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- .gitattributes +3 -0
- ME/GSE102504/GSE102504_RAW/GPL13534_450K_Manifest_header_Descriptions.xlsx +0 -0
- ME/GSE102504/meta/GSE102504_family.xml/GSE102504_family.xml +1897 -0
- ME/GSE111183/meta/GSE111183_family.xml/GSE111183_family.xml +1906 -0
- ME/GSE153667/GSE153667_RAW/GSM4649028_Control2_CpG.txt +0 -0
- ME/GSE153667/GSE153667_RAW/GSM4649033_Control7_CpG.txt +0 -0
- ME/GSE153667/GSE153667_RAW/GSM4649045_Patient9_CpG.txt +0 -0
- ME/GSE153667/meta/._GSE153667_family.soft +0 -0
- ME/GSE153667/meta/._GSE153667_family.xml +0 -0
- ME/GSE153667/meta/._GSE153667_series_matrix.txt +0 -0
- ME/GSE153667/meta/GSE153667_family.soft +853 -0
- ME/GSE153667/meta/GSE153667_family.xml +1056 -0
- ME/GSE153667/meta/GSE153667_series_matrix.txt +76 -0
- ME/GSE156792/._GSE156792_detection_pval.txt +0 -0
- ME/GSE156792/._GSE156792_meth_intensities.txt +0 -0
- ME/GSE166592/GSE166592_RAW/GSM5076049_ME007E_CpG.txt +0 -0
- ME/GSE166592/meta/._GSE166592_family.soft +0 -0
- ME/GSE166592/meta/._GSE166592_family.xml +0 -0
- ME/GSE166592/meta/._GSE166592_series_matrix.txt +0 -0
- ME/GSE166592/meta/GSE166592_family.soft +681 -0
- ME/GSE166592/meta/GSE166592_family.xml +965 -0
- ME/GSE166592/meta/GSE166592_series_matrix.txt +76 -0
- ME/GSE59489/GSE59489_RAW/GPL13534_450K_Manifest_header_Descriptions.xlsx +0 -0
- ME/GSE59489/meta/._GSE59489_family.soft +0 -0
- ME/GSE59489/meta/._GSE59489_family.xml +0 -0
- ME/GSE59489/meta/._GSE59489_series_matrix.txt +0 -0
- ME/GSE59489/meta/GSE59489_family.xml/._GPL13534-tbl-1.txt +0 -0
- ME/GSE59489/meta/GSE59489_family.xml/._GSE59489_family.xml +0 -0
- ME/GSE59489/meta/GSE59489_family.xml/._GSM1437759-tbl-1.txt +0 -0
- ME/GSE59489/meta/GSE59489_family.xml/._GSM1437761-tbl-1.txt +0 -0
- ME/GSE59489/meta/GSE59489_family.xml/._GSM1437762-tbl-1.txt +0 -0
- ME/GSE59489/meta/GSE59489_family.xml/._GSM1437763-tbl-1.txt +0 -0
- ME/GSE59489/meta/GSE59489_family.xml/._GSM1437764-tbl-1.txt +0 -0
- ME/GSE59489/meta/GSE59489_family.xml/._GSM1437765-tbl-1.txt +0 -0
- ME/GSE59489/meta/GSE59489_family.xml/._GSM1437766-tbl-1.txt +0 -0
- ME/GSE59489/meta/GSE59489_family.xml/._GSM1437767-tbl-1.txt +0 -0
- ME/GSE59489/meta/GSE59489_family.xml/._GSM1437768-tbl-1.txt +0 -0
- ME/GSE59489/meta/GSE59489_family.xml/._GSM1437769-tbl-1.txt +0 -0
- ME/GSE59489/meta/GSE59489_family.xml/._GSM1437770-tbl-1.txt +0 -0
- ME/GSE59489/meta/GSE59489_family.xml/._GSM1437771-tbl-1.txt +0 -0
- ME/GSE59489/meta/GSE59489_family.xml/._GSM1437772-tbl-1.txt +0 -0
- ME/GSE59489/meta/GSE59489_family.xml/._GSM1437773-tbl-1.txt +0 -0
- ME/GSE59489/meta/GSE59489_family.xml/._GSM1437775-tbl-1.txt +0 -0
- ME/GSE59489/meta/GSE59489_family.xml/._GSM1437776-tbl-1.txt +0 -0
- ME/GSE59489/meta/GSE59489_family.xml/._GSM1437777-tbl-1.txt +0 -0
- ME/GSE59489/meta/GSE59489_family.xml/._GSM1437778-tbl-1.txt +0 -0
- ME/GSE59489/meta/GSE59489_family.xml/._GSM1437780-tbl-1.txt +0 -0
- ME/GSE59489/meta/GSE59489_family.xml/._GSM1437781-tbl-1.txt +0 -0
- ME/GSE59489/meta/GSE59489_family.xml/._GSM1437782-tbl-1.txt +0 -0
- ME/GSE59489/meta/GSE59489_family.xml/GSE59489_family.xml +1926 -0
.gitattributes
CHANGED
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@@ -69,3 +69,6 @@ controls/GSE42861/GSE42861_methylation_signal_matrix_SUBSETS/GSE42861_methylatio
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| 69 |
controls/GSE40279/GSE40279_average_beta_GSM989991-GSM990299.txt filter=lfs diff=lfs merge=lfs -text
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| 70 |
controls/GSE40279/GSE40279_average_beta_GSM989827-GSM989990.txt filter=lfs diff=lfs merge=lfs -text
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| 71 |
controls/GSE40279/GSE40279_average_beta_GSM990300-GSM990463.txt filter=lfs diff=lfs merge=lfs -text
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| 69 |
controls/GSE40279/GSE40279_average_beta_GSM989991-GSM990299.txt filter=lfs diff=lfs merge=lfs -text
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controls/GSE40279/GSE40279_average_beta_GSM989827-GSM989990.txt filter=lfs diff=lfs merge=lfs -text
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| 71 |
controls/GSE40279/GSE40279_average_beta_GSM990300-GSM990463.txt filter=lfs diff=lfs merge=lfs -text
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| 72 |
+
controls/GSE42861/GSE42861_methylation_signal_matrix_SUBSETS/GSE42861_methylation_signal_matrix_13of13.txt filter=lfs diff=lfs merge=lfs -text
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| 73 |
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controls/GSE42861/GSE42861_methylation_signal_matrix_SUBSETS/GSE42861_methylation_signal_matrix_9of13.txt filter=lfs diff=lfs merge=lfs -text
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+
controls/GSE42861/GSE42861_methylation_signal_matrix_SUBSETS/GSE42861_methylation_signal_matrix_10of13.txt filter=lfs diff=lfs merge=lfs -text
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ME/GSE102504/GSE102504_RAW/GPL13534_450K_Manifest_header_Descriptions.xlsx
ADDED
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Binary file (9.85 kB). View file
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ME/GSE102504/meta/GSE102504_family.xml/GSE102504_family.xml
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|
| 1 |
+
<?xml version="1.0" encoding="UTF-8" standalone="no"?>
|
| 2 |
+
|
| 3 |
+
<MINiML
|
| 4 |
+
xmlns="http://www.ncbi.nlm.nih.gov/geo/info/MINiML"
|
| 5 |
+
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
|
| 6 |
+
xsi:schemaLocation="http://www.ncbi.nlm.nih.gov/geo/info/MINiML http://www.ncbi.nlm.nih.gov/geo/info/MINiML.xsd"
|
| 7 |
+
version="0.5.0" >
|
| 8 |
+
|
| 9 |
+
<Contributor iid="contrib1">
|
| 10 |
+
<Person><First>Patrick</First><Last>McGowan</Last></Person>
|
| 11 |
+
<Email>patrick.mcgowan@utoronto.ca</Email>
|
| 12 |
+
<Laboratory>SW326</Laboratory>
|
| 13 |
+
<Department>Biological Sciences</Department>
|
| 14 |
+
<Organization>University of Toronto Scarborough</Organization>
|
| 15 |
+
<Address>
|
| 16 |
+
<Line>1265 Military Trail</Line>
|
| 17 |
+
<City>Toronto</City>
|
| 18 |
+
<State>Ontario</State>
|
| 19 |
+
<Postal-Code>M1C 1A4</Postal-Code>
|
| 20 |
+
<Country>Canada</Country>
|
| 21 |
+
</Address>
|
| 22 |
+
</Contributor>
|
| 23 |
+
|
| 24 |
+
<Contributor iid="contrib2">
|
| 25 |
+
<Organization>Illumina Inc.</Organization>
|
| 26 |
+
<Email>expression@illumina.com, techsupport@illumina.com</Email>
|
| 27 |
+
<Phone>1 800 809 4566 </Phone>
|
| 28 |
+
<Organization>Illumina Inc.</Organization>
|
| 29 |
+
<Address>
|
| 30 |
+
<Line>9885 Towne Centre Drive</Line>
|
| 31 |
+
<City>San Diego</City>
|
| 32 |
+
<State>CA</State>
|
| 33 |
+
<Zip-Code>92121</Zip-Code>
|
| 34 |
+
<Country>USA</Country>
|
| 35 |
+
</Address>
|
| 36 |
+
<Web-Link>www.illumina.com</Web-Link>
|
| 37 |
+
</Contributor>
|
| 38 |
+
|
| 39 |
+
<Contributor iid="contrib3">
|
| 40 |
+
<Person><First>Wilfred</First><Middle>C</Middle><Last>de Vega</Last></Person>
|
| 41 |
+
</Contributor>
|
| 42 |
+
|
| 43 |
+
<Contributor iid="contrib4">
|
| 44 |
+
<Person><First>Suzanne</First><Middle>D</Middle><Last>Vernon</Last></Person>
|
| 45 |
+
</Contributor>
|
| 46 |
+
|
| 47 |
+
<Contributor iid="contrib5">
|
| 48 |
+
<Person><First>Patrick</First><Middle>O</Middle><Last>McGowan</Last></Person>
|
| 49 |
+
</Contributor>
|
| 50 |
+
|
| 51 |
+
<Database iid="GEO">
|
| 52 |
+
<Name>Gene Expression Omnibus (GEO)</Name>
|
| 53 |
+
<Public-ID>GEO</Public-ID>
|
| 54 |
+
<Organization>NCBI NLM NIH</Organization>
|
| 55 |
+
<Web-Link>http://www.ncbi.nlm.nih.gov/geo</Web-Link>
|
| 56 |
+
<Email>geo@ncbi.nlm.nih.gov</Email>
|
| 57 |
+
</Database>
|
| 58 |
+
|
| 59 |
+
<Platform iid="GPL13534">
|
| 60 |
+
<Status database="GEO">
|
| 61 |
+
<Submission-Date>2011-05-13</Submission-Date>
|
| 62 |
+
<Release-Date>2011-05-13</Release-Date>
|
| 63 |
+
<Last-Update-Date>2019-03-22</Last-Update-Date>
|
| 64 |
+
</Status>
|
| 65 |
+
<Title>Illumina HumanMethylation450 BeadChip (HumanMethylation450_15017482)</Title>
|
| 66 |
+
<Accession database="GEO">GPL13534</Accession>
|
| 67 |
+
<Technology>oligonucleotide beads</Technology>
|
| 68 |
+
<Distribution>commercial</Distribution>
|
| 69 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 70 |
+
<Manufacturer>Illumina, Inc.</Manufacturer>
|
| 71 |
+
<Manufacture-Protocol>
|
| 72 |
+
See manufacturer's website
|
| 73 |
+
</Manufacture-Protocol>
|
| 74 |
+
<Description>
|
| 75 |
+
1 difference between HumanMethylation450_15017482_v.1.1.bpm and HumanMethylation450_15017482_v.1.2.bpm:
|
| 76 |
+
|
| 77 |
+
1.1:
|
| 78 |
+
|
| 79 |
+
41636384,NEGATIVE,-99,Negative 604
|
| 80 |
+
|
| 81 |
+
1.2:
|
| 82 |
+
|
| 83 |
+
41636384,RESTORATION,Green,Restore
|
| 84 |
+
</Description>
|
| 85 |
+
<Contact-Ref ref="contrib2" />
|
| 86 |
+
<Supplementary-Data type="XLSX">
|
| 87 |
+
ftp://ftp.ncbi.nlm.nih.gov/geo/platforms/GPL13nnn/GPL13534/suppl/GPL13534_450K_Manifest_header_Descriptions.xlsx.gz
|
| 88 |
+
</Supplementary-Data>
|
| 89 |
+
<Supplementary-Data type="TXT">
|
| 90 |
+
ftp://ftp.ncbi.nlm.nih.gov/geo/platforms/GPL13nnn/GPL13534/suppl/GPL13534_HumanMethylation450_15017482_v.1.1.bpm.txt.gz
|
| 91 |
+
</Supplementary-Data>
|
| 92 |
+
<Supplementary-Data type="CSV">
|
| 93 |
+
ftp://ftp.ncbi.nlm.nih.gov/geo/platforms/GPL13nnn/GPL13534/suppl/GPL13534_HumanMethylation450_15017482_v.1.1.csv.gz
|
| 94 |
+
</Supplementary-Data>
|
| 95 |
+
<Supplementary-Data type="BPM">
|
| 96 |
+
ftp://ftp.ncbi.nlm.nih.gov/geo/platforms/GPL13nnn/GPL13534/suppl/GPL13534_HumanMethylation450_15017482_v.1.2.bpm.gz
|
| 97 |
+
</Supplementary-Data>
|
| 98 |
+
<Relation type="Alternative to" target="GPL16304" />
|
| 99 |
+
<Data-Table>
|
| 100 |
+
<Column position="1">
|
| 101 |
+
<Name>ID</Name>
|
| 102 |
+
</Column>
|
| 103 |
+
<Column position="2">
|
| 104 |
+
<Name>Name</Name>
|
| 105 |
+
</Column>
|
| 106 |
+
<Column position="3">
|
| 107 |
+
<Name>AddressA_ID</Name>
|
| 108 |
+
</Column>
|
| 109 |
+
<Column position="4">
|
| 110 |
+
<Name>AlleleA_ProbeSeq</Name>
|
| 111 |
+
</Column>
|
| 112 |
+
<Column position="5">
|
| 113 |
+
<Name>AddressB_ID</Name>
|
| 114 |
+
</Column>
|
| 115 |
+
<Column position="6">
|
| 116 |
+
<Name>AlleleB_ProbeSeq</Name>
|
| 117 |
+
</Column>
|
| 118 |
+
<Column position="7">
|
| 119 |
+
<Name>Infinium_Design_Type</Name>
|
| 120 |
+
</Column>
|
| 121 |
+
<Column position="8">
|
| 122 |
+
<Name>Next_Base</Name>
|
| 123 |
+
</Column>
|
| 124 |
+
<Column position="9">
|
| 125 |
+
<Name>Color_Channel</Name>
|
| 126 |
+
</Column>
|
| 127 |
+
<Column position="10">
|
| 128 |
+
<Name>Forward_Sequence</Name>
|
| 129 |
+
</Column>
|
| 130 |
+
<Column position="11">
|
| 131 |
+
<Name>Genome_Build</Name>
|
| 132 |
+
</Column>
|
| 133 |
+
<Column position="12">
|
| 134 |
+
<Name>CHR</Name>
|
| 135 |
+
</Column>
|
| 136 |
+
<Column position="13">
|
| 137 |
+
<Name>MAPINFO</Name>
|
| 138 |
+
</Column>
|
| 139 |
+
<Column position="14">
|
| 140 |
+
<Name>SourceSeq</Name>
|
| 141 |
+
</Column>
|
| 142 |
+
<Column position="15">
|
| 143 |
+
<Name>Chromosome_36</Name>
|
| 144 |
+
</Column>
|
| 145 |
+
<Column position="16">
|
| 146 |
+
<Name>Coordinate_36</Name>
|
| 147 |
+
</Column>
|
| 148 |
+
<Column position="17">
|
| 149 |
+
<Name>Strand</Name>
|
| 150 |
+
</Column>
|
| 151 |
+
<Column position="18">
|
| 152 |
+
<Name>Probe_SNPs</Name>
|
| 153 |
+
</Column>
|
| 154 |
+
<Column position="19">
|
| 155 |
+
<Name>Probe_SNPs_10</Name>
|
| 156 |
+
</Column>
|
| 157 |
+
<Column position="20">
|
| 158 |
+
<Name>Random_Loci</Name>
|
| 159 |
+
</Column>
|
| 160 |
+
<Column position="21">
|
| 161 |
+
<Name>Methyl27_Loci</Name>
|
| 162 |
+
</Column>
|
| 163 |
+
<Column position="22">
|
| 164 |
+
<Name>UCSC_RefGene_Name</Name>
|
| 165 |
+
</Column>
|
| 166 |
+
<Column position="23">
|
| 167 |
+
<Name>UCSC_RefGene_Accession</Name>
|
| 168 |
+
</Column>
|
| 169 |
+
<Column position="24">
|
| 170 |
+
<Name>UCSC_RefGene_Group</Name>
|
| 171 |
+
</Column>
|
| 172 |
+
<Column position="25">
|
| 173 |
+
<Name>UCSC_CpG_Islands_Name</Name>
|
| 174 |
+
</Column>
|
| 175 |
+
<Column position="26">
|
| 176 |
+
<Name>Relation_to_UCSC_CpG_Island</Name>
|
| 177 |
+
</Column>
|
| 178 |
+
<Column position="27">
|
| 179 |
+
<Name>Phantom</Name>
|
| 180 |
+
</Column>
|
| 181 |
+
<Column position="28">
|
| 182 |
+
<Name>DMR</Name>
|
| 183 |
+
</Column>
|
| 184 |
+
<Column position="29">
|
| 185 |
+
<Name>Enhancer</Name>
|
| 186 |
+
</Column>
|
| 187 |
+
<Column position="30">
|
| 188 |
+
<Name>HMM_Island</Name>
|
| 189 |
+
</Column>
|
| 190 |
+
<Column position="31">
|
| 191 |
+
<Name>Regulatory_Feature_Name</Name>
|
| 192 |
+
</Column>
|
| 193 |
+
<Column position="32">
|
| 194 |
+
<Name>Regulatory_Feature_Group</Name>
|
| 195 |
+
</Column>
|
| 196 |
+
<Column position="33">
|
| 197 |
+
<Name>DHS</Name>
|
| 198 |
+
</Column>
|
| 199 |
+
<Column position="34">
|
| 200 |
+
<Name>RANGE_START</Name>
|
| 201 |
+
</Column>
|
| 202 |
+
<Column position="35">
|
| 203 |
+
<Name>RANGE_END</Name>
|
| 204 |
+
</Column>
|
| 205 |
+
<Column position="36">
|
| 206 |
+
<Name>RANGE_GB</Name>
|
| 207 |
+
</Column>
|
| 208 |
+
<Column position="37">
|
| 209 |
+
<Name>SPOT_ID</Name>
|
| 210 |
+
</Column>
|
| 211 |
+
<External-Data rows="485577">
|
| 212 |
+
GPL13534-tbl-1.txt
|
| 213 |
+
</External-Data>
|
| 214 |
+
</Data-Table>
|
| 215 |
+
</Platform>
|
| 216 |
+
|
| 217 |
+
<Sample iid="GSM2739721">
|
| 218 |
+
<Status database="GEO">
|
| 219 |
+
<Submission-Date>2017-08-10</Submission-Date>
|
| 220 |
+
<Release-Date>2017-12-31</Release-Date>
|
| 221 |
+
<Last-Update-Date>2018-01-23</Last-Update-Date>
|
| 222 |
+
</Status>
|
| 223 |
+
<Title>PBMC Genomic DNA G00019</Title>
|
| 224 |
+
<Accession database="GEO">GSM2739721</Accession>
|
| 225 |
+
<Type>genomic</Type>
|
| 226 |
+
<Channel-Count>1</Channel-Count>
|
| 227 |
+
<Channel position="1">
|
| 228 |
+
<Source>PBMC</Source>
|
| 229 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 230 |
+
<Characteristics tag="Sex">
|
| 231 |
+
female
|
| 232 |
+
</Characteristics>
|
| 233 |
+
<Characteristics tag="disease state">
|
| 234 |
+
CFS
|
| 235 |
+
</Characteristics>
|
| 236 |
+
<Molecule>genomic DNA</Molecule>
|
| 237 |
+
<Extract-Protocol>
|
| 238 |
+
Genomic DNA was extracted and purified from Omega EZNA Tissue DNA Kit according to manufacturer's instructions
|
| 239 |
+
</Extract-Protocol>
|
| 240 |
+
<Label>Cy3 and Cy5</Label>
|
| 241 |
+
<Label-Protocol>
|
| 242 |
+
Standard Illumina Protocol
|
| 243 |
+
</Label-Protocol>
|
| 244 |
+
</Channel>
|
| 245 |
+
<Hybridization-Protocol>
|
| 246 |
+
Bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol
|
| 247 |
+
</Hybridization-Protocol>
|
| 248 |
+
<Scan-Protocol>
|
| 249 |
+
Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
|
| 250 |
+
</Scan-Protocol>
|
| 251 |
+
<Description>
|
| 252 |
+
CFS Genomic DNA
|
| 253 |
+
</Description>
|
| 254 |
+
<Data-Processing>
|
| 255 |
+
BeadStudio software v3.2
|
| 256 |
+
</Data-Processing>
|
| 257 |
+
<Platform-Ref ref="GPL13534" />
|
| 258 |
+
<Contact-Ref ref="contrib1" />
|
| 259 |
+
<Supplementary-Data type="IDAT">
|
| 260 |
+
ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2739nnn/GSM2739721/suppl/GSM2739721_3999356083_R01C01_Grn.idat.gz
|
| 261 |
+
</Supplementary-Data>
|
| 262 |
+
<Supplementary-Data type="IDAT">
|
| 263 |
+
ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2739nnn/GSM2739721/suppl/GSM2739721_3999356083_R01C01_Red.idat.gz
|
| 264 |
+
</Supplementary-Data>
|
| 265 |
+
<Data-Table>
|
| 266 |
+
<Column position="1">
|
| 267 |
+
<Name>ID_REF</Name>
|
| 268 |
+
</Column>
|
| 269 |
+
<Column position="2">
|
| 270 |
+
<Name>VALUE</Name>
|
| 271 |
+
<Description>Average Beta non-normalized Beta</Description>
|
| 272 |
+
</Column>
|
| 273 |
+
<Column position="3">
|
| 274 |
+
<Name>Detection Pval</Name>
|
| 275 |
+
</Column>
|
| 276 |
+
<External-Data rows="467971">
|
| 277 |
+
GSM2739721-tbl-1.txt
|
| 278 |
+
</External-Data>
|
| 279 |
+
</Data-Table>
|
| 280 |
+
</Sample>
|
| 281 |
+
|
| 282 |
+
<Sample iid="GSM2739722">
|
| 283 |
+
<Status database="GEO">
|
| 284 |
+
<Submission-Date>2017-08-10</Submission-Date>
|
| 285 |
+
<Release-Date>2017-12-31</Release-Date>
|
| 286 |
+
<Last-Update-Date>2018-01-23</Last-Update-Date>
|
| 287 |
+
</Status>
|
| 288 |
+
<Title>PBMC Genomic DNA G00041</Title>
|
| 289 |
+
<Accession database="GEO">GSM2739722</Accession>
|
| 290 |
+
<Type>genomic</Type>
|
| 291 |
+
<Channel-Count>1</Channel-Count>
|
| 292 |
+
<Channel position="1">
|
| 293 |
+
<Source>PBMC</Source>
|
| 294 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 295 |
+
<Characteristics tag="Sex">
|
| 296 |
+
female
|
| 297 |
+
</Characteristics>
|
| 298 |
+
<Characteristics tag="disease state">
|
| 299 |
+
CFS
|
| 300 |
+
</Characteristics>
|
| 301 |
+
<Molecule>genomic DNA</Molecule>
|
| 302 |
+
<Extract-Protocol>
|
| 303 |
+
Genomic DNA was extracted and purified from Omega EZNA Tissue DNA Kit according to manufacturer's instructions
|
| 304 |
+
</Extract-Protocol>
|
| 305 |
+
<Label>Cy3 and Cy5</Label>
|
| 306 |
+
<Label-Protocol>
|
| 307 |
+
Standard Illumina Protocol
|
| 308 |
+
</Label-Protocol>
|
| 309 |
+
</Channel>
|
| 310 |
+
<Hybridization-Protocol>
|
| 311 |
+
Bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol
|
| 312 |
+
</Hybridization-Protocol>
|
| 313 |
+
<Scan-Protocol>
|
| 314 |
+
Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
|
| 315 |
+
</Scan-Protocol>
|
| 316 |
+
<Description>
|
| 317 |
+
CFS Genomic DNA
|
| 318 |
+
</Description>
|
| 319 |
+
<Data-Processing>
|
| 320 |
+
BeadStudio software v3.2
|
| 321 |
+
</Data-Processing>
|
| 322 |
+
<Platform-Ref ref="GPL13534" />
|
| 323 |
+
<Contact-Ref ref="contrib1" />
|
| 324 |
+
<Supplementary-Data type="IDAT">
|
| 325 |
+
ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2739nnn/GSM2739722/suppl/GSM2739722_3999356083_R02C01_Grn.idat.gz
|
| 326 |
+
</Supplementary-Data>
|
| 327 |
+
<Supplementary-Data type="IDAT">
|
| 328 |
+
ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2739nnn/GSM2739722/suppl/GSM2739722_3999356083_R02C01_Red.idat.gz
|
| 329 |
+
</Supplementary-Data>
|
| 330 |
+
<Data-Table>
|
| 331 |
+
<Column position="1">
|
| 332 |
+
<Name>ID_REF</Name>
|
| 333 |
+
</Column>
|
| 334 |
+
<Column position="2">
|
| 335 |
+
<Name>VALUE</Name>
|
| 336 |
+
<Description>Average Beta non-normalized Beta</Description>
|
| 337 |
+
</Column>
|
| 338 |
+
<Column position="3">
|
| 339 |
+
<Name>Detection Pval</Name>
|
| 340 |
+
</Column>
|
| 341 |
+
<External-Data rows="467971">
|
| 342 |
+
GSM2739722-tbl-1.txt
|
| 343 |
+
</External-Data>
|
| 344 |
+
</Data-Table>
|
| 345 |
+
</Sample>
|
| 346 |
+
|
| 347 |
+
<Sample iid="GSM2739723">
|
| 348 |
+
<Status database="GEO">
|
| 349 |
+
<Submission-Date>2017-08-10</Submission-Date>
|
| 350 |
+
<Release-Date>2017-12-31</Release-Date>
|
| 351 |
+
<Last-Update-Date>2018-01-23</Last-Update-Date>
|
| 352 |
+
</Status>
|
| 353 |
+
<Title>PBMC Genomic DNA G00043</Title>
|
| 354 |
+
<Accession database="GEO">GSM2739723</Accession>
|
| 355 |
+
<Type>genomic</Type>
|
| 356 |
+
<Channel-Count>1</Channel-Count>
|
| 357 |
+
<Channel position="1">
|
| 358 |
+
<Source>PBMC</Source>
|
| 359 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 360 |
+
<Characteristics tag="Sex">
|
| 361 |
+
female
|
| 362 |
+
</Characteristics>
|
| 363 |
+
<Characteristics tag="disease state">
|
| 364 |
+
CFS
|
| 365 |
+
</Characteristics>
|
| 366 |
+
<Molecule>genomic DNA</Molecule>
|
| 367 |
+
<Extract-Protocol>
|
| 368 |
+
Genomic DNA was extracted and purified from Omega EZNA Tissue DNA Kit according to manufacturer's instructions
|
| 369 |
+
</Extract-Protocol>
|
| 370 |
+
<Label>Cy3 and Cy5</Label>
|
| 371 |
+
<Label-Protocol>
|
| 372 |
+
Standard Illumina Protocol
|
| 373 |
+
</Label-Protocol>
|
| 374 |
+
</Channel>
|
| 375 |
+
<Hybridization-Protocol>
|
| 376 |
+
Bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol
|
| 377 |
+
</Hybridization-Protocol>
|
| 378 |
+
<Scan-Protocol>
|
| 379 |
+
Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
|
| 380 |
+
</Scan-Protocol>
|
| 381 |
+
<Description>
|
| 382 |
+
CFS Genomic DNA
|
| 383 |
+
</Description>
|
| 384 |
+
<Data-Processing>
|
| 385 |
+
BeadStudio software v3.2
|
| 386 |
+
</Data-Processing>
|
| 387 |
+
<Platform-Ref ref="GPL13534" />
|
| 388 |
+
<Contact-Ref ref="contrib1" />
|
| 389 |
+
<Supplementary-Data type="IDAT">
|
| 390 |
+
ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2739nnn/GSM2739723/suppl/GSM2739723_3999356083_R03C01_Grn.idat.gz
|
| 391 |
+
</Supplementary-Data>
|
| 392 |
+
<Supplementary-Data type="IDAT">
|
| 393 |
+
ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2739nnn/GSM2739723/suppl/GSM2739723_3999356083_R03C01_Red.idat.gz
|
| 394 |
+
</Supplementary-Data>
|
| 395 |
+
<Data-Table>
|
| 396 |
+
<Column position="1">
|
| 397 |
+
<Name>ID_REF</Name>
|
| 398 |
+
</Column>
|
| 399 |
+
<Column position="2">
|
| 400 |
+
<Name>VALUE</Name>
|
| 401 |
+
<Description>Average Beta non-normalized Beta</Description>
|
| 402 |
+
</Column>
|
| 403 |
+
<Column position="3">
|
| 404 |
+
<Name>Detection Pval</Name>
|
| 405 |
+
</Column>
|
| 406 |
+
<External-Data rows="467971">
|
| 407 |
+
GSM2739723-tbl-1.txt
|
| 408 |
+
</External-Data>
|
| 409 |
+
</Data-Table>
|
| 410 |
+
</Sample>
|
| 411 |
+
|
| 412 |
+
<Sample iid="GSM2739724">
|
| 413 |
+
<Status database="GEO">
|
| 414 |
+
<Submission-Date>2017-08-10</Submission-Date>
|
| 415 |
+
<Release-Date>2017-12-31</Release-Date>
|
| 416 |
+
<Last-Update-Date>2018-01-23</Last-Update-Date>
|
| 417 |
+
</Status>
|
| 418 |
+
<Title>PBMC Genomic DNA G00052</Title>
|
| 419 |
+
<Accession database="GEO">GSM2739724</Accession>
|
| 420 |
+
<Type>genomic</Type>
|
| 421 |
+
<Channel-Count>1</Channel-Count>
|
| 422 |
+
<Channel position="1">
|
| 423 |
+
<Source>PBMC</Source>
|
| 424 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 425 |
+
<Characteristics tag="Sex">
|
| 426 |
+
female
|
| 427 |
+
</Characteristics>
|
| 428 |
+
<Characteristics tag="disease state">
|
| 429 |
+
CFS
|
| 430 |
+
</Characteristics>
|
| 431 |
+
<Molecule>genomic DNA</Molecule>
|
| 432 |
+
<Extract-Protocol>
|
| 433 |
+
Genomic DNA was extracted and purified from Omega EZNA Tissue DNA Kit according to manufacturer's instructions
|
| 434 |
+
</Extract-Protocol>
|
| 435 |
+
<Label>Cy3 and Cy5</Label>
|
| 436 |
+
<Label-Protocol>
|
| 437 |
+
Standard Illumina Protocol
|
| 438 |
+
</Label-Protocol>
|
| 439 |
+
</Channel>
|
| 440 |
+
<Hybridization-Protocol>
|
| 441 |
+
Bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol
|
| 442 |
+
</Hybridization-Protocol>
|
| 443 |
+
<Scan-Protocol>
|
| 444 |
+
Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
|
| 445 |
+
</Scan-Protocol>
|
| 446 |
+
<Description>
|
| 447 |
+
CFS Genomic DNA
|
| 448 |
+
</Description>
|
| 449 |
+
<Data-Processing>
|
| 450 |
+
BeadStudio software v3.2
|
| 451 |
+
</Data-Processing>
|
| 452 |
+
<Platform-Ref ref="GPL13534" />
|
| 453 |
+
<Contact-Ref ref="contrib1" />
|
| 454 |
+
<Supplementary-Data type="IDAT">
|
| 455 |
+
ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2739nnn/GSM2739724/suppl/GSM2739724_3999356083_R04C01_Grn.idat.gz
|
| 456 |
+
</Supplementary-Data>
|
| 457 |
+
<Supplementary-Data type="IDAT">
|
| 458 |
+
ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2739nnn/GSM2739724/suppl/GSM2739724_3999356083_R04C01_Red.idat.gz
|
| 459 |
+
</Supplementary-Data>
|
| 460 |
+
<Data-Table>
|
| 461 |
+
<Column position="1">
|
| 462 |
+
<Name>ID_REF</Name>
|
| 463 |
+
</Column>
|
| 464 |
+
<Column position="2">
|
| 465 |
+
<Name>VALUE</Name>
|
| 466 |
+
<Description>Average Beta non-normalized Beta</Description>
|
| 467 |
+
</Column>
|
| 468 |
+
<Column position="3">
|
| 469 |
+
<Name>Detection Pval</Name>
|
| 470 |
+
</Column>
|
| 471 |
+
<External-Data rows="467971">
|
| 472 |
+
GSM2739724-tbl-1.txt
|
| 473 |
+
</External-Data>
|
| 474 |
+
</Data-Table>
|
| 475 |
+
</Sample>
|
| 476 |
+
|
| 477 |
+
<Sample iid="GSM2739725">
|
| 478 |
+
<Status database="GEO">
|
| 479 |
+
<Submission-Date>2017-08-10</Submission-Date>
|
| 480 |
+
<Release-Date>2017-12-31</Release-Date>
|
| 481 |
+
<Last-Update-Date>2018-01-23</Last-Update-Date>
|
| 482 |
+
</Status>
|
| 483 |
+
<Title>PBMC Genomic DNA G00069</Title>
|
| 484 |
+
<Accession database="GEO">GSM2739725</Accession>
|
| 485 |
+
<Type>genomic</Type>
|
| 486 |
+
<Channel-Count>1</Channel-Count>
|
| 487 |
+
<Channel position="1">
|
| 488 |
+
<Source>PBMC</Source>
|
| 489 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 490 |
+
<Characteristics tag="Sex">
|
| 491 |
+
female
|
| 492 |
+
</Characteristics>
|
| 493 |
+
<Characteristics tag="disease state">
|
| 494 |
+
CFS
|
| 495 |
+
</Characteristics>
|
| 496 |
+
<Molecule>genomic DNA</Molecule>
|
| 497 |
+
<Extract-Protocol>
|
| 498 |
+
Genomic DNA was extracted and purified from Omega EZNA Tissue DNA Kit according to manufacturer's instructions
|
| 499 |
+
</Extract-Protocol>
|
| 500 |
+
<Label>Cy3 and Cy5</Label>
|
| 501 |
+
<Label-Protocol>
|
| 502 |
+
Standard Illumina Protocol
|
| 503 |
+
</Label-Protocol>
|
| 504 |
+
</Channel>
|
| 505 |
+
<Hybridization-Protocol>
|
| 506 |
+
Bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol
|
| 507 |
+
</Hybridization-Protocol>
|
| 508 |
+
<Scan-Protocol>
|
| 509 |
+
Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
|
| 510 |
+
</Scan-Protocol>
|
| 511 |
+
<Description>
|
| 512 |
+
CFS Genomic DNA
|
| 513 |
+
</Description>
|
| 514 |
+
<Data-Processing>
|
| 515 |
+
BeadStudio software v3.2
|
| 516 |
+
</Data-Processing>
|
| 517 |
+
<Platform-Ref ref="GPL13534" />
|
| 518 |
+
<Contact-Ref ref="contrib1" />
|
| 519 |
+
<Supplementary-Data type="IDAT">
|
| 520 |
+
ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2739nnn/GSM2739725/suppl/GSM2739725_3999356083_R06C01_Grn.idat.gz
|
| 521 |
+
</Supplementary-Data>
|
| 522 |
+
<Supplementary-Data type="IDAT">
|
| 523 |
+
ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2739nnn/GSM2739725/suppl/GSM2739725_3999356083_R06C01_Red.idat.gz
|
| 524 |
+
</Supplementary-Data>
|
| 525 |
+
<Data-Table>
|
| 526 |
+
<Column position="1">
|
| 527 |
+
<Name>ID_REF</Name>
|
| 528 |
+
</Column>
|
| 529 |
+
<Column position="2">
|
| 530 |
+
<Name>VALUE</Name>
|
| 531 |
+
<Description>Average Beta non-normalized Beta</Description>
|
| 532 |
+
</Column>
|
| 533 |
+
<Column position="3">
|
| 534 |
+
<Name>Detection Pval</Name>
|
| 535 |
+
</Column>
|
| 536 |
+
<External-Data rows="467971">
|
| 537 |
+
GSM2739725-tbl-1.txt
|
| 538 |
+
</External-Data>
|
| 539 |
+
</Data-Table>
|
| 540 |
+
</Sample>
|
| 541 |
+
|
| 542 |
+
<Sample iid="GSM2739726">
|
| 543 |
+
<Status database="GEO">
|
| 544 |
+
<Submission-Date>2017-08-10</Submission-Date>
|
| 545 |
+
<Release-Date>2017-12-31</Release-Date>
|
| 546 |
+
<Last-Update-Date>2018-01-23</Last-Update-Date>
|
| 547 |
+
</Status>
|
| 548 |
+
<Title>PBMC Genomic DNA G00074</Title>
|
| 549 |
+
<Accession database="GEO">GSM2739726</Accession>
|
| 550 |
+
<Type>genomic</Type>
|
| 551 |
+
<Channel-Count>1</Channel-Count>
|
| 552 |
+
<Channel position="1">
|
| 553 |
+
<Source>PBMC</Source>
|
| 554 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 555 |
+
<Characteristics tag="Sex">
|
| 556 |
+
female
|
| 557 |
+
</Characteristics>
|
| 558 |
+
<Characteristics tag="disease state">
|
| 559 |
+
CFS
|
| 560 |
+
</Characteristics>
|
| 561 |
+
<Molecule>genomic DNA</Molecule>
|
| 562 |
+
<Extract-Protocol>
|
| 563 |
+
Genomic DNA was extracted and purified from Omega EZNA Tissue DNA Kit according to manufacturer's instructions
|
| 564 |
+
</Extract-Protocol>
|
| 565 |
+
<Label>Cy3 and Cy5</Label>
|
| 566 |
+
<Label-Protocol>
|
| 567 |
+
Standard Illumina Protocol
|
| 568 |
+
</Label-Protocol>
|
| 569 |
+
</Channel>
|
| 570 |
+
<Hybridization-Protocol>
|
| 571 |
+
Bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol
|
| 572 |
+
</Hybridization-Protocol>
|
| 573 |
+
<Scan-Protocol>
|
| 574 |
+
Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
|
| 575 |
+
</Scan-Protocol>
|
| 576 |
+
<Description>
|
| 577 |
+
CFS Genomic DNA
|
| 578 |
+
</Description>
|
| 579 |
+
<Data-Processing>
|
| 580 |
+
BeadStudio software v3.2
|
| 581 |
+
</Data-Processing>
|
| 582 |
+
<Platform-Ref ref="GPL13534" />
|
| 583 |
+
<Contact-Ref ref="contrib1" />
|
| 584 |
+
<Supplementary-Data type="IDAT">
|
| 585 |
+
ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2739nnn/GSM2739726/suppl/GSM2739726_3999356083_R05C01_Grn.idat.gz
|
| 586 |
+
</Supplementary-Data>
|
| 587 |
+
<Supplementary-Data type="IDAT">
|
| 588 |
+
ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2739nnn/GSM2739726/suppl/GSM2739726_3999356083_R05C01_Red.idat.gz
|
| 589 |
+
</Supplementary-Data>
|
| 590 |
+
<Data-Table>
|
| 591 |
+
<Column position="1">
|
| 592 |
+
<Name>ID_REF</Name>
|
| 593 |
+
</Column>
|
| 594 |
+
<Column position="2">
|
| 595 |
+
<Name>VALUE</Name>
|
| 596 |
+
<Description>Average Beta non-normalized Beta</Description>
|
| 597 |
+
</Column>
|
| 598 |
+
<Column position="3">
|
| 599 |
+
<Name>Detection Pval</Name>
|
| 600 |
+
</Column>
|
| 601 |
+
<External-Data rows="467971">
|
| 602 |
+
GSM2739726-tbl-1.txt
|
| 603 |
+
</External-Data>
|
| 604 |
+
</Data-Table>
|
| 605 |
+
</Sample>
|
| 606 |
+
|
| 607 |
+
<Sample iid="GSM2739727">
|
| 608 |
+
<Status database="GEO">
|
| 609 |
+
<Submission-Date>2017-08-10</Submission-Date>
|
| 610 |
+
<Release-Date>2017-12-31</Release-Date>
|
| 611 |
+
<Last-Update-Date>2018-01-23</Last-Update-Date>
|
| 612 |
+
</Status>
|
| 613 |
+
<Title>PBMC Genomic DNA G00077</Title>
|
| 614 |
+
<Accession database="GEO">GSM2739727</Accession>
|
| 615 |
+
<Type>genomic</Type>
|
| 616 |
+
<Channel-Count>1</Channel-Count>
|
| 617 |
+
<Channel position="1">
|
| 618 |
+
<Source>PBMC</Source>
|
| 619 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 620 |
+
<Characteristics tag="Sex">
|
| 621 |
+
female
|
| 622 |
+
</Characteristics>
|
| 623 |
+
<Characteristics tag="disease state">
|
| 624 |
+
CFS
|
| 625 |
+
</Characteristics>
|
| 626 |
+
<Molecule>genomic DNA</Molecule>
|
| 627 |
+
<Extract-Protocol>
|
| 628 |
+
Genomic DNA was extracted and purified from Omega EZNA Tissue DNA Kit according to manufacturer's instructions
|
| 629 |
+
</Extract-Protocol>
|
| 630 |
+
<Label>Cy3 and Cy5</Label>
|
| 631 |
+
<Label-Protocol>
|
| 632 |
+
Standard Illumina Protocol
|
| 633 |
+
</Label-Protocol>
|
| 634 |
+
</Channel>
|
| 635 |
+
<Hybridization-Protocol>
|
| 636 |
+
Bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol
|
| 637 |
+
</Hybridization-Protocol>
|
| 638 |
+
<Scan-Protocol>
|
| 639 |
+
Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
|
| 640 |
+
</Scan-Protocol>
|
| 641 |
+
<Description>
|
| 642 |
+
CFS Genomic DNA
|
| 643 |
+
</Description>
|
| 644 |
+
<Data-Processing>
|
| 645 |
+
BeadStudio software v3.2
|
| 646 |
+
</Data-Processing>
|
| 647 |
+
<Platform-Ref ref="GPL13534" />
|
| 648 |
+
<Contact-Ref ref="contrib1" />
|
| 649 |
+
<Supplementary-Data type="IDAT">
|
| 650 |
+
ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2739nnn/GSM2739727/suppl/GSM2739727_3999356082_R01C01_Grn.idat.gz
|
| 651 |
+
</Supplementary-Data>
|
| 652 |
+
<Supplementary-Data type="IDAT">
|
| 653 |
+
ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2739nnn/GSM2739727/suppl/GSM2739727_3999356082_R01C01_Red.idat.gz
|
| 654 |
+
</Supplementary-Data>
|
| 655 |
+
<Data-Table>
|
| 656 |
+
<Column position="1">
|
| 657 |
+
<Name>ID_REF</Name>
|
| 658 |
+
</Column>
|
| 659 |
+
<Column position="2">
|
| 660 |
+
<Name>VALUE</Name>
|
| 661 |
+
<Description>Average Beta non-normalized Beta</Description>
|
| 662 |
+
</Column>
|
| 663 |
+
<Column position="3">
|
| 664 |
+
<Name>Detection Pval</Name>
|
| 665 |
+
</Column>
|
| 666 |
+
<External-Data rows="467971">
|
| 667 |
+
GSM2739727-tbl-1.txt
|
| 668 |
+
</External-Data>
|
| 669 |
+
</Data-Table>
|
| 670 |
+
</Sample>
|
| 671 |
+
|
| 672 |
+
<Sample iid="GSM2739728">
|
| 673 |
+
<Status database="GEO">
|
| 674 |
+
<Submission-Date>2017-08-10</Submission-Date>
|
| 675 |
+
<Release-Date>2017-12-31</Release-Date>
|
| 676 |
+
<Last-Update-Date>2018-01-23</Last-Update-Date>
|
| 677 |
+
</Status>
|
| 678 |
+
<Title>PBMC Genomic DNA G00100</Title>
|
| 679 |
+
<Accession database="GEO">GSM2739728</Accession>
|
| 680 |
+
<Type>genomic</Type>
|
| 681 |
+
<Channel-Count>1</Channel-Count>
|
| 682 |
+
<Channel position="1">
|
| 683 |
+
<Source>PBMC</Source>
|
| 684 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 685 |
+
<Characteristics tag="Sex">
|
| 686 |
+
female
|
| 687 |
+
</Characteristics>
|
| 688 |
+
<Characteristics tag="disease state">
|
| 689 |
+
CFS
|
| 690 |
+
</Characteristics>
|
| 691 |
+
<Molecule>genomic DNA</Molecule>
|
| 692 |
+
<Extract-Protocol>
|
| 693 |
+
Genomic DNA was extracted and purified from Omega EZNA Tissue DNA Kit according to manufacturer's instructions
|
| 694 |
+
</Extract-Protocol>
|
| 695 |
+
<Label>Cy3 and Cy5</Label>
|
| 696 |
+
<Label-Protocol>
|
| 697 |
+
Standard Illumina Protocol
|
| 698 |
+
</Label-Protocol>
|
| 699 |
+
</Channel>
|
| 700 |
+
<Hybridization-Protocol>
|
| 701 |
+
Bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol
|
| 702 |
+
</Hybridization-Protocol>
|
| 703 |
+
<Scan-Protocol>
|
| 704 |
+
Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
|
| 705 |
+
</Scan-Protocol>
|
| 706 |
+
<Description>
|
| 707 |
+
CFS Genomic DNA
|
| 708 |
+
</Description>
|
| 709 |
+
<Data-Processing>
|
| 710 |
+
BeadStudio software v3.2
|
| 711 |
+
</Data-Processing>
|
| 712 |
+
<Platform-Ref ref="GPL13534" />
|
| 713 |
+
<Contact-Ref ref="contrib1" />
|
| 714 |
+
<Supplementary-Data type="IDAT">
|
| 715 |
+
ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2739nnn/GSM2739728/suppl/GSM2739728_3999356082_R02C01_Grn.idat.gz
|
| 716 |
+
</Supplementary-Data>
|
| 717 |
+
<Supplementary-Data type="IDAT">
|
| 718 |
+
ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2739nnn/GSM2739728/suppl/GSM2739728_3999356082_R02C01_Red.idat.gz
|
| 719 |
+
</Supplementary-Data>
|
| 720 |
+
<Data-Table>
|
| 721 |
+
<Column position="1">
|
| 722 |
+
<Name>ID_REF</Name>
|
| 723 |
+
</Column>
|
| 724 |
+
<Column position="2">
|
| 725 |
+
<Name>VALUE</Name>
|
| 726 |
+
<Description>Average Beta non-normalized Beta</Description>
|
| 727 |
+
</Column>
|
| 728 |
+
<Column position="3">
|
| 729 |
+
<Name>Detection Pval</Name>
|
| 730 |
+
</Column>
|
| 731 |
+
<External-Data rows="467971">
|
| 732 |
+
GSM2739728-tbl-1.txt
|
| 733 |
+
</External-Data>
|
| 734 |
+
</Data-Table>
|
| 735 |
+
</Sample>
|
| 736 |
+
|
| 737 |
+
<Sample iid="GSM2739729">
|
| 738 |
+
<Status database="GEO">
|
| 739 |
+
<Submission-Date>2017-08-10</Submission-Date>
|
| 740 |
+
<Release-Date>2017-12-31</Release-Date>
|
| 741 |
+
<Last-Update-Date>2018-01-23</Last-Update-Date>
|
| 742 |
+
</Status>
|
| 743 |
+
<Title>PBMC Genomic DNA G00106</Title>
|
| 744 |
+
<Accession database="GEO">GSM2739729</Accession>
|
| 745 |
+
<Type>genomic</Type>
|
| 746 |
+
<Channel-Count>1</Channel-Count>
|
| 747 |
+
<Channel position="1">
|
| 748 |
+
<Source>PBMC</Source>
|
| 749 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 750 |
+
<Characteristics tag="Sex">
|
| 751 |
+
female
|
| 752 |
+
</Characteristics>
|
| 753 |
+
<Characteristics tag="disease state">
|
| 754 |
+
CFS
|
| 755 |
+
</Characteristics>
|
| 756 |
+
<Molecule>genomic DNA</Molecule>
|
| 757 |
+
<Extract-Protocol>
|
| 758 |
+
Genomic DNA was extracted and purified from Omega EZNA Tissue DNA Kit according to manufacturer's instructions
|
| 759 |
+
</Extract-Protocol>
|
| 760 |
+
<Label>Cy3 and Cy5</Label>
|
| 761 |
+
<Label-Protocol>
|
| 762 |
+
Standard Illumina Protocol
|
| 763 |
+
</Label-Protocol>
|
| 764 |
+
</Channel>
|
| 765 |
+
<Hybridization-Protocol>
|
| 766 |
+
Bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol
|
| 767 |
+
</Hybridization-Protocol>
|
| 768 |
+
<Scan-Protocol>
|
| 769 |
+
Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
|
| 770 |
+
</Scan-Protocol>
|
| 771 |
+
<Description>
|
| 772 |
+
CFS Genomic DNA
|
| 773 |
+
</Description>
|
| 774 |
+
<Data-Processing>
|
| 775 |
+
BeadStudio software v3.2
|
| 776 |
+
</Data-Processing>
|
| 777 |
+
<Platform-Ref ref="GPL13534" />
|
| 778 |
+
<Contact-Ref ref="contrib1" />
|
| 779 |
+
<Supplementary-Data type="IDAT">
|
| 780 |
+
ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2739nnn/GSM2739729/suppl/GSM2739729_3999356082_R03C01_Grn.idat.gz
|
| 781 |
+
</Supplementary-Data>
|
| 782 |
+
<Supplementary-Data type="IDAT">
|
| 783 |
+
ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2739nnn/GSM2739729/suppl/GSM2739729_3999356082_R03C01_Red.idat.gz
|
| 784 |
+
</Supplementary-Data>
|
| 785 |
+
<Data-Table>
|
| 786 |
+
<Column position="1">
|
| 787 |
+
<Name>ID_REF</Name>
|
| 788 |
+
</Column>
|
| 789 |
+
<Column position="2">
|
| 790 |
+
<Name>VALUE</Name>
|
| 791 |
+
<Description>Average Beta non-normalized Beta</Description>
|
| 792 |
+
</Column>
|
| 793 |
+
<Column position="3">
|
| 794 |
+
<Name>Detection Pval</Name>
|
| 795 |
+
</Column>
|
| 796 |
+
<External-Data rows="467971">
|
| 797 |
+
GSM2739729-tbl-1.txt
|
| 798 |
+
</External-Data>
|
| 799 |
+
</Data-Table>
|
| 800 |
+
</Sample>
|
| 801 |
+
|
| 802 |
+
<Sample iid="GSM2739730">
|
| 803 |
+
<Status database="GEO">
|
| 804 |
+
<Submission-Date>2017-08-10</Submission-Date>
|
| 805 |
+
<Release-Date>2017-12-31</Release-Date>
|
| 806 |
+
<Last-Update-Date>2018-01-23</Last-Update-Date>
|
| 807 |
+
</Status>
|
| 808 |
+
<Title>PBMC Genomic DNA G00111</Title>
|
| 809 |
+
<Accession database="GEO">GSM2739730</Accession>
|
| 810 |
+
<Type>genomic</Type>
|
| 811 |
+
<Channel-Count>1</Channel-Count>
|
| 812 |
+
<Channel position="1">
|
| 813 |
+
<Source>PBMC</Source>
|
| 814 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 815 |
+
<Characteristics tag="Sex">
|
| 816 |
+
female
|
| 817 |
+
</Characteristics>
|
| 818 |
+
<Characteristics tag="disease state">
|
| 819 |
+
CFS
|
| 820 |
+
</Characteristics>
|
| 821 |
+
<Molecule>genomic DNA</Molecule>
|
| 822 |
+
<Extract-Protocol>
|
| 823 |
+
Genomic DNA was extracted and purified from Omega EZNA Tissue DNA Kit according to manufacturer's instructions
|
| 824 |
+
</Extract-Protocol>
|
| 825 |
+
<Label>Cy3 and Cy5</Label>
|
| 826 |
+
<Label-Protocol>
|
| 827 |
+
Standard Illumina Protocol
|
| 828 |
+
</Label-Protocol>
|
| 829 |
+
</Channel>
|
| 830 |
+
<Hybridization-Protocol>
|
| 831 |
+
Bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol
|
| 832 |
+
</Hybridization-Protocol>
|
| 833 |
+
<Scan-Protocol>
|
| 834 |
+
Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
|
| 835 |
+
</Scan-Protocol>
|
| 836 |
+
<Description>
|
| 837 |
+
CFS Genomic DNA
|
| 838 |
+
</Description>
|
| 839 |
+
<Data-Processing>
|
| 840 |
+
BeadStudio software v3.2
|
| 841 |
+
</Data-Processing>
|
| 842 |
+
<Platform-Ref ref="GPL13534" />
|
| 843 |
+
<Contact-Ref ref="contrib1" />
|
| 844 |
+
<Supplementary-Data type="IDAT">
|
| 845 |
+
ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2739nnn/GSM2739730/suppl/GSM2739730_3999356082_R04C01_Grn.idat.gz
|
| 846 |
+
</Supplementary-Data>
|
| 847 |
+
<Supplementary-Data type="IDAT">
|
| 848 |
+
ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2739nnn/GSM2739730/suppl/GSM2739730_3999356082_R04C01_Red.idat.gz
|
| 849 |
+
</Supplementary-Data>
|
| 850 |
+
<Data-Table>
|
| 851 |
+
<Column position="1">
|
| 852 |
+
<Name>ID_REF</Name>
|
| 853 |
+
</Column>
|
| 854 |
+
<Column position="2">
|
| 855 |
+
<Name>VALUE</Name>
|
| 856 |
+
<Description>Average Beta non-normalized Beta</Description>
|
| 857 |
+
</Column>
|
| 858 |
+
<Column position="3">
|
| 859 |
+
<Name>Detection Pval</Name>
|
| 860 |
+
</Column>
|
| 861 |
+
<External-Data rows="467971">
|
| 862 |
+
GSM2739730-tbl-1.txt
|
| 863 |
+
</External-Data>
|
| 864 |
+
</Data-Table>
|
| 865 |
+
</Sample>
|
| 866 |
+
|
| 867 |
+
<Sample iid="GSM2739731">
|
| 868 |
+
<Status database="GEO">
|
| 869 |
+
<Submission-Date>2017-08-10</Submission-Date>
|
| 870 |
+
<Release-Date>2017-12-31</Release-Date>
|
| 871 |
+
<Last-Update-Date>2018-01-23</Last-Update-Date>
|
| 872 |
+
</Status>
|
| 873 |
+
<Title>PBMC Genomic DNA G00115</Title>
|
| 874 |
+
<Accession database="GEO">GSM2739731</Accession>
|
| 875 |
+
<Type>genomic</Type>
|
| 876 |
+
<Channel-Count>1</Channel-Count>
|
| 877 |
+
<Channel position="1">
|
| 878 |
+
<Source>PBMC</Source>
|
| 879 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 880 |
+
<Characteristics tag="Sex">
|
| 881 |
+
female
|
| 882 |
+
</Characteristics>
|
| 883 |
+
<Characteristics tag="disease state">
|
| 884 |
+
CFS
|
| 885 |
+
</Characteristics>
|
| 886 |
+
<Molecule>genomic DNA</Molecule>
|
| 887 |
+
<Extract-Protocol>
|
| 888 |
+
Genomic DNA was extracted and purified from Omega EZNA Tissue DNA Kit according to manufacturer's instructions
|
| 889 |
+
</Extract-Protocol>
|
| 890 |
+
<Label>Cy3 and Cy5</Label>
|
| 891 |
+
<Label-Protocol>
|
| 892 |
+
Standard Illumina Protocol
|
| 893 |
+
</Label-Protocol>
|
| 894 |
+
</Channel>
|
| 895 |
+
<Hybridization-Protocol>
|
| 896 |
+
Bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol
|
| 897 |
+
</Hybridization-Protocol>
|
| 898 |
+
<Scan-Protocol>
|
| 899 |
+
Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
|
| 900 |
+
</Scan-Protocol>
|
| 901 |
+
<Description>
|
| 902 |
+
CFS Genomic DNA
|
| 903 |
+
</Description>
|
| 904 |
+
<Data-Processing>
|
| 905 |
+
BeadStudio software v3.2
|
| 906 |
+
</Data-Processing>
|
| 907 |
+
<Platform-Ref ref="GPL13534" />
|
| 908 |
+
<Contact-Ref ref="contrib1" />
|
| 909 |
+
<Supplementary-Data type="IDAT">
|
| 910 |
+
ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2739nnn/GSM2739731/suppl/GSM2739731_3999356082_R05C01_Grn.idat.gz
|
| 911 |
+
</Supplementary-Data>
|
| 912 |
+
<Supplementary-Data type="IDAT">
|
| 913 |
+
ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2739nnn/GSM2739731/suppl/GSM2739731_3999356082_R05C01_Red.idat.gz
|
| 914 |
+
</Supplementary-Data>
|
| 915 |
+
<Data-Table>
|
| 916 |
+
<Column position="1">
|
| 917 |
+
<Name>ID_REF</Name>
|
| 918 |
+
</Column>
|
| 919 |
+
<Column position="2">
|
| 920 |
+
<Name>VALUE</Name>
|
| 921 |
+
<Description>Average Beta non-normalized Beta</Description>
|
| 922 |
+
</Column>
|
| 923 |
+
<Column position="3">
|
| 924 |
+
<Name>Detection Pval</Name>
|
| 925 |
+
</Column>
|
| 926 |
+
<External-Data rows="467971">
|
| 927 |
+
GSM2739731-tbl-1.txt
|
| 928 |
+
</External-Data>
|
| 929 |
+
</Data-Table>
|
| 930 |
+
</Sample>
|
| 931 |
+
|
| 932 |
+
<Sample iid="GSM2739732">
|
| 933 |
+
<Status database="GEO">
|
| 934 |
+
<Submission-Date>2017-08-10</Submission-Date>
|
| 935 |
+
<Release-Date>2017-12-31</Release-Date>
|
| 936 |
+
<Last-Update-Date>2018-01-23</Last-Update-Date>
|
| 937 |
+
</Status>
|
| 938 |
+
<Title>PBMC Genomic DNA G00124</Title>
|
| 939 |
+
<Accession database="GEO">GSM2739732</Accession>
|
| 940 |
+
<Type>genomic</Type>
|
| 941 |
+
<Channel-Count>1</Channel-Count>
|
| 942 |
+
<Channel position="1">
|
| 943 |
+
<Source>PBMC</Source>
|
| 944 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 945 |
+
<Characteristics tag="Sex">
|
| 946 |
+
female
|
| 947 |
+
</Characteristics>
|
| 948 |
+
<Characteristics tag="disease state">
|
| 949 |
+
CFS
|
| 950 |
+
</Characteristics>
|
| 951 |
+
<Molecule>genomic DNA</Molecule>
|
| 952 |
+
<Extract-Protocol>
|
| 953 |
+
Genomic DNA was extracted and purified from Omega EZNA Tissue DNA Kit according to manufacturer's instructions
|
| 954 |
+
</Extract-Protocol>
|
| 955 |
+
<Label>Cy3 and Cy5</Label>
|
| 956 |
+
<Label-Protocol>
|
| 957 |
+
Standard Illumina Protocol
|
| 958 |
+
</Label-Protocol>
|
| 959 |
+
</Channel>
|
| 960 |
+
<Hybridization-Protocol>
|
| 961 |
+
Bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol
|
| 962 |
+
</Hybridization-Protocol>
|
| 963 |
+
<Scan-Protocol>
|
| 964 |
+
Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
|
| 965 |
+
</Scan-Protocol>
|
| 966 |
+
<Description>
|
| 967 |
+
CFS Genomic DNA
|
| 968 |
+
</Description>
|
| 969 |
+
<Data-Processing>
|
| 970 |
+
BeadStudio software v3.2
|
| 971 |
+
</Data-Processing>
|
| 972 |
+
<Platform-Ref ref="GPL13534" />
|
| 973 |
+
<Contact-Ref ref="contrib1" />
|
| 974 |
+
<Supplementary-Data type="IDAT">
|
| 975 |
+
ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2739nnn/GSM2739732/suppl/GSM2739732_3999356064_R01C01_Grn.idat.gz
|
| 976 |
+
</Supplementary-Data>
|
| 977 |
+
<Supplementary-Data type="IDAT">
|
| 978 |
+
ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2739nnn/GSM2739732/suppl/GSM2739732_3999356064_R01C01_Red.idat.gz
|
| 979 |
+
</Supplementary-Data>
|
| 980 |
+
<Data-Table>
|
| 981 |
+
<Column position="1">
|
| 982 |
+
<Name>ID_REF</Name>
|
| 983 |
+
</Column>
|
| 984 |
+
<Column position="2">
|
| 985 |
+
<Name>VALUE</Name>
|
| 986 |
+
<Description>Average Beta non-normalized Beta</Description>
|
| 987 |
+
</Column>
|
| 988 |
+
<Column position="3">
|
| 989 |
+
<Name>Detection Pval</Name>
|
| 990 |
+
</Column>
|
| 991 |
+
<External-Data rows="467971">
|
| 992 |
+
GSM2739732-tbl-1.txt
|
| 993 |
+
</External-Data>
|
| 994 |
+
</Data-Table>
|
| 995 |
+
</Sample>
|
| 996 |
+
|
| 997 |
+
<Sample iid="GSM2739733">
|
| 998 |
+
<Status database="GEO">
|
| 999 |
+
<Submission-Date>2017-08-10</Submission-Date>
|
| 1000 |
+
<Release-Date>2017-12-31</Release-Date>
|
| 1001 |
+
<Last-Update-Date>2018-01-23</Last-Update-Date>
|
| 1002 |
+
</Status>
|
| 1003 |
+
<Title>PBMC Genomic DNA G00147</Title>
|
| 1004 |
+
<Accession database="GEO">GSM2739733</Accession>
|
| 1005 |
+
<Type>genomic</Type>
|
| 1006 |
+
<Channel-Count>1</Channel-Count>
|
| 1007 |
+
<Channel position="1">
|
| 1008 |
+
<Source>PBMC</Source>
|
| 1009 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 1010 |
+
<Characteristics tag="Sex">
|
| 1011 |
+
female
|
| 1012 |
+
</Characteristics>
|
| 1013 |
+
<Characteristics tag="disease state">
|
| 1014 |
+
CFS
|
| 1015 |
+
</Characteristics>
|
| 1016 |
+
<Molecule>genomic DNA</Molecule>
|
| 1017 |
+
<Extract-Protocol>
|
| 1018 |
+
Genomic DNA was extracted and purified from Omega EZNA Tissue DNA Kit according to manufacturer's instructions
|
| 1019 |
+
</Extract-Protocol>
|
| 1020 |
+
<Label>Cy3 and Cy5</Label>
|
| 1021 |
+
<Label-Protocol>
|
| 1022 |
+
Standard Illumina Protocol
|
| 1023 |
+
</Label-Protocol>
|
| 1024 |
+
</Channel>
|
| 1025 |
+
<Hybridization-Protocol>
|
| 1026 |
+
Bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol
|
| 1027 |
+
</Hybridization-Protocol>
|
| 1028 |
+
<Scan-Protocol>
|
| 1029 |
+
Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
|
| 1030 |
+
</Scan-Protocol>
|
| 1031 |
+
<Description>
|
| 1032 |
+
CFS Genomic DNA
|
| 1033 |
+
</Description>
|
| 1034 |
+
<Data-Processing>
|
| 1035 |
+
BeadStudio software v3.2
|
| 1036 |
+
</Data-Processing>
|
| 1037 |
+
<Platform-Ref ref="GPL13534" />
|
| 1038 |
+
<Contact-Ref ref="contrib1" />
|
| 1039 |
+
<Supplementary-Data type="IDAT">
|
| 1040 |
+
ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2739nnn/GSM2739733/suppl/GSM2739733_3999356064_R02C01_Grn.idat.gz
|
| 1041 |
+
</Supplementary-Data>
|
| 1042 |
+
<Supplementary-Data type="IDAT">
|
| 1043 |
+
ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2739nnn/GSM2739733/suppl/GSM2739733_3999356064_R02C01_Red.idat.gz
|
| 1044 |
+
</Supplementary-Data>
|
| 1045 |
+
<Data-Table>
|
| 1046 |
+
<Column position="1">
|
| 1047 |
+
<Name>ID_REF</Name>
|
| 1048 |
+
</Column>
|
| 1049 |
+
<Column position="2">
|
| 1050 |
+
<Name>VALUE</Name>
|
| 1051 |
+
<Description>Average Beta non-normalized Beta</Description>
|
| 1052 |
+
</Column>
|
| 1053 |
+
<Column position="3">
|
| 1054 |
+
<Name>Detection Pval</Name>
|
| 1055 |
+
</Column>
|
| 1056 |
+
<External-Data rows="467971">
|
| 1057 |
+
GSM2739733-tbl-1.txt
|
| 1058 |
+
</External-Data>
|
| 1059 |
+
</Data-Table>
|
| 1060 |
+
</Sample>
|
| 1061 |
+
|
| 1062 |
+
<Sample iid="GSM2739734">
|
| 1063 |
+
<Status database="GEO">
|
| 1064 |
+
<Submission-Date>2017-08-10</Submission-Date>
|
| 1065 |
+
<Release-Date>2017-12-31</Release-Date>
|
| 1066 |
+
<Last-Update-Date>2018-01-23</Last-Update-Date>
|
| 1067 |
+
</Status>
|
| 1068 |
+
<Title>PBMC Genomic DNA G00151</Title>
|
| 1069 |
+
<Accession database="GEO">GSM2739734</Accession>
|
| 1070 |
+
<Type>genomic</Type>
|
| 1071 |
+
<Channel-Count>1</Channel-Count>
|
| 1072 |
+
<Channel position="1">
|
| 1073 |
+
<Source>PBMC</Source>
|
| 1074 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 1075 |
+
<Characteristics tag="Sex">
|
| 1076 |
+
female
|
| 1077 |
+
</Characteristics>
|
| 1078 |
+
<Characteristics tag="disease state">
|
| 1079 |
+
CFS
|
| 1080 |
+
</Characteristics>
|
| 1081 |
+
<Molecule>genomic DNA</Molecule>
|
| 1082 |
+
<Extract-Protocol>
|
| 1083 |
+
Genomic DNA was extracted and purified from Omega EZNA Tissue DNA Kit according to manufacturer's instructions
|
| 1084 |
+
</Extract-Protocol>
|
| 1085 |
+
<Label>Cy3 and Cy5</Label>
|
| 1086 |
+
<Label-Protocol>
|
| 1087 |
+
Standard Illumina Protocol
|
| 1088 |
+
</Label-Protocol>
|
| 1089 |
+
</Channel>
|
| 1090 |
+
<Hybridization-Protocol>
|
| 1091 |
+
Bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol
|
| 1092 |
+
</Hybridization-Protocol>
|
| 1093 |
+
<Scan-Protocol>
|
| 1094 |
+
Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
|
| 1095 |
+
</Scan-Protocol>
|
| 1096 |
+
<Description>
|
| 1097 |
+
CFS Genomic DNA
|
| 1098 |
+
</Description>
|
| 1099 |
+
<Data-Processing>
|
| 1100 |
+
BeadStudio software v3.2
|
| 1101 |
+
</Data-Processing>
|
| 1102 |
+
<Platform-Ref ref="GPL13534" />
|
| 1103 |
+
<Contact-Ref ref="contrib1" />
|
| 1104 |
+
<Supplementary-Data type="IDAT">
|
| 1105 |
+
ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2739nnn/GSM2739734/suppl/GSM2739734_3999356064_R03C01_Grn.idat.gz
|
| 1106 |
+
</Supplementary-Data>
|
| 1107 |
+
<Supplementary-Data type="IDAT">
|
| 1108 |
+
ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2739nnn/GSM2739734/suppl/GSM2739734_3999356064_R03C01_Red.idat.gz
|
| 1109 |
+
</Supplementary-Data>
|
| 1110 |
+
<Data-Table>
|
| 1111 |
+
<Column position="1">
|
| 1112 |
+
<Name>ID_REF</Name>
|
| 1113 |
+
</Column>
|
| 1114 |
+
<Column position="2">
|
| 1115 |
+
<Name>VALUE</Name>
|
| 1116 |
+
<Description>Average Beta non-normalized Beta</Description>
|
| 1117 |
+
</Column>
|
| 1118 |
+
<Column position="3">
|
| 1119 |
+
<Name>Detection Pval</Name>
|
| 1120 |
+
</Column>
|
| 1121 |
+
<External-Data rows="467971">
|
| 1122 |
+
GSM2739734-tbl-1.txt
|
| 1123 |
+
</External-Data>
|
| 1124 |
+
</Data-Table>
|
| 1125 |
+
</Sample>
|
| 1126 |
+
|
| 1127 |
+
<Sample iid="GSM2739735">
|
| 1128 |
+
<Status database="GEO">
|
| 1129 |
+
<Submission-Date>2017-08-10</Submission-Date>
|
| 1130 |
+
<Release-Date>2017-12-31</Release-Date>
|
| 1131 |
+
<Last-Update-Date>2018-01-23</Last-Update-Date>
|
| 1132 |
+
</Status>
|
| 1133 |
+
<Title>PBMC Genomic DNA G00159</Title>
|
| 1134 |
+
<Accession database="GEO">GSM2739735</Accession>
|
| 1135 |
+
<Type>genomic</Type>
|
| 1136 |
+
<Channel-Count>1</Channel-Count>
|
| 1137 |
+
<Channel position="1">
|
| 1138 |
+
<Source>PBMC</Source>
|
| 1139 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 1140 |
+
<Characteristics tag="Sex">
|
| 1141 |
+
female
|
| 1142 |
+
</Characteristics>
|
| 1143 |
+
<Characteristics tag="disease state">
|
| 1144 |
+
CFS
|
| 1145 |
+
</Characteristics>
|
| 1146 |
+
<Molecule>genomic DNA</Molecule>
|
| 1147 |
+
<Extract-Protocol>
|
| 1148 |
+
Genomic DNA was extracted and purified from Omega EZNA Tissue DNA Kit according to manufacturer's instructions
|
| 1149 |
+
</Extract-Protocol>
|
| 1150 |
+
<Label>Cy3 and Cy5</Label>
|
| 1151 |
+
<Label-Protocol>
|
| 1152 |
+
Standard Illumina Protocol
|
| 1153 |
+
</Label-Protocol>
|
| 1154 |
+
</Channel>
|
| 1155 |
+
<Hybridization-Protocol>
|
| 1156 |
+
Bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol
|
| 1157 |
+
</Hybridization-Protocol>
|
| 1158 |
+
<Scan-Protocol>
|
| 1159 |
+
Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
|
| 1160 |
+
</Scan-Protocol>
|
| 1161 |
+
<Description>
|
| 1162 |
+
CFS Genomic DNA
|
| 1163 |
+
</Description>
|
| 1164 |
+
<Data-Processing>
|
| 1165 |
+
BeadStudio software v3.2
|
| 1166 |
+
</Data-Processing>
|
| 1167 |
+
<Platform-Ref ref="GPL13534" />
|
| 1168 |
+
<Contact-Ref ref="contrib1" />
|
| 1169 |
+
<Supplementary-Data type="IDAT">
|
| 1170 |
+
ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2739nnn/GSM2739735/suppl/GSM2739735_3999356064_R04C01_Grn.idat.gz
|
| 1171 |
+
</Supplementary-Data>
|
| 1172 |
+
<Supplementary-Data type="IDAT">
|
| 1173 |
+
ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2739nnn/GSM2739735/suppl/GSM2739735_3999356064_R04C01_Red.idat.gz
|
| 1174 |
+
</Supplementary-Data>
|
| 1175 |
+
<Data-Table>
|
| 1176 |
+
<Column position="1">
|
| 1177 |
+
<Name>ID_REF</Name>
|
| 1178 |
+
</Column>
|
| 1179 |
+
<Column position="2">
|
| 1180 |
+
<Name>VALUE</Name>
|
| 1181 |
+
<Description>Average Beta non-normalized Beta</Description>
|
| 1182 |
+
</Column>
|
| 1183 |
+
<Column position="3">
|
| 1184 |
+
<Name>Detection Pval</Name>
|
| 1185 |
+
</Column>
|
| 1186 |
+
<External-Data rows="467971">
|
| 1187 |
+
GSM2739735-tbl-1.txt
|
| 1188 |
+
</External-Data>
|
| 1189 |
+
</Data-Table>
|
| 1190 |
+
</Sample>
|
| 1191 |
+
|
| 1192 |
+
<Sample iid="GSM2739736">
|
| 1193 |
+
<Status database="GEO">
|
| 1194 |
+
<Submission-Date>2017-08-10</Submission-Date>
|
| 1195 |
+
<Release-Date>2017-12-31</Release-Date>
|
| 1196 |
+
<Last-Update-Date>2018-01-23</Last-Update-Date>
|
| 1197 |
+
</Status>
|
| 1198 |
+
<Title>PBMC Genomic DNA G00166</Title>
|
| 1199 |
+
<Accession database="GEO">GSM2739736</Accession>
|
| 1200 |
+
<Type>genomic</Type>
|
| 1201 |
+
<Channel-Count>1</Channel-Count>
|
| 1202 |
+
<Channel position="1">
|
| 1203 |
+
<Source>PBMC</Source>
|
| 1204 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 1205 |
+
<Characteristics tag="Sex">
|
| 1206 |
+
female
|
| 1207 |
+
</Characteristics>
|
| 1208 |
+
<Characteristics tag="disease state">
|
| 1209 |
+
CFS
|
| 1210 |
+
</Characteristics>
|
| 1211 |
+
<Molecule>genomic DNA</Molecule>
|
| 1212 |
+
<Extract-Protocol>
|
| 1213 |
+
Genomic DNA was extracted and purified from Omega EZNA Tissue DNA Kit according to manufacturer's instructions
|
| 1214 |
+
</Extract-Protocol>
|
| 1215 |
+
<Label>Cy3 and Cy5</Label>
|
| 1216 |
+
<Label-Protocol>
|
| 1217 |
+
Standard Illumina Protocol
|
| 1218 |
+
</Label-Protocol>
|
| 1219 |
+
</Channel>
|
| 1220 |
+
<Hybridization-Protocol>
|
| 1221 |
+
Bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol
|
| 1222 |
+
</Hybridization-Protocol>
|
| 1223 |
+
<Scan-Protocol>
|
| 1224 |
+
Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
|
| 1225 |
+
</Scan-Protocol>
|
| 1226 |
+
<Description>
|
| 1227 |
+
CFS Genomic DNA
|
| 1228 |
+
</Description>
|
| 1229 |
+
<Data-Processing>
|
| 1230 |
+
BeadStudio software v3.2
|
| 1231 |
+
</Data-Processing>
|
| 1232 |
+
<Platform-Ref ref="GPL13534" />
|
| 1233 |
+
<Contact-Ref ref="contrib1" />
|
| 1234 |
+
<Supplementary-Data type="IDAT">
|
| 1235 |
+
ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2739nnn/GSM2739736/suppl/GSM2739736_3999356064_R05C01_Grn.idat.gz
|
| 1236 |
+
</Supplementary-Data>
|
| 1237 |
+
<Supplementary-Data type="IDAT">
|
| 1238 |
+
ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2739nnn/GSM2739736/suppl/GSM2739736_3999356064_R05C01_Red.idat.gz
|
| 1239 |
+
</Supplementary-Data>
|
| 1240 |
+
<Data-Table>
|
| 1241 |
+
<Column position="1">
|
| 1242 |
+
<Name>ID_REF</Name>
|
| 1243 |
+
</Column>
|
| 1244 |
+
<Column position="2">
|
| 1245 |
+
<Name>VALUE</Name>
|
| 1246 |
+
<Description>Average Beta non-normalized Beta</Description>
|
| 1247 |
+
</Column>
|
| 1248 |
+
<Column position="3">
|
| 1249 |
+
<Name>Detection Pval</Name>
|
| 1250 |
+
</Column>
|
| 1251 |
+
<External-Data rows="467971">
|
| 1252 |
+
GSM2739736-tbl-1.txt
|
| 1253 |
+
</External-Data>
|
| 1254 |
+
</Data-Table>
|
| 1255 |
+
</Sample>
|
| 1256 |
+
|
| 1257 |
+
<Sample iid="GSM2739737">
|
| 1258 |
+
<Status database="GEO">
|
| 1259 |
+
<Submission-Date>2017-08-10</Submission-Date>
|
| 1260 |
+
<Release-Date>2017-12-31</Release-Date>
|
| 1261 |
+
<Last-Update-Date>2018-01-23</Last-Update-Date>
|
| 1262 |
+
</Status>
|
| 1263 |
+
<Title>PBMC Genomic DNA G00172</Title>
|
| 1264 |
+
<Accession database="GEO">GSM2739737</Accession>
|
| 1265 |
+
<Type>genomic</Type>
|
| 1266 |
+
<Channel-Count>1</Channel-Count>
|
| 1267 |
+
<Channel position="1">
|
| 1268 |
+
<Source>PBMC</Source>
|
| 1269 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 1270 |
+
<Characteristics tag="Sex">
|
| 1271 |
+
female
|
| 1272 |
+
</Characteristics>
|
| 1273 |
+
<Characteristics tag="disease state">
|
| 1274 |
+
CFS
|
| 1275 |
+
</Characteristics>
|
| 1276 |
+
<Molecule>genomic DNA</Molecule>
|
| 1277 |
+
<Extract-Protocol>
|
| 1278 |
+
Genomic DNA was extracted and purified from Omega EZNA Tissue DNA Kit according to manufacturer's instructions
|
| 1279 |
+
</Extract-Protocol>
|
| 1280 |
+
<Label>Cy3 and Cy5</Label>
|
| 1281 |
+
<Label-Protocol>
|
| 1282 |
+
Standard Illumina Protocol
|
| 1283 |
+
</Label-Protocol>
|
| 1284 |
+
</Channel>
|
| 1285 |
+
<Hybridization-Protocol>
|
| 1286 |
+
Bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol
|
| 1287 |
+
</Hybridization-Protocol>
|
| 1288 |
+
<Scan-Protocol>
|
| 1289 |
+
Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
|
| 1290 |
+
</Scan-Protocol>
|
| 1291 |
+
<Description>
|
| 1292 |
+
CFS Genomic DNA
|
| 1293 |
+
</Description>
|
| 1294 |
+
<Data-Processing>
|
| 1295 |
+
BeadStudio software v3.2
|
| 1296 |
+
</Data-Processing>
|
| 1297 |
+
<Platform-Ref ref="GPL13534" />
|
| 1298 |
+
<Contact-Ref ref="contrib1" />
|
| 1299 |
+
<Supplementary-Data type="IDAT">
|
| 1300 |
+
ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2739nnn/GSM2739737/suppl/GSM2739737_3999356064_R06C01_Grn.idat.gz
|
| 1301 |
+
</Supplementary-Data>
|
| 1302 |
+
<Supplementary-Data type="IDAT">
|
| 1303 |
+
ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2739nnn/GSM2739737/suppl/GSM2739737_3999356064_R06C01_Red.idat.gz
|
| 1304 |
+
</Supplementary-Data>
|
| 1305 |
+
<Data-Table>
|
| 1306 |
+
<Column position="1">
|
| 1307 |
+
<Name>ID_REF</Name>
|
| 1308 |
+
</Column>
|
| 1309 |
+
<Column position="2">
|
| 1310 |
+
<Name>VALUE</Name>
|
| 1311 |
+
<Description>Average Beta non-normalized Beta</Description>
|
| 1312 |
+
</Column>
|
| 1313 |
+
<Column position="3">
|
| 1314 |
+
<Name>Detection Pval</Name>
|
| 1315 |
+
</Column>
|
| 1316 |
+
<External-Data rows="467971">
|
| 1317 |
+
GSM2739737-tbl-1.txt
|
| 1318 |
+
</External-Data>
|
| 1319 |
+
</Data-Table>
|
| 1320 |
+
</Sample>
|
| 1321 |
+
|
| 1322 |
+
<Sample iid="GSM2739738">
|
| 1323 |
+
<Status database="GEO">
|
| 1324 |
+
<Submission-Date>2017-08-10</Submission-Date>
|
| 1325 |
+
<Release-Date>2017-12-31</Release-Date>
|
| 1326 |
+
<Last-Update-Date>2018-01-23</Last-Update-Date>
|
| 1327 |
+
</Status>
|
| 1328 |
+
<Title>PBMC Genomic DNA G00181</Title>
|
| 1329 |
+
<Accession database="GEO">GSM2739738</Accession>
|
| 1330 |
+
<Type>genomic</Type>
|
| 1331 |
+
<Channel-Count>1</Channel-Count>
|
| 1332 |
+
<Channel position="1">
|
| 1333 |
+
<Source>PBMC</Source>
|
| 1334 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 1335 |
+
<Characteristics tag="Sex">
|
| 1336 |
+
female
|
| 1337 |
+
</Characteristics>
|
| 1338 |
+
<Characteristics tag="disease state">
|
| 1339 |
+
CFS
|
| 1340 |
+
</Characteristics>
|
| 1341 |
+
<Molecule>genomic DNA</Molecule>
|
| 1342 |
+
<Extract-Protocol>
|
| 1343 |
+
Genomic DNA was extracted and purified from Omega EZNA Tissue DNA Kit according to manufacturer's instructions
|
| 1344 |
+
</Extract-Protocol>
|
| 1345 |
+
<Label>Cy3 and Cy5</Label>
|
| 1346 |
+
<Label-Protocol>
|
| 1347 |
+
Standard Illumina Protocol
|
| 1348 |
+
</Label-Protocol>
|
| 1349 |
+
</Channel>
|
| 1350 |
+
<Hybridization-Protocol>
|
| 1351 |
+
Bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol
|
| 1352 |
+
</Hybridization-Protocol>
|
| 1353 |
+
<Scan-Protocol>
|
| 1354 |
+
Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
|
| 1355 |
+
</Scan-Protocol>
|
| 1356 |
+
<Description>
|
| 1357 |
+
CFS Genomic DNA
|
| 1358 |
+
</Description>
|
| 1359 |
+
<Data-Processing>
|
| 1360 |
+
BeadStudio software v3.2
|
| 1361 |
+
</Data-Processing>
|
| 1362 |
+
<Platform-Ref ref="GPL13534" />
|
| 1363 |
+
<Contact-Ref ref="contrib1" />
|
| 1364 |
+
<Supplementary-Data type="IDAT">
|
| 1365 |
+
ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2739nnn/GSM2739738/suppl/GSM2739738_3999356028_R01C01_Grn.idat.gz
|
| 1366 |
+
</Supplementary-Data>
|
| 1367 |
+
<Supplementary-Data type="IDAT">
|
| 1368 |
+
ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2739nnn/GSM2739738/suppl/GSM2739738_3999356028_R01C01_Red.idat.gz
|
| 1369 |
+
</Supplementary-Data>
|
| 1370 |
+
<Data-Table>
|
| 1371 |
+
<Column position="1">
|
| 1372 |
+
<Name>ID_REF</Name>
|
| 1373 |
+
</Column>
|
| 1374 |
+
<Column position="2">
|
| 1375 |
+
<Name>VALUE</Name>
|
| 1376 |
+
<Description>Average Beta non-normalized Beta</Description>
|
| 1377 |
+
</Column>
|
| 1378 |
+
<Column position="3">
|
| 1379 |
+
<Name>Detection Pval</Name>
|
| 1380 |
+
</Column>
|
| 1381 |
+
<External-Data rows="467971">
|
| 1382 |
+
GSM2739738-tbl-1.txt
|
| 1383 |
+
</External-Data>
|
| 1384 |
+
</Data-Table>
|
| 1385 |
+
</Sample>
|
| 1386 |
+
|
| 1387 |
+
<Sample iid="GSM2739739">
|
| 1388 |
+
<Status database="GEO">
|
| 1389 |
+
<Submission-Date>2017-08-10</Submission-Date>
|
| 1390 |
+
<Release-Date>2017-12-31</Release-Date>
|
| 1391 |
+
<Last-Update-Date>2018-01-23</Last-Update-Date>
|
| 1392 |
+
</Status>
|
| 1393 |
+
<Title>PBMC Genomic DNA G00194</Title>
|
| 1394 |
+
<Accession database="GEO">GSM2739739</Accession>
|
| 1395 |
+
<Type>genomic</Type>
|
| 1396 |
+
<Channel-Count>1</Channel-Count>
|
| 1397 |
+
<Channel position="1">
|
| 1398 |
+
<Source>PBMC</Source>
|
| 1399 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 1400 |
+
<Characteristics tag="Sex">
|
| 1401 |
+
female
|
| 1402 |
+
</Characteristics>
|
| 1403 |
+
<Characteristics tag="disease state">
|
| 1404 |
+
CFS
|
| 1405 |
+
</Characteristics>
|
| 1406 |
+
<Molecule>genomic DNA</Molecule>
|
| 1407 |
+
<Extract-Protocol>
|
| 1408 |
+
Genomic DNA was extracted and purified from Omega EZNA Tissue DNA Kit according to manufacturer's instructions
|
| 1409 |
+
</Extract-Protocol>
|
| 1410 |
+
<Label>Cy3 and Cy5</Label>
|
| 1411 |
+
<Label-Protocol>
|
| 1412 |
+
Standard Illumina Protocol
|
| 1413 |
+
</Label-Protocol>
|
| 1414 |
+
</Channel>
|
| 1415 |
+
<Hybridization-Protocol>
|
| 1416 |
+
Bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol
|
| 1417 |
+
</Hybridization-Protocol>
|
| 1418 |
+
<Scan-Protocol>
|
| 1419 |
+
Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
|
| 1420 |
+
</Scan-Protocol>
|
| 1421 |
+
<Description>
|
| 1422 |
+
CFS Genomic DNA
|
| 1423 |
+
</Description>
|
| 1424 |
+
<Data-Processing>
|
| 1425 |
+
BeadStudio software v3.2
|
| 1426 |
+
</Data-Processing>
|
| 1427 |
+
<Platform-Ref ref="GPL13534" />
|
| 1428 |
+
<Contact-Ref ref="contrib1" />
|
| 1429 |
+
<Supplementary-Data type="IDAT">
|
| 1430 |
+
ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2739nnn/GSM2739739/suppl/GSM2739739_3999356028_R02C01_Grn.idat.gz
|
| 1431 |
+
</Supplementary-Data>
|
| 1432 |
+
<Supplementary-Data type="IDAT">
|
| 1433 |
+
ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2739nnn/GSM2739739/suppl/GSM2739739_3999356028_R02C01_Red.idat.gz
|
| 1434 |
+
</Supplementary-Data>
|
| 1435 |
+
<Data-Table>
|
| 1436 |
+
<Column position="1">
|
| 1437 |
+
<Name>ID_REF</Name>
|
| 1438 |
+
</Column>
|
| 1439 |
+
<Column position="2">
|
| 1440 |
+
<Name>VALUE</Name>
|
| 1441 |
+
<Description>Average Beta non-normalized Beta</Description>
|
| 1442 |
+
</Column>
|
| 1443 |
+
<Column position="3">
|
| 1444 |
+
<Name>Detection Pval</Name>
|
| 1445 |
+
</Column>
|
| 1446 |
+
<External-Data rows="467971">
|
| 1447 |
+
GSM2739739-tbl-1.txt
|
| 1448 |
+
</External-Data>
|
| 1449 |
+
</Data-Table>
|
| 1450 |
+
</Sample>
|
| 1451 |
+
|
| 1452 |
+
<Sample iid="GSM2739740">
|
| 1453 |
+
<Status database="GEO">
|
| 1454 |
+
<Submission-Date>2017-08-10</Submission-Date>
|
| 1455 |
+
<Release-Date>2017-12-31</Release-Date>
|
| 1456 |
+
<Last-Update-Date>2018-01-23</Last-Update-Date>
|
| 1457 |
+
</Status>
|
| 1458 |
+
<Title>PBMC Genomic DNA G00198</Title>
|
| 1459 |
+
<Accession database="GEO">GSM2739740</Accession>
|
| 1460 |
+
<Type>genomic</Type>
|
| 1461 |
+
<Channel-Count>1</Channel-Count>
|
| 1462 |
+
<Channel position="1">
|
| 1463 |
+
<Source>PBMC</Source>
|
| 1464 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 1465 |
+
<Characteristics tag="Sex">
|
| 1466 |
+
female
|
| 1467 |
+
</Characteristics>
|
| 1468 |
+
<Characteristics tag="disease state">
|
| 1469 |
+
CFS
|
| 1470 |
+
</Characteristics>
|
| 1471 |
+
<Molecule>genomic DNA</Molecule>
|
| 1472 |
+
<Extract-Protocol>
|
| 1473 |
+
Genomic DNA was extracted and purified from Omega EZNA Tissue DNA Kit according to manufacturer's instructions
|
| 1474 |
+
</Extract-Protocol>
|
| 1475 |
+
<Label>Cy3 and Cy5</Label>
|
| 1476 |
+
<Label-Protocol>
|
| 1477 |
+
Standard Illumina Protocol
|
| 1478 |
+
</Label-Protocol>
|
| 1479 |
+
</Channel>
|
| 1480 |
+
<Hybridization-Protocol>
|
| 1481 |
+
Bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol
|
| 1482 |
+
</Hybridization-Protocol>
|
| 1483 |
+
<Scan-Protocol>
|
| 1484 |
+
Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
|
| 1485 |
+
</Scan-Protocol>
|
| 1486 |
+
<Description>
|
| 1487 |
+
CFS Genomic DNA
|
| 1488 |
+
</Description>
|
| 1489 |
+
<Data-Processing>
|
| 1490 |
+
BeadStudio software v3.2
|
| 1491 |
+
</Data-Processing>
|
| 1492 |
+
<Platform-Ref ref="GPL13534" />
|
| 1493 |
+
<Contact-Ref ref="contrib1" />
|
| 1494 |
+
<Supplementary-Data type="IDAT">
|
| 1495 |
+
ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2739nnn/GSM2739740/suppl/GSM2739740_3999356028_R03C01_Grn.idat.gz
|
| 1496 |
+
</Supplementary-Data>
|
| 1497 |
+
<Supplementary-Data type="IDAT">
|
| 1498 |
+
ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2739nnn/GSM2739740/suppl/GSM2739740_3999356028_R03C01_Red.idat.gz
|
| 1499 |
+
</Supplementary-Data>
|
| 1500 |
+
<Data-Table>
|
| 1501 |
+
<Column position="1">
|
| 1502 |
+
<Name>ID_REF</Name>
|
| 1503 |
+
</Column>
|
| 1504 |
+
<Column position="2">
|
| 1505 |
+
<Name>VALUE</Name>
|
| 1506 |
+
<Description>Average Beta non-normalized Beta</Description>
|
| 1507 |
+
</Column>
|
| 1508 |
+
<Column position="3">
|
| 1509 |
+
<Name>Detection Pval</Name>
|
| 1510 |
+
</Column>
|
| 1511 |
+
<External-Data rows="467971">
|
| 1512 |
+
GSM2739740-tbl-1.txt
|
| 1513 |
+
</External-Data>
|
| 1514 |
+
</Data-Table>
|
| 1515 |
+
</Sample>
|
| 1516 |
+
|
| 1517 |
+
<Sample iid="GSM2739741">
|
| 1518 |
+
<Status database="GEO">
|
| 1519 |
+
<Submission-Date>2017-08-10</Submission-Date>
|
| 1520 |
+
<Release-Date>2017-12-31</Release-Date>
|
| 1521 |
+
<Last-Update-Date>2018-01-23</Last-Update-Date>
|
| 1522 |
+
</Status>
|
| 1523 |
+
<Title>PBMC Genomic DNA G00222</Title>
|
| 1524 |
+
<Accession database="GEO">GSM2739741</Accession>
|
| 1525 |
+
<Type>genomic</Type>
|
| 1526 |
+
<Channel-Count>1</Channel-Count>
|
| 1527 |
+
<Channel position="1">
|
| 1528 |
+
<Source>PBMC</Source>
|
| 1529 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 1530 |
+
<Characteristics tag="Sex">
|
| 1531 |
+
female
|
| 1532 |
+
</Characteristics>
|
| 1533 |
+
<Characteristics tag="disease state">
|
| 1534 |
+
CFS
|
| 1535 |
+
</Characteristics>
|
| 1536 |
+
<Molecule>genomic DNA</Molecule>
|
| 1537 |
+
<Extract-Protocol>
|
| 1538 |
+
Genomic DNA was extracted and purified from Omega EZNA Tissue DNA Kit according to manufacturer's instructions
|
| 1539 |
+
</Extract-Protocol>
|
| 1540 |
+
<Label>Cy3 and Cy5</Label>
|
| 1541 |
+
<Label-Protocol>
|
| 1542 |
+
Standard Illumina Protocol
|
| 1543 |
+
</Label-Protocol>
|
| 1544 |
+
</Channel>
|
| 1545 |
+
<Hybridization-Protocol>
|
| 1546 |
+
Bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol
|
| 1547 |
+
</Hybridization-Protocol>
|
| 1548 |
+
<Scan-Protocol>
|
| 1549 |
+
Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
|
| 1550 |
+
</Scan-Protocol>
|
| 1551 |
+
<Description>
|
| 1552 |
+
CFS Genomic DNA
|
| 1553 |
+
</Description>
|
| 1554 |
+
<Data-Processing>
|
| 1555 |
+
BeadStudio software v3.2
|
| 1556 |
+
</Data-Processing>
|
| 1557 |
+
<Platform-Ref ref="GPL13534" />
|
| 1558 |
+
<Contact-Ref ref="contrib1" />
|
| 1559 |
+
<Supplementary-Data type="IDAT">
|
| 1560 |
+
ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2739nnn/GSM2739741/suppl/GSM2739741_3999356028_R04C01_Grn.idat.gz
|
| 1561 |
+
</Supplementary-Data>
|
| 1562 |
+
<Supplementary-Data type="IDAT">
|
| 1563 |
+
ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2739nnn/GSM2739741/suppl/GSM2739741_3999356028_R04C01_Red.idat.gz
|
| 1564 |
+
</Supplementary-Data>
|
| 1565 |
+
<Data-Table>
|
| 1566 |
+
<Column position="1">
|
| 1567 |
+
<Name>ID_REF</Name>
|
| 1568 |
+
</Column>
|
| 1569 |
+
<Column position="2">
|
| 1570 |
+
<Name>VALUE</Name>
|
| 1571 |
+
<Description>Average Beta non-normalized Beta</Description>
|
| 1572 |
+
</Column>
|
| 1573 |
+
<Column position="3">
|
| 1574 |
+
<Name>Detection Pval</Name>
|
| 1575 |
+
</Column>
|
| 1576 |
+
<External-Data rows="467971">
|
| 1577 |
+
GSM2739741-tbl-1.txt
|
| 1578 |
+
</External-Data>
|
| 1579 |
+
</Data-Table>
|
| 1580 |
+
</Sample>
|
| 1581 |
+
|
| 1582 |
+
<Sample iid="GSM2739742">
|
| 1583 |
+
<Status database="GEO">
|
| 1584 |
+
<Submission-Date>2017-08-10</Submission-Date>
|
| 1585 |
+
<Release-Date>2017-12-31</Release-Date>
|
| 1586 |
+
<Last-Update-Date>2018-01-23</Last-Update-Date>
|
| 1587 |
+
</Status>
|
| 1588 |
+
<Title>PBMC Genomic DNA G00244</Title>
|
| 1589 |
+
<Accession database="GEO">GSM2739742</Accession>
|
| 1590 |
+
<Type>genomic</Type>
|
| 1591 |
+
<Channel-Count>1</Channel-Count>
|
| 1592 |
+
<Channel position="1">
|
| 1593 |
+
<Source>PBMC</Source>
|
| 1594 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 1595 |
+
<Characteristics tag="Sex">
|
| 1596 |
+
female
|
| 1597 |
+
</Characteristics>
|
| 1598 |
+
<Characteristics tag="disease state">
|
| 1599 |
+
CFS
|
| 1600 |
+
</Characteristics>
|
| 1601 |
+
<Molecule>genomic DNA</Molecule>
|
| 1602 |
+
<Extract-Protocol>
|
| 1603 |
+
Genomic DNA was extracted and purified from Omega EZNA Tissue DNA Kit according to manufacturer's instructions
|
| 1604 |
+
</Extract-Protocol>
|
| 1605 |
+
<Label>Cy3 and Cy5</Label>
|
| 1606 |
+
<Label-Protocol>
|
| 1607 |
+
Standard Illumina Protocol
|
| 1608 |
+
</Label-Protocol>
|
| 1609 |
+
</Channel>
|
| 1610 |
+
<Hybridization-Protocol>
|
| 1611 |
+
Bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol
|
| 1612 |
+
</Hybridization-Protocol>
|
| 1613 |
+
<Scan-Protocol>
|
| 1614 |
+
Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
|
| 1615 |
+
</Scan-Protocol>
|
| 1616 |
+
<Description>
|
| 1617 |
+
CFS Genomic DNA
|
| 1618 |
+
</Description>
|
| 1619 |
+
<Data-Processing>
|
| 1620 |
+
BeadStudio software v3.2
|
| 1621 |
+
</Data-Processing>
|
| 1622 |
+
<Platform-Ref ref="GPL13534" />
|
| 1623 |
+
<Contact-Ref ref="contrib1" />
|
| 1624 |
+
<Supplementary-Data type="IDAT">
|
| 1625 |
+
ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2739nnn/GSM2739742/suppl/GSM2739742_3999356028_R05C01_Grn.idat.gz
|
| 1626 |
+
</Supplementary-Data>
|
| 1627 |
+
<Supplementary-Data type="IDAT">
|
| 1628 |
+
ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2739nnn/GSM2739742/suppl/GSM2739742_3999356028_R05C01_Red.idat.gz
|
| 1629 |
+
</Supplementary-Data>
|
| 1630 |
+
<Data-Table>
|
| 1631 |
+
<Column position="1">
|
| 1632 |
+
<Name>ID_REF</Name>
|
| 1633 |
+
</Column>
|
| 1634 |
+
<Column position="2">
|
| 1635 |
+
<Name>VALUE</Name>
|
| 1636 |
+
<Description>Average Beta non-normalized Beta</Description>
|
| 1637 |
+
</Column>
|
| 1638 |
+
<Column position="3">
|
| 1639 |
+
<Name>Detection Pval</Name>
|
| 1640 |
+
</Column>
|
| 1641 |
+
<External-Data rows="467971">
|
| 1642 |
+
GSM2739742-tbl-1.txt
|
| 1643 |
+
</External-Data>
|
| 1644 |
+
</Data-Table>
|
| 1645 |
+
</Sample>
|
| 1646 |
+
|
| 1647 |
+
<Sample iid="GSM2739743">
|
| 1648 |
+
<Status database="GEO">
|
| 1649 |
+
<Submission-Date>2017-08-10</Submission-Date>
|
| 1650 |
+
<Release-Date>2017-12-31</Release-Date>
|
| 1651 |
+
<Last-Update-Date>2018-01-23</Last-Update-Date>
|
| 1652 |
+
</Status>
|
| 1653 |
+
<Title>PBMC Genomic DNA G00256</Title>
|
| 1654 |
+
<Accession database="GEO">GSM2739743</Accession>
|
| 1655 |
+
<Type>genomic</Type>
|
| 1656 |
+
<Channel-Count>1</Channel-Count>
|
| 1657 |
+
<Channel position="1">
|
| 1658 |
+
<Source>PBMC</Source>
|
| 1659 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 1660 |
+
<Characteristics tag="Sex">
|
| 1661 |
+
female
|
| 1662 |
+
</Characteristics>
|
| 1663 |
+
<Characteristics tag="disease state">
|
| 1664 |
+
CFS
|
| 1665 |
+
</Characteristics>
|
| 1666 |
+
<Molecule>genomic DNA</Molecule>
|
| 1667 |
+
<Extract-Protocol>
|
| 1668 |
+
Genomic DNA was extracted and purified from Omega EZNA Tissue DNA Kit according to manufacturer's instructions
|
| 1669 |
+
</Extract-Protocol>
|
| 1670 |
+
<Label>Cy3 and Cy5</Label>
|
| 1671 |
+
<Label-Protocol>
|
| 1672 |
+
Standard Illumina Protocol
|
| 1673 |
+
</Label-Protocol>
|
| 1674 |
+
</Channel>
|
| 1675 |
+
<Hybridization-Protocol>
|
| 1676 |
+
Bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol
|
| 1677 |
+
</Hybridization-Protocol>
|
| 1678 |
+
<Scan-Protocol>
|
| 1679 |
+
Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
|
| 1680 |
+
</Scan-Protocol>
|
| 1681 |
+
<Description>
|
| 1682 |
+
CFS Genomic DNA
|
| 1683 |
+
</Description>
|
| 1684 |
+
<Data-Processing>
|
| 1685 |
+
BeadStudio software v3.2
|
| 1686 |
+
</Data-Processing>
|
| 1687 |
+
<Platform-Ref ref="GPL13534" />
|
| 1688 |
+
<Contact-Ref ref="contrib1" />
|
| 1689 |
+
<Supplementary-Data type="IDAT">
|
| 1690 |
+
ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2739nnn/GSM2739743/suppl/GSM2739743_3999356028_R06C01_Grn.idat.gz
|
| 1691 |
+
</Supplementary-Data>
|
| 1692 |
+
<Supplementary-Data type="IDAT">
|
| 1693 |
+
ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2739nnn/GSM2739743/suppl/GSM2739743_3999356028_R06C01_Red.idat.gz
|
| 1694 |
+
</Supplementary-Data>
|
| 1695 |
+
<Data-Table>
|
| 1696 |
+
<Column position="1">
|
| 1697 |
+
<Name>ID_REF</Name>
|
| 1698 |
+
</Column>
|
| 1699 |
+
<Column position="2">
|
| 1700 |
+
<Name>VALUE</Name>
|
| 1701 |
+
<Description>Average Beta non-normalized Beta</Description>
|
| 1702 |
+
</Column>
|
| 1703 |
+
<Column position="3">
|
| 1704 |
+
<Name>Detection Pval</Name>
|
| 1705 |
+
</Column>
|
| 1706 |
+
<External-Data rows="467971">
|
| 1707 |
+
GSM2739743-tbl-1.txt
|
| 1708 |
+
</External-Data>
|
| 1709 |
+
</Data-Table>
|
| 1710 |
+
</Sample>
|
| 1711 |
+
|
| 1712 |
+
<Sample iid="GSM2739744">
|
| 1713 |
+
<Status database="GEO">
|
| 1714 |
+
<Submission-Date>2017-08-10</Submission-Date>
|
| 1715 |
+
<Release-Date>2017-12-31</Release-Date>
|
| 1716 |
+
<Last-Update-Date>2018-01-23</Last-Update-Date>
|
| 1717 |
+
</Status>
|
| 1718 |
+
<Title>PBMC Genomic DNA G00262</Title>
|
| 1719 |
+
<Accession database="GEO">GSM2739744</Accession>
|
| 1720 |
+
<Type>genomic</Type>
|
| 1721 |
+
<Channel-Count>1</Channel-Count>
|
| 1722 |
+
<Channel position="1">
|
| 1723 |
+
<Source>PBMC</Source>
|
| 1724 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 1725 |
+
<Characteristics tag="Sex">
|
| 1726 |
+
female
|
| 1727 |
+
</Characteristics>
|
| 1728 |
+
<Characteristics tag="disease state">
|
| 1729 |
+
CFS
|
| 1730 |
+
</Characteristics>
|
| 1731 |
+
<Molecule>genomic DNA</Molecule>
|
| 1732 |
+
<Extract-Protocol>
|
| 1733 |
+
Genomic DNA was extracted and purified from Omega EZNA Tissue DNA Kit according to manufacturer's instructions
|
| 1734 |
+
</Extract-Protocol>
|
| 1735 |
+
<Label>Cy3 and Cy5</Label>
|
| 1736 |
+
<Label-Protocol>
|
| 1737 |
+
Standard Illumina Protocol
|
| 1738 |
+
</Label-Protocol>
|
| 1739 |
+
</Channel>
|
| 1740 |
+
<Hybridization-Protocol>
|
| 1741 |
+
Bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol
|
| 1742 |
+
</Hybridization-Protocol>
|
| 1743 |
+
<Scan-Protocol>
|
| 1744 |
+
Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
|
| 1745 |
+
</Scan-Protocol>
|
| 1746 |
+
<Description>
|
| 1747 |
+
CFS Genomic DNA
|
| 1748 |
+
</Description>
|
| 1749 |
+
<Data-Processing>
|
| 1750 |
+
BeadStudio software v3.2
|
| 1751 |
+
</Data-Processing>
|
| 1752 |
+
<Platform-Ref ref="GPL13534" />
|
| 1753 |
+
<Contact-Ref ref="contrib1" />
|
| 1754 |
+
<Supplementary-Data type="IDAT">
|
| 1755 |
+
ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2739nnn/GSM2739744/suppl/GSM2739744_3999834039_R01C01_Grn.idat.gz
|
| 1756 |
+
</Supplementary-Data>
|
| 1757 |
+
<Supplementary-Data type="IDAT">
|
| 1758 |
+
ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2739nnn/GSM2739744/suppl/GSM2739744_3999834039_R01C01_Red.idat.gz
|
| 1759 |
+
</Supplementary-Data>
|
| 1760 |
+
<Data-Table>
|
| 1761 |
+
<Column position="1">
|
| 1762 |
+
<Name>ID_REF</Name>
|
| 1763 |
+
</Column>
|
| 1764 |
+
<Column position="2">
|
| 1765 |
+
<Name>VALUE</Name>
|
| 1766 |
+
<Description>Average Beta non-normalized Beta</Description>
|
| 1767 |
+
</Column>
|
| 1768 |
+
<Column position="3">
|
| 1769 |
+
<Name>Detection Pval</Name>
|
| 1770 |
+
</Column>
|
| 1771 |
+
<External-Data rows="467971">
|
| 1772 |
+
GSM2739744-tbl-1.txt
|
| 1773 |
+
</External-Data>
|
| 1774 |
+
</Data-Table>
|
| 1775 |
+
</Sample>
|
| 1776 |
+
|
| 1777 |
+
<Sample iid="GSM2739745">
|
| 1778 |
+
<Status database="GEO">
|
| 1779 |
+
<Submission-Date>2017-08-10</Submission-Date>
|
| 1780 |
+
<Release-Date>2017-12-31</Release-Date>
|
| 1781 |
+
<Last-Update-Date>2018-01-23</Last-Update-Date>
|
| 1782 |
+
</Status>
|
| 1783 |
+
<Title>PBMC Genomic DNA G00263</Title>
|
| 1784 |
+
<Accession database="GEO">GSM2739745</Accession>
|
| 1785 |
+
<Type>genomic</Type>
|
| 1786 |
+
<Channel-Count>1</Channel-Count>
|
| 1787 |
+
<Channel position="1">
|
| 1788 |
+
<Source>PBMC</Source>
|
| 1789 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 1790 |
+
<Characteristics tag="Sex">
|
| 1791 |
+
female
|
| 1792 |
+
</Characteristics>
|
| 1793 |
+
<Characteristics tag="disease state">
|
| 1794 |
+
CFS
|
| 1795 |
+
</Characteristics>
|
| 1796 |
+
<Molecule>genomic DNA</Molecule>
|
| 1797 |
+
<Extract-Protocol>
|
| 1798 |
+
Genomic DNA was extracted and purified from Omega EZNA Tissue DNA Kit according to manufacturer's instructions
|
| 1799 |
+
</Extract-Protocol>
|
| 1800 |
+
<Label>Cy3 and Cy5</Label>
|
| 1801 |
+
<Label-Protocol>
|
| 1802 |
+
Standard Illumina Protocol
|
| 1803 |
+
</Label-Protocol>
|
| 1804 |
+
</Channel>
|
| 1805 |
+
<Hybridization-Protocol>
|
| 1806 |
+
Bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol
|
| 1807 |
+
</Hybridization-Protocol>
|
| 1808 |
+
<Scan-Protocol>
|
| 1809 |
+
Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
|
| 1810 |
+
</Scan-Protocol>
|
| 1811 |
+
<Description>
|
| 1812 |
+
CFS Genomic DNA
|
| 1813 |
+
</Description>
|
| 1814 |
+
<Data-Processing>
|
| 1815 |
+
BeadStudio software v3.2
|
| 1816 |
+
</Data-Processing>
|
| 1817 |
+
<Platform-Ref ref="GPL13534" />
|
| 1818 |
+
<Contact-Ref ref="contrib1" />
|
| 1819 |
+
<Supplementary-Data type="IDAT">
|
| 1820 |
+
ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2739nnn/GSM2739745/suppl/GSM2739745_3999834039_R02C01_Grn.idat.gz
|
| 1821 |
+
</Supplementary-Data>
|
| 1822 |
+
<Supplementary-Data type="IDAT">
|
| 1823 |
+
ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2739nnn/GSM2739745/suppl/GSM2739745_3999834039_R02C01_Red.idat.gz
|
| 1824 |
+
</Supplementary-Data>
|
| 1825 |
+
<Data-Table>
|
| 1826 |
+
<Column position="1">
|
| 1827 |
+
<Name>ID_REF</Name>
|
| 1828 |
+
</Column>
|
| 1829 |
+
<Column position="2">
|
| 1830 |
+
<Name>VALUE</Name>
|
| 1831 |
+
<Description>Average Beta non-normalized Beta</Description>
|
| 1832 |
+
</Column>
|
| 1833 |
+
<Column position="3">
|
| 1834 |
+
<Name>Detection Pval</Name>
|
| 1835 |
+
</Column>
|
| 1836 |
+
<External-Data rows="467971">
|
| 1837 |
+
GSM2739745-tbl-1.txt
|
| 1838 |
+
</External-Data>
|
| 1839 |
+
</Data-Table>
|
| 1840 |
+
</Sample>
|
| 1841 |
+
|
| 1842 |
+
<Series iid="GSE102504">
|
| 1843 |
+
<Status database="GEO">
|
| 1844 |
+
<Submission-Date>2017-08-10</Submission-Date>
|
| 1845 |
+
<Release-Date>2017-12-31</Release-Date>
|
| 1846 |
+
<Last-Update-Date>2021-07-25</Last-Update-Date>
|
| 1847 |
+
</Status>
|
| 1848 |
+
<Title>DNA methylome modifications and subtyping in ME/CFS</Title>
|
| 1849 |
+
<Accession database="GEO">GSE102504</Accession>
|
| 1850 |
+
<Pubmed-ID>29692205</Pubmed-ID>
|
| 1851 |
+
<Summary>
|
| 1852 |
+
Examination of DNA methylome patterns for potential subtypes in a larger cohort of ME/CFS samples using the Illumina Infinium HumanMethylation450 Beadchip Array
|
| 1853 |
+
Bisulfite-converted DNA from 25 samples were hybridised onto the Illumina Infinium HumanMethylation450 Beadchip Array
|
| 1854 |
+
</Summary>
|
| 1855 |
+
<Overall-Design>
|
| 1856 |
+
Bisulfite-converted DNA from 25 samples were hybridised onto the Illumina Infinium HumanMethylation450 Beadchip Array
|
| 1857 |
+
</Overall-Design>
|
| 1858 |
+
<Type>Methylation profiling by array</Type>
|
| 1859 |
+
<Contributor-Ref ref="contrib3" position="1" />
|
| 1860 |
+
<Contributor-Ref ref="contrib4" position="2" />
|
| 1861 |
+
<Contributor-Ref ref="contrib5" position="3" />
|
| 1862 |
+
<Contact-Ref ref="contrib1" />
|
| 1863 |
+
<Sample-Ref ref="GSM2739721" />
|
| 1864 |
+
<Sample-Ref ref="GSM2739722" />
|
| 1865 |
+
<Sample-Ref ref="GSM2739723" />
|
| 1866 |
+
<Sample-Ref ref="GSM2739724" />
|
| 1867 |
+
<Sample-Ref ref="GSM2739725" />
|
| 1868 |
+
<Sample-Ref ref="GSM2739726" />
|
| 1869 |
+
<Sample-Ref ref="GSM2739727" />
|
| 1870 |
+
<Sample-Ref ref="GSM2739728" />
|
| 1871 |
+
<Sample-Ref ref="GSM2739729" />
|
| 1872 |
+
<Sample-Ref ref="GSM2739730" />
|
| 1873 |
+
<Sample-Ref ref="GSM2739731" />
|
| 1874 |
+
<Sample-Ref ref="GSM2739732" />
|
| 1875 |
+
<Sample-Ref ref="GSM2739733" />
|
| 1876 |
+
<Sample-Ref ref="GSM2739734" />
|
| 1877 |
+
<Sample-Ref ref="GSM2739735" />
|
| 1878 |
+
<Sample-Ref ref="GSM2739736" />
|
| 1879 |
+
<Sample-Ref ref="GSM2739737" />
|
| 1880 |
+
<Sample-Ref ref="GSM2739738" />
|
| 1881 |
+
<Sample-Ref ref="GSM2739739" />
|
| 1882 |
+
<Sample-Ref ref="GSM2739740" />
|
| 1883 |
+
<Sample-Ref ref="GSM2739741" />
|
| 1884 |
+
<Sample-Ref ref="GSM2739742" />
|
| 1885 |
+
<Sample-Ref ref="GSM2739743" />
|
| 1886 |
+
<Sample-Ref ref="GSM2739744" />
|
| 1887 |
+
<Sample-Ref ref="GSM2739745" />
|
| 1888 |
+
<Supplementary-Data type="TAR">
|
| 1889 |
+
ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE102nnn/GSE102504/suppl/GSE102504_RAW.tar
|
| 1890 |
+
</Supplementary-Data>
|
| 1891 |
+
<Supplementary-Data type="TXT">
|
| 1892 |
+
ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE102nnn/GSE102504/suppl/GSE102504_signal_intensities.txt.gz
|
| 1893 |
+
</Supplementary-Data>
|
| 1894 |
+
<Relation type="BioProject" target="https://www.ncbi.nlm.nih.gov/bioproject/PRJNA397901" />
|
| 1895 |
+
</Series>
|
| 1896 |
+
|
| 1897 |
+
</MINiML>
|
ME/GSE111183/meta/GSE111183_family.xml/GSE111183_family.xml
ADDED
|
@@ -0,0 +1,1906 @@
|
|
|
|
|
|
|
|
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|
|
|
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|
|
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|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
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|
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|
|
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|
|
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|
|
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|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
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|
|
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|
| 1 |
+
<?xml version="1.0" encoding="UTF-8" standalone="no"?>
|
| 2 |
+
|
| 3 |
+
<MINiML
|
| 4 |
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xmlns="http://www.ncbi.nlm.nih.gov/geo/info/MINiML"
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| 5 |
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xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
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| 6 |
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xsi:schemaLocation="http://www.ncbi.nlm.nih.gov/geo/info/MINiML http://www.ncbi.nlm.nih.gov/geo/info/MINiML.xsd"
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| 7 |
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version="0.5.0" >
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| 9 |
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|
| 10 |
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|
| 11 |
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<Email>lnathanson@nova.edu</Email>
|
| 12 |
+
<Department>INIM</Department>
|
| 13 |
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<Organization>Nova Southeastern University</Organization>
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| 14 |
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<Address>
|
| 15 |
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<Line>3321 College Ave.</Line>
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| 16 |
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<City>Fort Lauderdale</City>
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| 17 |
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<State>Florida</State>
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| 18 |
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<Zip-Code>33314</Zip-Code>
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| 19 |
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<Country>USA</Country>
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| 20 |
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</Address>
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| 21 |
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| 22 |
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|
| 23 |
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<Contributor iid="contrib2">
|
| 24 |
+
<Organization>Illumina Inc.</Organization>
|
| 25 |
+
<Email>expression@illumina.com, techsupport@illumina.com</Email>
|
| 26 |
+
<Phone>1 800 809 4566 </Phone>
|
| 27 |
+
<Organization>Illumina Inc.</Organization>
|
| 28 |
+
<Address>
|
| 29 |
+
<Line>9885 Towne Centre Drive</Line>
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| 30 |
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<City>San Diego</City>
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| 31 |
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<State>CA</State>
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| 32 |
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<Zip-Code>92121</Zip-Code>
|
| 33 |
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<Country>USA</Country>
|
| 34 |
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</Address>
|
| 35 |
+
<Web-Link>www.illumina.com</Web-Link>
|
| 36 |
+
</Contributor>
|
| 37 |
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|
| 38 |
+
<Contributor iid="contrib3">
|
| 39 |
+
<Person><First>Malav</First><Middle>S</Middle><Last>Trivedi</Last></Person>
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| 40 |
+
</Contributor>
|
| 41 |
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|
| 42 |
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<Contributor iid="contrib4">
|
| 43 |
+
<Person><First>Elisa</First><Last>Oltra</Last></Person>
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| 44 |
+
</Contributor>
|
| 45 |
+
|
| 46 |
+
<Contributor iid="contrib5">
|
| 47 |
+
<Person><First>Leonor</First><Last>Sarria</Last></Person>
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| 48 |
+
</Contributor>
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| 49 |
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|
| 50 |
+
<Contributor iid="contrib6">
|
| 51 |
+
<Person><First>Natasha</First><Last>Rose</Last></Person>
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| 52 |
+
</Contributor>
|
| 53 |
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|
| 54 |
+
<Contributor iid="contrib7">
|
| 55 |
+
<Person><First>Vladimir</First><Last>Beljanski</Last></Person>
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| 56 |
+
</Contributor>
|
| 57 |
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|
| 58 |
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<Contributor iid="contrib8">
|
| 59 |
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<Person><First>Mary</First><Middle>A</Middle><Last>Fletcher</Last></Person>
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| 60 |
+
</Contributor>
|
| 61 |
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|
| 62 |
+
<Contributor iid="contrib9">
|
| 63 |
+
<Person><First>Nancy</First><Middle>G</Middle><Last>Klimas</Last></Person>
|
| 64 |
+
</Contributor>
|
| 65 |
+
|
| 66 |
+
<Database iid="GEO">
|
| 67 |
+
<Name>Gene Expression Omnibus (GEO)</Name>
|
| 68 |
+
<Public-ID>GEO</Public-ID>
|
| 69 |
+
<Organization>NCBI NLM NIH</Organization>
|
| 70 |
+
<Web-Link>http://www.ncbi.nlm.nih.gov/geo</Web-Link>
|
| 71 |
+
<Email>geo@ncbi.nlm.nih.gov</Email>
|
| 72 |
+
</Database>
|
| 73 |
+
|
| 74 |
+
<Platform iid="GPL21145">
|
| 75 |
+
<Status database="GEO">
|
| 76 |
+
<Submission-Date>2015-11-16</Submission-Date>
|
| 77 |
+
<Release-Date>2015-11-16</Release-Date>
|
| 78 |
+
<Last-Update-Date>2019-01-20</Last-Update-Date>
|
| 79 |
+
</Status>
|
| 80 |
+
<Title>Infinium MethylationEPIC</Title>
|
| 81 |
+
<Accession database="GEO">GPL21145</Accession>
|
| 82 |
+
<Technology>oligonucleotide beads</Technology>
|
| 83 |
+
<Distribution>commercial</Distribution>
|
| 84 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 85 |
+
<Manufacturer>Illumina, Inc.</Manufacturer>
|
| 86 |
+
<Manufacture-Protocol>
|
| 87 |
+
See manufacturer's website
|
| 88 |
+
</Manufacture-Protocol>
|
| 89 |
+
<Contact-Ref ref="contrib2" />
|
| 90 |
+
<Supplementary-Data type="CSV">
|
| 91 |
+
ftp://ftp.ncbi.nlm.nih.gov/geo/platforms/GPL21nnn/GPL21145/suppl/GPL21145_MethylationEPIC_15073387_v-1-0.csv.gz
|
| 92 |
+
</Supplementary-Data>
|
| 93 |
+
<Relation type="Alternative to" target="GPL23976" />
|
| 94 |
+
<Data-Table>
|
| 95 |
+
<Column position="1">
|
| 96 |
+
<Name>ID</Name>
|
| 97 |
+
<Description>IlmnID</Description>
|
| 98 |
+
</Column>
|
| 99 |
+
<Column position="2">
|
| 100 |
+
<Name>SPOT_ID</Name>
|
| 101 |
+
</Column>
|
| 102 |
+
<Column position="3">
|
| 103 |
+
<Name>AddressA_ID</Name>
|
| 104 |
+
</Column>
|
| 105 |
+
<Column position="4">
|
| 106 |
+
<Name>AlleleA_ProbeSeq</Name>
|
| 107 |
+
</Column>
|
| 108 |
+
<Column position="5">
|
| 109 |
+
<Name>AddressB_ID</Name>
|
| 110 |
+
</Column>
|
| 111 |
+
<Column position="6">
|
| 112 |
+
<Name>AlleleB_ProbeSeq</Name>
|
| 113 |
+
</Column>
|
| 114 |
+
<Column position="7">
|
| 115 |
+
<Name>Infinium_Design_Type</Name>
|
| 116 |
+
</Column>
|
| 117 |
+
<Column position="8">
|
| 118 |
+
<Name>Next_Base</Name>
|
| 119 |
+
</Column>
|
| 120 |
+
<Column position="9">
|
| 121 |
+
<Name>Color_Channel</Name>
|
| 122 |
+
</Column>
|
| 123 |
+
<Column position="10">
|
| 124 |
+
<Name>Forward_Sequence</Name>
|
| 125 |
+
</Column>
|
| 126 |
+
<Column position="11">
|
| 127 |
+
<Name>Genome_Build</Name>
|
| 128 |
+
</Column>
|
| 129 |
+
<Column position="12">
|
| 130 |
+
<Name>CHR</Name>
|
| 131 |
+
</Column>
|
| 132 |
+
<Column position="13">
|
| 133 |
+
<Name>MAPINFO</Name>
|
| 134 |
+
</Column>
|
| 135 |
+
<Column position="14">
|
| 136 |
+
<Name>SourceSeq</Name>
|
| 137 |
+
</Column>
|
| 138 |
+
<External-Data rows="868564">
|
| 139 |
+
GPL21145-tbl-1.txt
|
| 140 |
+
</External-Data>
|
| 141 |
+
</Data-Table>
|
| 142 |
+
</Platform>
|
| 143 |
+
|
| 144 |
+
<Sample iid="GSM3024927">
|
| 145 |
+
<Status database="GEO">
|
| 146 |
+
<Submission-Date>2018-02-27</Submission-Date>
|
| 147 |
+
<Release-Date>2018-07-23</Release-Date>
|
| 148 |
+
<Last-Update-Date>2018-07-23</Last-Update-Date>
|
| 149 |
+
</Status>
|
| 150 |
+
<Title>PBMC genomic DNA ME/CFS 1</Title>
|
| 151 |
+
<Accession database="GEO">GSM3024927</Accession>
|
| 152 |
+
<Type>genomic</Type>
|
| 153 |
+
<Channel-Count>1</Channel-Count>
|
| 154 |
+
<Channel position="1">
|
| 155 |
+
<Source>ME/CFS PBMC</Source>
|
| 156 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 157 |
+
<Characteristics tag="gender">
|
| 158 |
+
female
|
| 159 |
+
</Characteristics>
|
| 160 |
+
<Characteristics tag="subject id">
|
| 161 |
+
ME/CFS subject 1
|
| 162 |
+
</Characteristics>
|
| 163 |
+
<Characteristics tag="disease state">
|
| 164 |
+
Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS)
|
| 165 |
+
</Characteristics>
|
| 166 |
+
<Characteristics tag="cell type">
|
| 167 |
+
peripheral blood mononuclear cells (PBMC)
|
| 168 |
+
</Characteristics>
|
| 169 |
+
<Molecule>genomic DNA</Molecule>
|
| 170 |
+
<Extract-Protocol>
|
| 171 |
+
genomic DNA was extracted and purified from PBMC samples using Qiagen DNeasy Blood & Tissue Kit according to manufacturer instructions
|
| 172 |
+
</Extract-Protocol>
|
| 173 |
+
<Label>Cy3, Cy5</Label>
|
| 174 |
+
<Label-Protocol>
|
| 175 |
+
Standard Illumina Protocol
|
| 176 |
+
</Label-Protocol>
|
| 177 |
+
</Channel>
|
| 178 |
+
<Hybridization-Protocol>
|
| 179 |
+
bisulphite converted DNA was hybridised to Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol
|
| 180 |
+
</Hybridization-Protocol>
|
| 181 |
+
<Scan-Protocol>
|
| 182 |
+
Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
|
| 183 |
+
</Scan-Protocol>
|
| 184 |
+
<Description>
|
| 185 |
+
PBMC genomic DNA from ME/CFS subject 1
|
| 186 |
+
</Description>
|
| 187 |
+
<Data-Processing>
|
| 188 |
+
Illumina Genome Studio; Matrix signal intensities contains unmethylated and methylated signal intensities; Matrix processed contains non-normalized average beta values.
|
| 189 |
+
</Data-Processing>
|
| 190 |
+
<Platform-Ref ref="GPL21145" />
|
| 191 |
+
<Contact-Ref ref="contrib1" />
|
| 192 |
+
<Supplementary-Data type="unknown">
|
| 193 |
+
NONE
|
| 194 |
+
</Supplementary-Data>
|
| 195 |
+
<Data-Table>
|
| 196 |
+
<Column position="1">
|
| 197 |
+
<Name>ID_REF</Name>
|
| 198 |
+
</Column>
|
| 199 |
+
<Column position="2">
|
| 200 |
+
<Name>VALUE</Name>
|
| 201 |
+
<Description>Average Beta</Description>
|
| 202 |
+
</Column>
|
| 203 |
+
<Column position="3">
|
| 204 |
+
<Name>Detection Pval</Name>
|
| 205 |
+
</Column>
|
| 206 |
+
<External-Data rows="866895">
|
| 207 |
+
GSM3024927-tbl-1.txt
|
| 208 |
+
</External-Data>
|
| 209 |
+
</Data-Table>
|
| 210 |
+
</Sample>
|
| 211 |
+
|
| 212 |
+
<Sample iid="GSM3024928">
|
| 213 |
+
<Status database="GEO">
|
| 214 |
+
<Submission-Date>2018-02-27</Submission-Date>
|
| 215 |
+
<Release-Date>2018-07-23</Release-Date>
|
| 216 |
+
<Last-Update-Date>2018-07-23</Last-Update-Date>
|
| 217 |
+
</Status>
|
| 218 |
+
<Title>PBMC genomic DNA Healthy Control (HC) 1</Title>
|
| 219 |
+
<Accession database="GEO">GSM3024928</Accession>
|
| 220 |
+
<Type>genomic</Type>
|
| 221 |
+
<Channel-Count>1</Channel-Count>
|
| 222 |
+
<Channel position="1">
|
| 223 |
+
<Source>HC PBMC</Source>
|
| 224 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 225 |
+
<Characteristics tag="gender">
|
| 226 |
+
female
|
| 227 |
+
</Characteristics>
|
| 228 |
+
<Characteristics tag="subject id">
|
| 229 |
+
HC subject 1
|
| 230 |
+
</Characteristics>
|
| 231 |
+
<Characteristics tag="disease state">
|
| 232 |
+
Healthy Control (HC)
|
| 233 |
+
</Characteristics>
|
| 234 |
+
<Characteristics tag="cell type">
|
| 235 |
+
peripheral blood mononuclear cells (PBMC)
|
| 236 |
+
</Characteristics>
|
| 237 |
+
<Molecule>genomic DNA</Molecule>
|
| 238 |
+
<Extract-Protocol>
|
| 239 |
+
genomic DNA was extracted and purified from PBMC samples using Qiagen DNeasy Blood & Tissue Kit according to manufacturer instructions
|
| 240 |
+
</Extract-Protocol>
|
| 241 |
+
<Label>Cy3, Cy5</Label>
|
| 242 |
+
<Label-Protocol>
|
| 243 |
+
Standard Illumina Protocol
|
| 244 |
+
</Label-Protocol>
|
| 245 |
+
</Channel>
|
| 246 |
+
<Hybridization-Protocol>
|
| 247 |
+
bisulphite converted DNA was hybridised to Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol
|
| 248 |
+
</Hybridization-Protocol>
|
| 249 |
+
<Scan-Protocol>
|
| 250 |
+
Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
|
| 251 |
+
</Scan-Protocol>
|
| 252 |
+
<Description>
|
| 253 |
+
PBMC genomic DNA from HC subject 1
|
| 254 |
+
</Description>
|
| 255 |
+
<Data-Processing>
|
| 256 |
+
Illumina Genome Studio; Matrix signal intensities contains unmethylated and methylated signal intensities; Matrix processed contains non-normalized average beta values.
|
| 257 |
+
</Data-Processing>
|
| 258 |
+
<Platform-Ref ref="GPL21145" />
|
| 259 |
+
<Contact-Ref ref="contrib1" />
|
| 260 |
+
<Supplementary-Data type="unknown">
|
| 261 |
+
NONE
|
| 262 |
+
</Supplementary-Data>
|
| 263 |
+
<Data-Table>
|
| 264 |
+
<Column position="1">
|
| 265 |
+
<Name>ID_REF</Name>
|
| 266 |
+
</Column>
|
| 267 |
+
<Column position="2">
|
| 268 |
+
<Name>VALUE</Name>
|
| 269 |
+
<Description>Average Beta</Description>
|
| 270 |
+
</Column>
|
| 271 |
+
<Column position="3">
|
| 272 |
+
<Name>Detection Pval</Name>
|
| 273 |
+
</Column>
|
| 274 |
+
<External-Data rows="866895">
|
| 275 |
+
GSM3024928-tbl-1.txt
|
| 276 |
+
</External-Data>
|
| 277 |
+
</Data-Table>
|
| 278 |
+
</Sample>
|
| 279 |
+
|
| 280 |
+
<Sample iid="GSM3024929">
|
| 281 |
+
<Status database="GEO">
|
| 282 |
+
<Submission-Date>2018-02-27</Submission-Date>
|
| 283 |
+
<Release-Date>2018-07-23</Release-Date>
|
| 284 |
+
<Last-Update-Date>2018-07-23</Last-Update-Date>
|
| 285 |
+
</Status>
|
| 286 |
+
<Title>PBMC genomic DNA ME/CFS 2</Title>
|
| 287 |
+
<Accession database="GEO">GSM3024929</Accession>
|
| 288 |
+
<Type>genomic</Type>
|
| 289 |
+
<Channel-Count>1</Channel-Count>
|
| 290 |
+
<Channel position="1">
|
| 291 |
+
<Source>ME/CFS PBMC</Source>
|
| 292 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 293 |
+
<Characteristics tag="gender">
|
| 294 |
+
female
|
| 295 |
+
</Characteristics>
|
| 296 |
+
<Characteristics tag="subject id">
|
| 297 |
+
ME/CFS subject 2
|
| 298 |
+
</Characteristics>
|
| 299 |
+
<Characteristics tag="disease state">
|
| 300 |
+
Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS)
|
| 301 |
+
</Characteristics>
|
| 302 |
+
<Characteristics tag="cell type">
|
| 303 |
+
peripheral blood mononuclear cells (PBMC)
|
| 304 |
+
</Characteristics>
|
| 305 |
+
<Molecule>genomic DNA</Molecule>
|
| 306 |
+
<Extract-Protocol>
|
| 307 |
+
genomic DNA was extracted and purified from PBMC samples using Qiagen DNeasy Blood & Tissue Kit according to manufacturer instructions
|
| 308 |
+
</Extract-Protocol>
|
| 309 |
+
<Label>Cy3, Cy5</Label>
|
| 310 |
+
<Label-Protocol>
|
| 311 |
+
Standard Illumina Protocol
|
| 312 |
+
</Label-Protocol>
|
| 313 |
+
</Channel>
|
| 314 |
+
<Hybridization-Protocol>
|
| 315 |
+
bisulphite converted DNA was hybridised to Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol
|
| 316 |
+
</Hybridization-Protocol>
|
| 317 |
+
<Scan-Protocol>
|
| 318 |
+
Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
|
| 319 |
+
</Scan-Protocol>
|
| 320 |
+
<Description>
|
| 321 |
+
PBMC genomic DNA from ME/CFS subject 2
|
| 322 |
+
</Description>
|
| 323 |
+
<Data-Processing>
|
| 324 |
+
Illumina Genome Studio; Matrix signal intensities contains unmethylated and methylated signal intensities; Matrix processed contains non-normalized average beta values.
|
| 325 |
+
</Data-Processing>
|
| 326 |
+
<Platform-Ref ref="GPL21145" />
|
| 327 |
+
<Contact-Ref ref="contrib1" />
|
| 328 |
+
<Supplementary-Data type="unknown">
|
| 329 |
+
NONE
|
| 330 |
+
</Supplementary-Data>
|
| 331 |
+
<Data-Table>
|
| 332 |
+
<Column position="1">
|
| 333 |
+
<Name>ID_REF</Name>
|
| 334 |
+
</Column>
|
| 335 |
+
<Column position="2">
|
| 336 |
+
<Name>VALUE</Name>
|
| 337 |
+
<Description>Average Beta</Description>
|
| 338 |
+
</Column>
|
| 339 |
+
<Column position="3">
|
| 340 |
+
<Name>Detection Pval</Name>
|
| 341 |
+
</Column>
|
| 342 |
+
<External-Data rows="866895">
|
| 343 |
+
GSM3024929-tbl-1.txt
|
| 344 |
+
</External-Data>
|
| 345 |
+
</Data-Table>
|
| 346 |
+
</Sample>
|
| 347 |
+
|
| 348 |
+
<Sample iid="GSM3024930">
|
| 349 |
+
<Status database="GEO">
|
| 350 |
+
<Submission-Date>2018-02-27</Submission-Date>
|
| 351 |
+
<Release-Date>2018-07-23</Release-Date>
|
| 352 |
+
<Last-Update-Date>2018-07-23</Last-Update-Date>
|
| 353 |
+
</Status>
|
| 354 |
+
<Title>PBMC genomic DNA ME/CFS 3</Title>
|
| 355 |
+
<Accession database="GEO">GSM3024930</Accession>
|
| 356 |
+
<Type>genomic</Type>
|
| 357 |
+
<Channel-Count>1</Channel-Count>
|
| 358 |
+
<Channel position="1">
|
| 359 |
+
<Source>ME/CFS PBMC</Source>
|
| 360 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 361 |
+
<Characteristics tag="gender">
|
| 362 |
+
female
|
| 363 |
+
</Characteristics>
|
| 364 |
+
<Characteristics tag="subject id">
|
| 365 |
+
ME/CFS subject 3
|
| 366 |
+
</Characteristics>
|
| 367 |
+
<Characteristics tag="disease state">
|
| 368 |
+
Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS)
|
| 369 |
+
</Characteristics>
|
| 370 |
+
<Characteristics tag="cell type">
|
| 371 |
+
peripheral blood mononuclear cells (PBMC)
|
| 372 |
+
</Characteristics>
|
| 373 |
+
<Molecule>genomic DNA</Molecule>
|
| 374 |
+
<Extract-Protocol>
|
| 375 |
+
genomic DNA was extracted and purified from PBMC samples using Qiagen DNeasy Blood & Tissue Kit according to manufacturer instructions
|
| 376 |
+
</Extract-Protocol>
|
| 377 |
+
<Label>Cy3, Cy5</Label>
|
| 378 |
+
<Label-Protocol>
|
| 379 |
+
Standard Illumina Protocol
|
| 380 |
+
</Label-Protocol>
|
| 381 |
+
</Channel>
|
| 382 |
+
<Hybridization-Protocol>
|
| 383 |
+
bisulphite converted DNA was hybridised to Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol
|
| 384 |
+
</Hybridization-Protocol>
|
| 385 |
+
<Scan-Protocol>
|
| 386 |
+
Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
|
| 387 |
+
</Scan-Protocol>
|
| 388 |
+
<Description>
|
| 389 |
+
PBMC genomic DNA from ME/CFS subject 3
|
| 390 |
+
</Description>
|
| 391 |
+
<Data-Processing>
|
| 392 |
+
Illumina Genome Studio; Matrix signal intensities contains unmethylated and methylated signal intensities; Matrix processed contains non-normalized average beta values.
|
| 393 |
+
</Data-Processing>
|
| 394 |
+
<Platform-Ref ref="GPL21145" />
|
| 395 |
+
<Contact-Ref ref="contrib1" />
|
| 396 |
+
<Supplementary-Data type="unknown">
|
| 397 |
+
NONE
|
| 398 |
+
</Supplementary-Data>
|
| 399 |
+
<Data-Table>
|
| 400 |
+
<Column position="1">
|
| 401 |
+
<Name>ID_REF</Name>
|
| 402 |
+
</Column>
|
| 403 |
+
<Column position="2">
|
| 404 |
+
<Name>VALUE</Name>
|
| 405 |
+
<Description>Average Beta</Description>
|
| 406 |
+
</Column>
|
| 407 |
+
<Column position="3">
|
| 408 |
+
<Name>Detection Pval</Name>
|
| 409 |
+
</Column>
|
| 410 |
+
<External-Data rows="866895">
|
| 411 |
+
GSM3024930-tbl-1.txt
|
| 412 |
+
</External-Data>
|
| 413 |
+
</Data-Table>
|
| 414 |
+
</Sample>
|
| 415 |
+
|
| 416 |
+
<Sample iid="GSM3024931">
|
| 417 |
+
<Status database="GEO">
|
| 418 |
+
<Submission-Date>2018-02-27</Submission-Date>
|
| 419 |
+
<Release-Date>2018-07-23</Release-Date>
|
| 420 |
+
<Last-Update-Date>2018-07-23</Last-Update-Date>
|
| 421 |
+
</Status>
|
| 422 |
+
<Title>PBMC genomic DNA Healthy Control (HC) 2</Title>
|
| 423 |
+
<Accession database="GEO">GSM3024931</Accession>
|
| 424 |
+
<Type>genomic</Type>
|
| 425 |
+
<Channel-Count>1</Channel-Count>
|
| 426 |
+
<Channel position="1">
|
| 427 |
+
<Source>HC PBMC</Source>
|
| 428 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 429 |
+
<Characteristics tag="gender">
|
| 430 |
+
female
|
| 431 |
+
</Characteristics>
|
| 432 |
+
<Characteristics tag="subject id">
|
| 433 |
+
HC subject 2
|
| 434 |
+
</Characteristics>
|
| 435 |
+
<Characteristics tag="disease state">
|
| 436 |
+
Healthy Control (HC)
|
| 437 |
+
</Characteristics>
|
| 438 |
+
<Characteristics tag="cell type">
|
| 439 |
+
peripheral blood mononuclear cells (PBMC)
|
| 440 |
+
</Characteristics>
|
| 441 |
+
<Molecule>genomic DNA</Molecule>
|
| 442 |
+
<Extract-Protocol>
|
| 443 |
+
genomic DNA was extracted and purified from PBMC samples using Qiagen DNeasy Blood & Tissue Kit according to manufacturer instructions
|
| 444 |
+
</Extract-Protocol>
|
| 445 |
+
<Label>Cy3, Cy5</Label>
|
| 446 |
+
<Label-Protocol>
|
| 447 |
+
Standard Illumina Protocol
|
| 448 |
+
</Label-Protocol>
|
| 449 |
+
</Channel>
|
| 450 |
+
<Hybridization-Protocol>
|
| 451 |
+
bisulphite converted DNA was hybridised to Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol
|
| 452 |
+
</Hybridization-Protocol>
|
| 453 |
+
<Scan-Protocol>
|
| 454 |
+
Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
|
| 455 |
+
</Scan-Protocol>
|
| 456 |
+
<Description>
|
| 457 |
+
PBMC genomic DNA from HC subject 2
|
| 458 |
+
</Description>
|
| 459 |
+
<Data-Processing>
|
| 460 |
+
Illumina Genome Studio; Matrix signal intensities contains unmethylated and methylated signal intensities; Matrix processed contains non-normalized average beta values.
|
| 461 |
+
</Data-Processing>
|
| 462 |
+
<Platform-Ref ref="GPL21145" />
|
| 463 |
+
<Contact-Ref ref="contrib1" />
|
| 464 |
+
<Supplementary-Data type="unknown">
|
| 465 |
+
NONE
|
| 466 |
+
</Supplementary-Data>
|
| 467 |
+
<Data-Table>
|
| 468 |
+
<Column position="1">
|
| 469 |
+
<Name>ID_REF</Name>
|
| 470 |
+
</Column>
|
| 471 |
+
<Column position="2">
|
| 472 |
+
<Name>VALUE</Name>
|
| 473 |
+
<Description>Average Beta</Description>
|
| 474 |
+
</Column>
|
| 475 |
+
<Column position="3">
|
| 476 |
+
<Name>Detection Pval</Name>
|
| 477 |
+
</Column>
|
| 478 |
+
<External-Data rows="866895">
|
| 479 |
+
GSM3024931-tbl-1.txt
|
| 480 |
+
</External-Data>
|
| 481 |
+
</Data-Table>
|
| 482 |
+
</Sample>
|
| 483 |
+
|
| 484 |
+
<Sample iid="GSM3024932">
|
| 485 |
+
<Status database="GEO">
|
| 486 |
+
<Submission-Date>2018-02-27</Submission-Date>
|
| 487 |
+
<Release-Date>2018-07-23</Release-Date>
|
| 488 |
+
<Last-Update-Date>2018-07-23</Last-Update-Date>
|
| 489 |
+
</Status>
|
| 490 |
+
<Title>PBMC genomic DNA Healthy Control (HC) 3</Title>
|
| 491 |
+
<Accession database="GEO">GSM3024932</Accession>
|
| 492 |
+
<Type>genomic</Type>
|
| 493 |
+
<Channel-Count>1</Channel-Count>
|
| 494 |
+
<Channel position="1">
|
| 495 |
+
<Source>HC PBMC</Source>
|
| 496 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 497 |
+
<Characteristics tag="gender">
|
| 498 |
+
female
|
| 499 |
+
</Characteristics>
|
| 500 |
+
<Characteristics tag="subject id">
|
| 501 |
+
HC subject 3
|
| 502 |
+
</Characteristics>
|
| 503 |
+
<Characteristics tag="disease state">
|
| 504 |
+
Healthy Control (HC)
|
| 505 |
+
</Characteristics>
|
| 506 |
+
<Characteristics tag="cell type">
|
| 507 |
+
peripheral blood mononuclear cells (PBMC)
|
| 508 |
+
</Characteristics>
|
| 509 |
+
<Molecule>genomic DNA</Molecule>
|
| 510 |
+
<Extract-Protocol>
|
| 511 |
+
genomic DNA was extracted and purified from PBMC samples using Qiagen DNeasy Blood & Tissue Kit according to manufacturer instructions
|
| 512 |
+
</Extract-Protocol>
|
| 513 |
+
<Label>Cy3, Cy5</Label>
|
| 514 |
+
<Label-Protocol>
|
| 515 |
+
Standard Illumina Protocol
|
| 516 |
+
</Label-Protocol>
|
| 517 |
+
</Channel>
|
| 518 |
+
<Hybridization-Protocol>
|
| 519 |
+
bisulphite converted DNA was hybridised to Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol
|
| 520 |
+
</Hybridization-Protocol>
|
| 521 |
+
<Scan-Protocol>
|
| 522 |
+
Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
|
| 523 |
+
</Scan-Protocol>
|
| 524 |
+
<Description>
|
| 525 |
+
PBMC genomic DNA from HC subject 3
|
| 526 |
+
</Description>
|
| 527 |
+
<Data-Processing>
|
| 528 |
+
Illumina Genome Studio; Matrix signal intensities contains unmethylated and methylated signal intensities; Matrix processed contains non-normalized average beta values.
|
| 529 |
+
</Data-Processing>
|
| 530 |
+
<Platform-Ref ref="GPL21145" />
|
| 531 |
+
<Contact-Ref ref="contrib1" />
|
| 532 |
+
<Supplementary-Data type="unknown">
|
| 533 |
+
NONE
|
| 534 |
+
</Supplementary-Data>
|
| 535 |
+
<Data-Table>
|
| 536 |
+
<Column position="1">
|
| 537 |
+
<Name>ID_REF</Name>
|
| 538 |
+
</Column>
|
| 539 |
+
<Column position="2">
|
| 540 |
+
<Name>VALUE</Name>
|
| 541 |
+
<Description>Average Beta</Description>
|
| 542 |
+
</Column>
|
| 543 |
+
<Column position="3">
|
| 544 |
+
<Name>Detection Pval</Name>
|
| 545 |
+
</Column>
|
| 546 |
+
<External-Data rows="866895">
|
| 547 |
+
GSM3024932-tbl-1.txt
|
| 548 |
+
</External-Data>
|
| 549 |
+
</Data-Table>
|
| 550 |
+
</Sample>
|
| 551 |
+
|
| 552 |
+
<Sample iid="GSM3024933">
|
| 553 |
+
<Status database="GEO">
|
| 554 |
+
<Submission-Date>2018-02-27</Submission-Date>
|
| 555 |
+
<Release-Date>2018-07-23</Release-Date>
|
| 556 |
+
<Last-Update-Date>2018-07-23</Last-Update-Date>
|
| 557 |
+
</Status>
|
| 558 |
+
<Title>PBMC genomic DNA ME/CFS 4</Title>
|
| 559 |
+
<Accession database="GEO">GSM3024933</Accession>
|
| 560 |
+
<Type>genomic</Type>
|
| 561 |
+
<Channel-Count>1</Channel-Count>
|
| 562 |
+
<Channel position="1">
|
| 563 |
+
<Source>ME/CFS PBMC</Source>
|
| 564 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 565 |
+
<Characteristics tag="gender">
|
| 566 |
+
female
|
| 567 |
+
</Characteristics>
|
| 568 |
+
<Characteristics tag="subject id">
|
| 569 |
+
ME/CFS subject 4
|
| 570 |
+
</Characteristics>
|
| 571 |
+
<Characteristics tag="disease state">
|
| 572 |
+
Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS)
|
| 573 |
+
</Characteristics>
|
| 574 |
+
<Characteristics tag="cell type">
|
| 575 |
+
peripheral blood mononuclear cells (PBMC)
|
| 576 |
+
</Characteristics>
|
| 577 |
+
<Molecule>genomic DNA</Molecule>
|
| 578 |
+
<Extract-Protocol>
|
| 579 |
+
genomic DNA was extracted and purified from PBMC samples using Qiagen DNeasy Blood & Tissue Kit according to manufacturer instructions
|
| 580 |
+
</Extract-Protocol>
|
| 581 |
+
<Label>Cy3, Cy5</Label>
|
| 582 |
+
<Label-Protocol>
|
| 583 |
+
Standard Illumina Protocol
|
| 584 |
+
</Label-Protocol>
|
| 585 |
+
</Channel>
|
| 586 |
+
<Hybridization-Protocol>
|
| 587 |
+
bisulphite converted DNA was hybridised to Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol
|
| 588 |
+
</Hybridization-Protocol>
|
| 589 |
+
<Scan-Protocol>
|
| 590 |
+
Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
|
| 591 |
+
</Scan-Protocol>
|
| 592 |
+
<Description>
|
| 593 |
+
PBMC genomic DNA from ME/CFS subject 4
|
| 594 |
+
</Description>
|
| 595 |
+
<Data-Processing>
|
| 596 |
+
Illumina Genome Studio; Matrix signal intensities contains unmethylated and methylated signal intensities; Matrix processed contains non-normalized average beta values.
|
| 597 |
+
</Data-Processing>
|
| 598 |
+
<Platform-Ref ref="GPL21145" />
|
| 599 |
+
<Contact-Ref ref="contrib1" />
|
| 600 |
+
<Supplementary-Data type="unknown">
|
| 601 |
+
NONE
|
| 602 |
+
</Supplementary-Data>
|
| 603 |
+
<Data-Table>
|
| 604 |
+
<Column position="1">
|
| 605 |
+
<Name>ID_REF</Name>
|
| 606 |
+
</Column>
|
| 607 |
+
<Column position="2">
|
| 608 |
+
<Name>VALUE</Name>
|
| 609 |
+
<Description>Average Beta</Description>
|
| 610 |
+
</Column>
|
| 611 |
+
<Column position="3">
|
| 612 |
+
<Name>Detection Pval</Name>
|
| 613 |
+
</Column>
|
| 614 |
+
<External-Data rows="866895">
|
| 615 |
+
GSM3024933-tbl-1.txt
|
| 616 |
+
</External-Data>
|
| 617 |
+
</Data-Table>
|
| 618 |
+
</Sample>
|
| 619 |
+
|
| 620 |
+
<Sample iid="GSM3024934">
|
| 621 |
+
<Status database="GEO">
|
| 622 |
+
<Submission-Date>2018-02-27</Submission-Date>
|
| 623 |
+
<Release-Date>2018-07-23</Release-Date>
|
| 624 |
+
<Last-Update-Date>2018-07-23</Last-Update-Date>
|
| 625 |
+
</Status>
|
| 626 |
+
<Title>PBMC genomic DNA ME/CFS 5</Title>
|
| 627 |
+
<Accession database="GEO">GSM3024934</Accession>
|
| 628 |
+
<Type>genomic</Type>
|
| 629 |
+
<Channel-Count>1</Channel-Count>
|
| 630 |
+
<Channel position="1">
|
| 631 |
+
<Source>ME/CFS PBMC</Source>
|
| 632 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 633 |
+
<Characteristics tag="gender">
|
| 634 |
+
female
|
| 635 |
+
</Characteristics>
|
| 636 |
+
<Characteristics tag="subject id">
|
| 637 |
+
ME/CFS subject 5
|
| 638 |
+
</Characteristics>
|
| 639 |
+
<Characteristics tag="disease state">
|
| 640 |
+
Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS)
|
| 641 |
+
</Characteristics>
|
| 642 |
+
<Characteristics tag="cell type">
|
| 643 |
+
peripheral blood mononuclear cells (PBMC)
|
| 644 |
+
</Characteristics>
|
| 645 |
+
<Molecule>genomic DNA</Molecule>
|
| 646 |
+
<Extract-Protocol>
|
| 647 |
+
genomic DNA was extracted and purified from PBMC samples using Qiagen DNeasy Blood & Tissue Kit according to manufacturer instructions
|
| 648 |
+
</Extract-Protocol>
|
| 649 |
+
<Label>Cy3, Cy5</Label>
|
| 650 |
+
<Label-Protocol>
|
| 651 |
+
Standard Illumina Protocol
|
| 652 |
+
</Label-Protocol>
|
| 653 |
+
</Channel>
|
| 654 |
+
<Hybridization-Protocol>
|
| 655 |
+
bisulphite converted DNA was hybridised to Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol
|
| 656 |
+
</Hybridization-Protocol>
|
| 657 |
+
<Scan-Protocol>
|
| 658 |
+
Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
|
| 659 |
+
</Scan-Protocol>
|
| 660 |
+
<Description>
|
| 661 |
+
PBMC genomic DNA from ME/CFS subject 5
|
| 662 |
+
</Description>
|
| 663 |
+
<Data-Processing>
|
| 664 |
+
Illumina Genome Studio; Matrix signal intensities contains unmethylated and methylated signal intensities; Matrix processed contains non-normalized average beta values.
|
| 665 |
+
</Data-Processing>
|
| 666 |
+
<Platform-Ref ref="GPL21145" />
|
| 667 |
+
<Contact-Ref ref="contrib1" />
|
| 668 |
+
<Supplementary-Data type="unknown">
|
| 669 |
+
NONE
|
| 670 |
+
</Supplementary-Data>
|
| 671 |
+
<Data-Table>
|
| 672 |
+
<Column position="1">
|
| 673 |
+
<Name>ID_REF</Name>
|
| 674 |
+
</Column>
|
| 675 |
+
<Column position="2">
|
| 676 |
+
<Name>VALUE</Name>
|
| 677 |
+
<Description>Average Beta</Description>
|
| 678 |
+
</Column>
|
| 679 |
+
<Column position="3">
|
| 680 |
+
<Name>Detection Pval</Name>
|
| 681 |
+
</Column>
|
| 682 |
+
<External-Data rows="866895">
|
| 683 |
+
GSM3024934-tbl-1.txt
|
| 684 |
+
</External-Data>
|
| 685 |
+
</Data-Table>
|
| 686 |
+
</Sample>
|
| 687 |
+
|
| 688 |
+
<Sample iid="GSM3024935">
|
| 689 |
+
<Status database="GEO">
|
| 690 |
+
<Submission-Date>2018-02-27</Submission-Date>
|
| 691 |
+
<Release-Date>2018-07-23</Release-Date>
|
| 692 |
+
<Last-Update-Date>2018-07-23</Last-Update-Date>
|
| 693 |
+
</Status>
|
| 694 |
+
<Title>PBMC genomic DNA ME/CFS 6</Title>
|
| 695 |
+
<Accession database="GEO">GSM3024935</Accession>
|
| 696 |
+
<Type>genomic</Type>
|
| 697 |
+
<Channel-Count>1</Channel-Count>
|
| 698 |
+
<Channel position="1">
|
| 699 |
+
<Source>ME/CFS PBMC</Source>
|
| 700 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 701 |
+
<Characteristics tag="gender">
|
| 702 |
+
female
|
| 703 |
+
</Characteristics>
|
| 704 |
+
<Characteristics tag="subject id">
|
| 705 |
+
ME/CFS subject 6
|
| 706 |
+
</Characteristics>
|
| 707 |
+
<Characteristics tag="disease state">
|
| 708 |
+
Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS)
|
| 709 |
+
</Characteristics>
|
| 710 |
+
<Characteristics tag="cell type">
|
| 711 |
+
peripheral blood mononuclear cells (PBMC)
|
| 712 |
+
</Characteristics>
|
| 713 |
+
<Molecule>genomic DNA</Molecule>
|
| 714 |
+
<Extract-Protocol>
|
| 715 |
+
genomic DNA was extracted and purified from PBMC samples using Qiagen DNeasy Blood & Tissue Kit according to manufacturer instructions
|
| 716 |
+
</Extract-Protocol>
|
| 717 |
+
<Label>Cy3, Cy5</Label>
|
| 718 |
+
<Label-Protocol>
|
| 719 |
+
Standard Illumina Protocol
|
| 720 |
+
</Label-Protocol>
|
| 721 |
+
</Channel>
|
| 722 |
+
<Hybridization-Protocol>
|
| 723 |
+
bisulphite converted DNA was hybridised to Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol
|
| 724 |
+
</Hybridization-Protocol>
|
| 725 |
+
<Scan-Protocol>
|
| 726 |
+
Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
|
| 727 |
+
</Scan-Protocol>
|
| 728 |
+
<Description>
|
| 729 |
+
PBMC genomic DNA from ME/CFS subject 6
|
| 730 |
+
</Description>
|
| 731 |
+
<Data-Processing>
|
| 732 |
+
Illumina Genome Studio; Matrix signal intensities contains unmethylated and methylated signal intensities; Matrix processed contains non-normalized average beta values.
|
| 733 |
+
</Data-Processing>
|
| 734 |
+
<Platform-Ref ref="GPL21145" />
|
| 735 |
+
<Contact-Ref ref="contrib1" />
|
| 736 |
+
<Supplementary-Data type="unknown">
|
| 737 |
+
NONE
|
| 738 |
+
</Supplementary-Data>
|
| 739 |
+
<Data-Table>
|
| 740 |
+
<Column position="1">
|
| 741 |
+
<Name>ID_REF</Name>
|
| 742 |
+
</Column>
|
| 743 |
+
<Column position="2">
|
| 744 |
+
<Name>VALUE</Name>
|
| 745 |
+
<Description>Average Beta</Description>
|
| 746 |
+
</Column>
|
| 747 |
+
<Column position="3">
|
| 748 |
+
<Name>Detection Pval</Name>
|
| 749 |
+
</Column>
|
| 750 |
+
<External-Data rows="866895">
|
| 751 |
+
GSM3024935-tbl-1.txt
|
| 752 |
+
</External-Data>
|
| 753 |
+
</Data-Table>
|
| 754 |
+
</Sample>
|
| 755 |
+
|
| 756 |
+
<Sample iid="GSM3024936">
|
| 757 |
+
<Status database="GEO">
|
| 758 |
+
<Submission-Date>2018-02-27</Submission-Date>
|
| 759 |
+
<Release-Date>2018-07-23</Release-Date>
|
| 760 |
+
<Last-Update-Date>2018-07-23</Last-Update-Date>
|
| 761 |
+
</Status>
|
| 762 |
+
<Title>PBMC genomic DNA ME/CFS 7</Title>
|
| 763 |
+
<Accession database="GEO">GSM3024936</Accession>
|
| 764 |
+
<Type>genomic</Type>
|
| 765 |
+
<Channel-Count>1</Channel-Count>
|
| 766 |
+
<Channel position="1">
|
| 767 |
+
<Source>ME/CFS PBMC</Source>
|
| 768 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 769 |
+
<Characteristics tag="gender">
|
| 770 |
+
female
|
| 771 |
+
</Characteristics>
|
| 772 |
+
<Characteristics tag="subject id">
|
| 773 |
+
ME/CFS subject 7
|
| 774 |
+
</Characteristics>
|
| 775 |
+
<Characteristics tag="disease state">
|
| 776 |
+
Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS)
|
| 777 |
+
</Characteristics>
|
| 778 |
+
<Characteristics tag="cell type">
|
| 779 |
+
peripheral blood mononuclear cells (PBMC)
|
| 780 |
+
</Characteristics>
|
| 781 |
+
<Molecule>genomic DNA</Molecule>
|
| 782 |
+
<Extract-Protocol>
|
| 783 |
+
genomic DNA was extracted and purified from PBMC samples using Qiagen DNeasy Blood & Tissue Kit according to manufacturer instructions
|
| 784 |
+
</Extract-Protocol>
|
| 785 |
+
<Label>Cy3, Cy5</Label>
|
| 786 |
+
<Label-Protocol>
|
| 787 |
+
Standard Illumina Protocol
|
| 788 |
+
</Label-Protocol>
|
| 789 |
+
</Channel>
|
| 790 |
+
<Hybridization-Protocol>
|
| 791 |
+
bisulphite converted DNA was hybridised to Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol
|
| 792 |
+
</Hybridization-Protocol>
|
| 793 |
+
<Scan-Protocol>
|
| 794 |
+
Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
|
| 795 |
+
</Scan-Protocol>
|
| 796 |
+
<Description>
|
| 797 |
+
PBMC genomic DNA from ME/CFS subject 7
|
| 798 |
+
</Description>
|
| 799 |
+
<Data-Processing>
|
| 800 |
+
Illumina Genome Studio; Matrix signal intensities contains unmethylated and methylated signal intensities; Matrix processed contains non-normalized average beta values.
|
| 801 |
+
</Data-Processing>
|
| 802 |
+
<Platform-Ref ref="GPL21145" />
|
| 803 |
+
<Contact-Ref ref="contrib1" />
|
| 804 |
+
<Supplementary-Data type="unknown">
|
| 805 |
+
NONE
|
| 806 |
+
</Supplementary-Data>
|
| 807 |
+
<Data-Table>
|
| 808 |
+
<Column position="1">
|
| 809 |
+
<Name>ID_REF</Name>
|
| 810 |
+
</Column>
|
| 811 |
+
<Column position="2">
|
| 812 |
+
<Name>VALUE</Name>
|
| 813 |
+
<Description>Average Beta</Description>
|
| 814 |
+
</Column>
|
| 815 |
+
<Column position="3">
|
| 816 |
+
<Name>Detection Pval</Name>
|
| 817 |
+
</Column>
|
| 818 |
+
<External-Data rows="866895">
|
| 819 |
+
GSM3024936-tbl-1.txt
|
| 820 |
+
</External-Data>
|
| 821 |
+
</Data-Table>
|
| 822 |
+
</Sample>
|
| 823 |
+
|
| 824 |
+
<Sample iid="GSM3024937">
|
| 825 |
+
<Status database="GEO">
|
| 826 |
+
<Submission-Date>2018-02-27</Submission-Date>
|
| 827 |
+
<Release-Date>2018-07-23</Release-Date>
|
| 828 |
+
<Last-Update-Date>2018-07-23</Last-Update-Date>
|
| 829 |
+
</Status>
|
| 830 |
+
<Title>PBMC genomic DNA ME/CFS 8</Title>
|
| 831 |
+
<Accession database="GEO">GSM3024937</Accession>
|
| 832 |
+
<Type>genomic</Type>
|
| 833 |
+
<Channel-Count>1</Channel-Count>
|
| 834 |
+
<Channel position="1">
|
| 835 |
+
<Source>ME/CFS PBMC</Source>
|
| 836 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 837 |
+
<Characteristics tag="gender">
|
| 838 |
+
female
|
| 839 |
+
</Characteristics>
|
| 840 |
+
<Characteristics tag="subject id">
|
| 841 |
+
ME/CFS subject 8
|
| 842 |
+
</Characteristics>
|
| 843 |
+
<Characteristics tag="disease state">
|
| 844 |
+
Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS)
|
| 845 |
+
</Characteristics>
|
| 846 |
+
<Characteristics tag="cell type">
|
| 847 |
+
peripheral blood mononuclear cells (PBMC)
|
| 848 |
+
</Characteristics>
|
| 849 |
+
<Molecule>genomic DNA</Molecule>
|
| 850 |
+
<Extract-Protocol>
|
| 851 |
+
genomic DNA was extracted and purified from PBMC samples using Qiagen DNeasy Blood & Tissue Kit according to manufacturer instructions
|
| 852 |
+
</Extract-Protocol>
|
| 853 |
+
<Label>Cy3, Cy5</Label>
|
| 854 |
+
<Label-Protocol>
|
| 855 |
+
Standard Illumina Protocol
|
| 856 |
+
</Label-Protocol>
|
| 857 |
+
</Channel>
|
| 858 |
+
<Hybridization-Protocol>
|
| 859 |
+
bisulphite converted DNA was hybridised to Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol
|
| 860 |
+
</Hybridization-Protocol>
|
| 861 |
+
<Scan-Protocol>
|
| 862 |
+
Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
|
| 863 |
+
</Scan-Protocol>
|
| 864 |
+
<Description>
|
| 865 |
+
PBMC genomic DNA from ME/CFS subject 8
|
| 866 |
+
</Description>
|
| 867 |
+
<Data-Processing>
|
| 868 |
+
Illumina Genome Studio; Matrix signal intensities contains unmethylated and methylated signal intensities; Matrix processed contains non-normalized average beta values.
|
| 869 |
+
</Data-Processing>
|
| 870 |
+
<Platform-Ref ref="GPL21145" />
|
| 871 |
+
<Contact-Ref ref="contrib1" />
|
| 872 |
+
<Supplementary-Data type="unknown">
|
| 873 |
+
NONE
|
| 874 |
+
</Supplementary-Data>
|
| 875 |
+
<Data-Table>
|
| 876 |
+
<Column position="1">
|
| 877 |
+
<Name>ID_REF</Name>
|
| 878 |
+
</Column>
|
| 879 |
+
<Column position="2">
|
| 880 |
+
<Name>VALUE</Name>
|
| 881 |
+
<Description>Average Beta</Description>
|
| 882 |
+
</Column>
|
| 883 |
+
<Column position="3">
|
| 884 |
+
<Name>Detection Pval</Name>
|
| 885 |
+
</Column>
|
| 886 |
+
<External-Data rows="866895">
|
| 887 |
+
GSM3024937-tbl-1.txt
|
| 888 |
+
</External-Data>
|
| 889 |
+
</Data-Table>
|
| 890 |
+
</Sample>
|
| 891 |
+
|
| 892 |
+
<Sample iid="GSM3024938">
|
| 893 |
+
<Status database="GEO">
|
| 894 |
+
<Submission-Date>2018-02-27</Submission-Date>
|
| 895 |
+
<Release-Date>2018-07-23</Release-Date>
|
| 896 |
+
<Last-Update-Date>2018-07-23</Last-Update-Date>
|
| 897 |
+
</Status>
|
| 898 |
+
<Title>PBMC genomic DNA Healthy Control (HC) 4</Title>
|
| 899 |
+
<Accession database="GEO">GSM3024938</Accession>
|
| 900 |
+
<Type>genomic</Type>
|
| 901 |
+
<Channel-Count>1</Channel-Count>
|
| 902 |
+
<Channel position="1">
|
| 903 |
+
<Source>HC PBMC</Source>
|
| 904 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 905 |
+
<Characteristics tag="gender">
|
| 906 |
+
female
|
| 907 |
+
</Characteristics>
|
| 908 |
+
<Characteristics tag="subject id">
|
| 909 |
+
HC subject 4
|
| 910 |
+
</Characteristics>
|
| 911 |
+
<Characteristics tag="disease state">
|
| 912 |
+
Healthy Control (HC)
|
| 913 |
+
</Characteristics>
|
| 914 |
+
<Characteristics tag="cell type">
|
| 915 |
+
peripheral blood mononuclear cells (PBMC)
|
| 916 |
+
</Characteristics>
|
| 917 |
+
<Molecule>genomic DNA</Molecule>
|
| 918 |
+
<Extract-Protocol>
|
| 919 |
+
genomic DNA was extracted and purified from PBMC samples using Qiagen DNeasy Blood & Tissue Kit according to manufacturer instructions
|
| 920 |
+
</Extract-Protocol>
|
| 921 |
+
<Label>Cy3, Cy5</Label>
|
| 922 |
+
<Label-Protocol>
|
| 923 |
+
Standard Illumina Protocol
|
| 924 |
+
</Label-Protocol>
|
| 925 |
+
</Channel>
|
| 926 |
+
<Hybridization-Protocol>
|
| 927 |
+
bisulphite converted DNA was hybridised to Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol
|
| 928 |
+
</Hybridization-Protocol>
|
| 929 |
+
<Scan-Protocol>
|
| 930 |
+
Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
|
| 931 |
+
</Scan-Protocol>
|
| 932 |
+
<Description>
|
| 933 |
+
PBMC genomic DNA from HC subject 4
|
| 934 |
+
</Description>
|
| 935 |
+
<Data-Processing>
|
| 936 |
+
Illumina Genome Studio; Matrix signal intensities contains unmethylated and methylated signal intensities; Matrix processed contains non-normalized average beta values.
|
| 937 |
+
</Data-Processing>
|
| 938 |
+
<Platform-Ref ref="GPL21145" />
|
| 939 |
+
<Contact-Ref ref="contrib1" />
|
| 940 |
+
<Supplementary-Data type="unknown">
|
| 941 |
+
NONE
|
| 942 |
+
</Supplementary-Data>
|
| 943 |
+
<Data-Table>
|
| 944 |
+
<Column position="1">
|
| 945 |
+
<Name>ID_REF</Name>
|
| 946 |
+
</Column>
|
| 947 |
+
<Column position="2">
|
| 948 |
+
<Name>VALUE</Name>
|
| 949 |
+
<Description>Average Beta</Description>
|
| 950 |
+
</Column>
|
| 951 |
+
<Column position="3">
|
| 952 |
+
<Name>Detection Pval</Name>
|
| 953 |
+
</Column>
|
| 954 |
+
<External-Data rows="866895">
|
| 955 |
+
GSM3024938-tbl-1.txt
|
| 956 |
+
</External-Data>
|
| 957 |
+
</Data-Table>
|
| 958 |
+
</Sample>
|
| 959 |
+
|
| 960 |
+
<Sample iid="GSM3024939">
|
| 961 |
+
<Status database="GEO">
|
| 962 |
+
<Submission-Date>2018-02-27</Submission-Date>
|
| 963 |
+
<Release-Date>2018-07-23</Release-Date>
|
| 964 |
+
<Last-Update-Date>2018-07-23</Last-Update-Date>
|
| 965 |
+
</Status>
|
| 966 |
+
<Title>PBMC genomic DNA Healthy Control (HC) 5</Title>
|
| 967 |
+
<Accession database="GEO">GSM3024939</Accession>
|
| 968 |
+
<Type>genomic</Type>
|
| 969 |
+
<Channel-Count>1</Channel-Count>
|
| 970 |
+
<Channel position="1">
|
| 971 |
+
<Source>HC PBMC</Source>
|
| 972 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 973 |
+
<Characteristics tag="gender">
|
| 974 |
+
female
|
| 975 |
+
</Characteristics>
|
| 976 |
+
<Characteristics tag="subject id">
|
| 977 |
+
HC subject 5
|
| 978 |
+
</Characteristics>
|
| 979 |
+
<Characteristics tag="disease state">
|
| 980 |
+
Healthy Control (HC)
|
| 981 |
+
</Characteristics>
|
| 982 |
+
<Characteristics tag="cell type">
|
| 983 |
+
peripheral blood mononuclear cells (PBMC)
|
| 984 |
+
</Characteristics>
|
| 985 |
+
<Molecule>genomic DNA</Molecule>
|
| 986 |
+
<Extract-Protocol>
|
| 987 |
+
genomic DNA was extracted and purified from PBMC samples using Qiagen DNeasy Blood & Tissue Kit according to manufacturer instructions
|
| 988 |
+
</Extract-Protocol>
|
| 989 |
+
<Label>Cy3, Cy5</Label>
|
| 990 |
+
<Label-Protocol>
|
| 991 |
+
Standard Illumina Protocol
|
| 992 |
+
</Label-Protocol>
|
| 993 |
+
</Channel>
|
| 994 |
+
<Hybridization-Protocol>
|
| 995 |
+
bisulphite converted DNA was hybridised to Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol
|
| 996 |
+
</Hybridization-Protocol>
|
| 997 |
+
<Scan-Protocol>
|
| 998 |
+
Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
|
| 999 |
+
</Scan-Protocol>
|
| 1000 |
+
<Description>
|
| 1001 |
+
PBMC genomic DNA from HC subject 5
|
| 1002 |
+
</Description>
|
| 1003 |
+
<Data-Processing>
|
| 1004 |
+
Illumina Genome Studio; Matrix signal intensities contains unmethylated and methylated signal intensities; Matrix processed contains non-normalized average beta values.
|
| 1005 |
+
</Data-Processing>
|
| 1006 |
+
<Platform-Ref ref="GPL21145" />
|
| 1007 |
+
<Contact-Ref ref="contrib1" />
|
| 1008 |
+
<Supplementary-Data type="unknown">
|
| 1009 |
+
NONE
|
| 1010 |
+
</Supplementary-Data>
|
| 1011 |
+
<Data-Table>
|
| 1012 |
+
<Column position="1">
|
| 1013 |
+
<Name>ID_REF</Name>
|
| 1014 |
+
</Column>
|
| 1015 |
+
<Column position="2">
|
| 1016 |
+
<Name>VALUE</Name>
|
| 1017 |
+
<Description>Average Beta</Description>
|
| 1018 |
+
</Column>
|
| 1019 |
+
<Column position="3">
|
| 1020 |
+
<Name>Detection Pval</Name>
|
| 1021 |
+
</Column>
|
| 1022 |
+
<External-Data rows="866895">
|
| 1023 |
+
GSM3024939-tbl-1.txt
|
| 1024 |
+
</External-Data>
|
| 1025 |
+
</Data-Table>
|
| 1026 |
+
</Sample>
|
| 1027 |
+
|
| 1028 |
+
<Sample iid="GSM3024940">
|
| 1029 |
+
<Status database="GEO">
|
| 1030 |
+
<Submission-Date>2018-02-27</Submission-Date>
|
| 1031 |
+
<Release-Date>2018-07-23</Release-Date>
|
| 1032 |
+
<Last-Update-Date>2018-07-23</Last-Update-Date>
|
| 1033 |
+
</Status>
|
| 1034 |
+
<Title>PBMC genomic DNA ME/CFS 9</Title>
|
| 1035 |
+
<Accession database="GEO">GSM3024940</Accession>
|
| 1036 |
+
<Type>genomic</Type>
|
| 1037 |
+
<Channel-Count>1</Channel-Count>
|
| 1038 |
+
<Channel position="1">
|
| 1039 |
+
<Source>ME/CFS PBMC</Source>
|
| 1040 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 1041 |
+
<Characteristics tag="gender">
|
| 1042 |
+
female
|
| 1043 |
+
</Characteristics>
|
| 1044 |
+
<Characteristics tag="subject id">
|
| 1045 |
+
ME/CFS subject 9
|
| 1046 |
+
</Characteristics>
|
| 1047 |
+
<Characteristics tag="disease state">
|
| 1048 |
+
Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS)
|
| 1049 |
+
</Characteristics>
|
| 1050 |
+
<Characteristics tag="cell type">
|
| 1051 |
+
peripheral blood mononuclear cells (PBMC)
|
| 1052 |
+
</Characteristics>
|
| 1053 |
+
<Molecule>genomic DNA</Molecule>
|
| 1054 |
+
<Extract-Protocol>
|
| 1055 |
+
genomic DNA was extracted and purified from PBMC samples using Qiagen DNeasy Blood & Tissue Kit according to manufacturer instructions
|
| 1056 |
+
</Extract-Protocol>
|
| 1057 |
+
<Label>Cy3, Cy5</Label>
|
| 1058 |
+
<Label-Protocol>
|
| 1059 |
+
Standard Illumina Protocol
|
| 1060 |
+
</Label-Protocol>
|
| 1061 |
+
</Channel>
|
| 1062 |
+
<Hybridization-Protocol>
|
| 1063 |
+
bisulphite converted DNA was hybridised to Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol
|
| 1064 |
+
</Hybridization-Protocol>
|
| 1065 |
+
<Scan-Protocol>
|
| 1066 |
+
Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
|
| 1067 |
+
</Scan-Protocol>
|
| 1068 |
+
<Description>
|
| 1069 |
+
PBMC genomic DNA from ME/CFS subject 9
|
| 1070 |
+
</Description>
|
| 1071 |
+
<Data-Processing>
|
| 1072 |
+
Illumina Genome Studio; Matrix signal intensities contains unmethylated and methylated signal intensities; Matrix processed contains non-normalized average beta values.
|
| 1073 |
+
</Data-Processing>
|
| 1074 |
+
<Platform-Ref ref="GPL21145" />
|
| 1075 |
+
<Contact-Ref ref="contrib1" />
|
| 1076 |
+
<Supplementary-Data type="unknown">
|
| 1077 |
+
NONE
|
| 1078 |
+
</Supplementary-Data>
|
| 1079 |
+
<Data-Table>
|
| 1080 |
+
<Column position="1">
|
| 1081 |
+
<Name>ID_REF</Name>
|
| 1082 |
+
</Column>
|
| 1083 |
+
<Column position="2">
|
| 1084 |
+
<Name>VALUE</Name>
|
| 1085 |
+
<Description>Average Beta</Description>
|
| 1086 |
+
</Column>
|
| 1087 |
+
<Column position="3">
|
| 1088 |
+
<Name>Detection Pval</Name>
|
| 1089 |
+
</Column>
|
| 1090 |
+
<External-Data rows="866895">
|
| 1091 |
+
GSM3024940-tbl-1.txt
|
| 1092 |
+
</External-Data>
|
| 1093 |
+
</Data-Table>
|
| 1094 |
+
</Sample>
|
| 1095 |
+
|
| 1096 |
+
<Sample iid="GSM3024941">
|
| 1097 |
+
<Status database="GEO">
|
| 1098 |
+
<Submission-Date>2018-02-27</Submission-Date>
|
| 1099 |
+
<Release-Date>2018-07-23</Release-Date>
|
| 1100 |
+
<Last-Update-Date>2018-07-23</Last-Update-Date>
|
| 1101 |
+
</Status>
|
| 1102 |
+
<Title>PBMC genomic DNA Healthy Control (HC) 6</Title>
|
| 1103 |
+
<Accession database="GEO">GSM3024941</Accession>
|
| 1104 |
+
<Type>genomic</Type>
|
| 1105 |
+
<Channel-Count>1</Channel-Count>
|
| 1106 |
+
<Channel position="1">
|
| 1107 |
+
<Source>HC PBMC</Source>
|
| 1108 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 1109 |
+
<Characteristics tag="gender">
|
| 1110 |
+
female
|
| 1111 |
+
</Characteristics>
|
| 1112 |
+
<Characteristics tag="subject id">
|
| 1113 |
+
HC subject 6
|
| 1114 |
+
</Characteristics>
|
| 1115 |
+
<Characteristics tag="disease state">
|
| 1116 |
+
Healthy Control (HC)
|
| 1117 |
+
</Characteristics>
|
| 1118 |
+
<Characteristics tag="cell type">
|
| 1119 |
+
peripheral blood mononuclear cells (PBMC)
|
| 1120 |
+
</Characteristics>
|
| 1121 |
+
<Molecule>genomic DNA</Molecule>
|
| 1122 |
+
<Extract-Protocol>
|
| 1123 |
+
genomic DNA was extracted and purified from PBMC samples using Qiagen DNeasy Blood & Tissue Kit according to manufacturer instructions
|
| 1124 |
+
</Extract-Protocol>
|
| 1125 |
+
<Label>Cy3, Cy5</Label>
|
| 1126 |
+
<Label-Protocol>
|
| 1127 |
+
Standard Illumina Protocol
|
| 1128 |
+
</Label-Protocol>
|
| 1129 |
+
</Channel>
|
| 1130 |
+
<Hybridization-Protocol>
|
| 1131 |
+
bisulphite converted DNA was hybridised to Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol
|
| 1132 |
+
</Hybridization-Protocol>
|
| 1133 |
+
<Scan-Protocol>
|
| 1134 |
+
Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
|
| 1135 |
+
</Scan-Protocol>
|
| 1136 |
+
<Description>
|
| 1137 |
+
PBMC genomic DNA from HC subject 6
|
| 1138 |
+
</Description>
|
| 1139 |
+
<Data-Processing>
|
| 1140 |
+
Illumina Genome Studio; Matrix signal intensities contains unmethylated and methylated signal intensities; Matrix processed contains non-normalized average beta values.
|
| 1141 |
+
</Data-Processing>
|
| 1142 |
+
<Platform-Ref ref="GPL21145" />
|
| 1143 |
+
<Contact-Ref ref="contrib1" />
|
| 1144 |
+
<Supplementary-Data type="unknown">
|
| 1145 |
+
NONE
|
| 1146 |
+
</Supplementary-Data>
|
| 1147 |
+
<Data-Table>
|
| 1148 |
+
<Column position="1">
|
| 1149 |
+
<Name>ID_REF</Name>
|
| 1150 |
+
</Column>
|
| 1151 |
+
<Column position="2">
|
| 1152 |
+
<Name>VALUE</Name>
|
| 1153 |
+
<Description>Average Beta</Description>
|
| 1154 |
+
</Column>
|
| 1155 |
+
<Column position="3">
|
| 1156 |
+
<Name>Detection Pval</Name>
|
| 1157 |
+
</Column>
|
| 1158 |
+
<External-Data rows="866895">
|
| 1159 |
+
GSM3024941-tbl-1.txt
|
| 1160 |
+
</External-Data>
|
| 1161 |
+
</Data-Table>
|
| 1162 |
+
</Sample>
|
| 1163 |
+
|
| 1164 |
+
<Sample iid="GSM3024942">
|
| 1165 |
+
<Status database="GEO">
|
| 1166 |
+
<Submission-Date>2018-02-27</Submission-Date>
|
| 1167 |
+
<Release-Date>2018-07-23</Release-Date>
|
| 1168 |
+
<Last-Update-Date>2018-07-23</Last-Update-Date>
|
| 1169 |
+
</Status>
|
| 1170 |
+
<Title>PBMC genomic DNA ME/CFS 10</Title>
|
| 1171 |
+
<Accession database="GEO">GSM3024942</Accession>
|
| 1172 |
+
<Type>genomic</Type>
|
| 1173 |
+
<Channel-Count>1</Channel-Count>
|
| 1174 |
+
<Channel position="1">
|
| 1175 |
+
<Source>ME/CFS PBMC</Source>
|
| 1176 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 1177 |
+
<Characteristics tag="gender">
|
| 1178 |
+
female
|
| 1179 |
+
</Characteristics>
|
| 1180 |
+
<Characteristics tag="subject id">
|
| 1181 |
+
ME/CFS subject 10
|
| 1182 |
+
</Characteristics>
|
| 1183 |
+
<Characteristics tag="disease state">
|
| 1184 |
+
Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS)
|
| 1185 |
+
</Characteristics>
|
| 1186 |
+
<Characteristics tag="cell type">
|
| 1187 |
+
peripheral blood mononuclear cells (PBMC)
|
| 1188 |
+
</Characteristics>
|
| 1189 |
+
<Molecule>genomic DNA</Molecule>
|
| 1190 |
+
<Extract-Protocol>
|
| 1191 |
+
genomic DNA was extracted and purified from PBMC samples using Qiagen DNeasy Blood & Tissue Kit according to manufacturer instructions
|
| 1192 |
+
</Extract-Protocol>
|
| 1193 |
+
<Label>Cy3, Cy5</Label>
|
| 1194 |
+
<Label-Protocol>
|
| 1195 |
+
Standard Illumina Protocol
|
| 1196 |
+
</Label-Protocol>
|
| 1197 |
+
</Channel>
|
| 1198 |
+
<Hybridization-Protocol>
|
| 1199 |
+
bisulphite converted DNA was hybridised to Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol
|
| 1200 |
+
</Hybridization-Protocol>
|
| 1201 |
+
<Scan-Protocol>
|
| 1202 |
+
Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
|
| 1203 |
+
</Scan-Protocol>
|
| 1204 |
+
<Description>
|
| 1205 |
+
PBMC genomic DNA from ME/CFS subject 10
|
| 1206 |
+
</Description>
|
| 1207 |
+
<Data-Processing>
|
| 1208 |
+
Illumina Genome Studio; Matrix signal intensities contains unmethylated and methylated signal intensities; Matrix processed contains non-normalized average beta values.
|
| 1209 |
+
</Data-Processing>
|
| 1210 |
+
<Platform-Ref ref="GPL21145" />
|
| 1211 |
+
<Contact-Ref ref="contrib1" />
|
| 1212 |
+
<Supplementary-Data type="unknown">
|
| 1213 |
+
NONE
|
| 1214 |
+
</Supplementary-Data>
|
| 1215 |
+
<Data-Table>
|
| 1216 |
+
<Column position="1">
|
| 1217 |
+
<Name>ID_REF</Name>
|
| 1218 |
+
</Column>
|
| 1219 |
+
<Column position="2">
|
| 1220 |
+
<Name>VALUE</Name>
|
| 1221 |
+
<Description>Average Beta</Description>
|
| 1222 |
+
</Column>
|
| 1223 |
+
<Column position="3">
|
| 1224 |
+
<Name>Detection Pval</Name>
|
| 1225 |
+
</Column>
|
| 1226 |
+
<External-Data rows="866895">
|
| 1227 |
+
GSM3024942-tbl-1.txt
|
| 1228 |
+
</External-Data>
|
| 1229 |
+
</Data-Table>
|
| 1230 |
+
</Sample>
|
| 1231 |
+
|
| 1232 |
+
<Sample iid="GSM3024943">
|
| 1233 |
+
<Status database="GEO">
|
| 1234 |
+
<Submission-Date>2018-02-27</Submission-Date>
|
| 1235 |
+
<Release-Date>2018-07-23</Release-Date>
|
| 1236 |
+
<Last-Update-Date>2018-07-23</Last-Update-Date>
|
| 1237 |
+
</Status>
|
| 1238 |
+
<Title>PBMC genomic DNA Healthy Control (HC) 7</Title>
|
| 1239 |
+
<Accession database="GEO">GSM3024943</Accession>
|
| 1240 |
+
<Type>genomic</Type>
|
| 1241 |
+
<Channel-Count>1</Channel-Count>
|
| 1242 |
+
<Channel position="1">
|
| 1243 |
+
<Source>HC PBMC</Source>
|
| 1244 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 1245 |
+
<Characteristics tag="gender">
|
| 1246 |
+
female
|
| 1247 |
+
</Characteristics>
|
| 1248 |
+
<Characteristics tag="subject id">
|
| 1249 |
+
HC subject 7
|
| 1250 |
+
</Characteristics>
|
| 1251 |
+
<Characteristics tag="disease state">
|
| 1252 |
+
Healthy Control (HC)
|
| 1253 |
+
</Characteristics>
|
| 1254 |
+
<Characteristics tag="cell type">
|
| 1255 |
+
peripheral blood mononuclear cells (PBMC)
|
| 1256 |
+
</Characteristics>
|
| 1257 |
+
<Molecule>genomic DNA</Molecule>
|
| 1258 |
+
<Extract-Protocol>
|
| 1259 |
+
genomic DNA was extracted and purified from PBMC samples using Qiagen DNeasy Blood & Tissue Kit according to manufacturer instructions
|
| 1260 |
+
</Extract-Protocol>
|
| 1261 |
+
<Label>Cy3, Cy5</Label>
|
| 1262 |
+
<Label-Protocol>
|
| 1263 |
+
Standard Illumina Protocol
|
| 1264 |
+
</Label-Protocol>
|
| 1265 |
+
</Channel>
|
| 1266 |
+
<Hybridization-Protocol>
|
| 1267 |
+
bisulphite converted DNA was hybridised to Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol
|
| 1268 |
+
</Hybridization-Protocol>
|
| 1269 |
+
<Scan-Protocol>
|
| 1270 |
+
Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
|
| 1271 |
+
</Scan-Protocol>
|
| 1272 |
+
<Description>
|
| 1273 |
+
PBMC genomic DNA from HC subject 7
|
| 1274 |
+
</Description>
|
| 1275 |
+
<Data-Processing>
|
| 1276 |
+
Illumina Genome Studio; Matrix signal intensities contains unmethylated and methylated signal intensities; Matrix processed contains non-normalized average beta values.
|
| 1277 |
+
</Data-Processing>
|
| 1278 |
+
<Platform-Ref ref="GPL21145" />
|
| 1279 |
+
<Contact-Ref ref="contrib1" />
|
| 1280 |
+
<Supplementary-Data type="unknown">
|
| 1281 |
+
NONE
|
| 1282 |
+
</Supplementary-Data>
|
| 1283 |
+
<Data-Table>
|
| 1284 |
+
<Column position="1">
|
| 1285 |
+
<Name>ID_REF</Name>
|
| 1286 |
+
</Column>
|
| 1287 |
+
<Column position="2">
|
| 1288 |
+
<Name>VALUE</Name>
|
| 1289 |
+
<Description>Average Beta</Description>
|
| 1290 |
+
</Column>
|
| 1291 |
+
<Column position="3">
|
| 1292 |
+
<Name>Detection Pval</Name>
|
| 1293 |
+
</Column>
|
| 1294 |
+
<External-Data rows="866895">
|
| 1295 |
+
GSM3024943-tbl-1.txt
|
| 1296 |
+
</External-Data>
|
| 1297 |
+
</Data-Table>
|
| 1298 |
+
</Sample>
|
| 1299 |
+
|
| 1300 |
+
<Sample iid="GSM3024944">
|
| 1301 |
+
<Status database="GEO">
|
| 1302 |
+
<Submission-Date>2018-02-27</Submission-Date>
|
| 1303 |
+
<Release-Date>2018-07-23</Release-Date>
|
| 1304 |
+
<Last-Update-Date>2018-07-23</Last-Update-Date>
|
| 1305 |
+
</Status>
|
| 1306 |
+
<Title>PBMC genomic DNA ME/CFS 11</Title>
|
| 1307 |
+
<Accession database="GEO">GSM3024944</Accession>
|
| 1308 |
+
<Type>genomic</Type>
|
| 1309 |
+
<Channel-Count>1</Channel-Count>
|
| 1310 |
+
<Channel position="1">
|
| 1311 |
+
<Source>ME/CFS PBMC</Source>
|
| 1312 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 1313 |
+
<Characteristics tag="gender">
|
| 1314 |
+
female
|
| 1315 |
+
</Characteristics>
|
| 1316 |
+
<Characteristics tag="subject id">
|
| 1317 |
+
ME/CFS subject 11
|
| 1318 |
+
</Characteristics>
|
| 1319 |
+
<Characteristics tag="disease state">
|
| 1320 |
+
Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS)
|
| 1321 |
+
</Characteristics>
|
| 1322 |
+
<Characteristics tag="cell type">
|
| 1323 |
+
peripheral blood mononuclear cells (PBMC)
|
| 1324 |
+
</Characteristics>
|
| 1325 |
+
<Molecule>genomic DNA</Molecule>
|
| 1326 |
+
<Extract-Protocol>
|
| 1327 |
+
genomic DNA was extracted and purified from PBMC samples using Qiagen DNeasy Blood & Tissue Kit according to manufacturer instructions
|
| 1328 |
+
</Extract-Protocol>
|
| 1329 |
+
<Label>Cy3, Cy5</Label>
|
| 1330 |
+
<Label-Protocol>
|
| 1331 |
+
Standard Illumina Protocol
|
| 1332 |
+
</Label-Protocol>
|
| 1333 |
+
</Channel>
|
| 1334 |
+
<Hybridization-Protocol>
|
| 1335 |
+
bisulphite converted DNA was hybridised to Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol
|
| 1336 |
+
</Hybridization-Protocol>
|
| 1337 |
+
<Scan-Protocol>
|
| 1338 |
+
Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
|
| 1339 |
+
</Scan-Protocol>
|
| 1340 |
+
<Description>
|
| 1341 |
+
PBMC genomic DNA from ME/CFS subject 11
|
| 1342 |
+
</Description>
|
| 1343 |
+
<Data-Processing>
|
| 1344 |
+
Illumina Genome Studio; Matrix signal intensities contains unmethylated and methylated signal intensities; Matrix processed contains non-normalized average beta values.
|
| 1345 |
+
</Data-Processing>
|
| 1346 |
+
<Platform-Ref ref="GPL21145" />
|
| 1347 |
+
<Contact-Ref ref="contrib1" />
|
| 1348 |
+
<Supplementary-Data type="unknown">
|
| 1349 |
+
NONE
|
| 1350 |
+
</Supplementary-Data>
|
| 1351 |
+
<Data-Table>
|
| 1352 |
+
<Column position="1">
|
| 1353 |
+
<Name>ID_REF</Name>
|
| 1354 |
+
</Column>
|
| 1355 |
+
<Column position="2">
|
| 1356 |
+
<Name>VALUE</Name>
|
| 1357 |
+
<Description>Average Beta</Description>
|
| 1358 |
+
</Column>
|
| 1359 |
+
<Column position="3">
|
| 1360 |
+
<Name>Detection Pval</Name>
|
| 1361 |
+
</Column>
|
| 1362 |
+
<External-Data rows="866895">
|
| 1363 |
+
GSM3024944-tbl-1.txt
|
| 1364 |
+
</External-Data>
|
| 1365 |
+
</Data-Table>
|
| 1366 |
+
</Sample>
|
| 1367 |
+
|
| 1368 |
+
<Sample iid="GSM3024945">
|
| 1369 |
+
<Status database="GEO">
|
| 1370 |
+
<Submission-Date>2018-02-27</Submission-Date>
|
| 1371 |
+
<Release-Date>2018-07-23</Release-Date>
|
| 1372 |
+
<Last-Update-Date>2018-07-23</Last-Update-Date>
|
| 1373 |
+
</Status>
|
| 1374 |
+
<Title>PBMC genomic DNA Healthy Control (HC) 8</Title>
|
| 1375 |
+
<Accession database="GEO">GSM3024945</Accession>
|
| 1376 |
+
<Type>genomic</Type>
|
| 1377 |
+
<Channel-Count>1</Channel-Count>
|
| 1378 |
+
<Channel position="1">
|
| 1379 |
+
<Source>HC PBMC</Source>
|
| 1380 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 1381 |
+
<Characteristics tag="gender">
|
| 1382 |
+
female
|
| 1383 |
+
</Characteristics>
|
| 1384 |
+
<Characteristics tag="subject id">
|
| 1385 |
+
HC subject 8
|
| 1386 |
+
</Characteristics>
|
| 1387 |
+
<Characteristics tag="disease state">
|
| 1388 |
+
Healthy Control (HC)
|
| 1389 |
+
</Characteristics>
|
| 1390 |
+
<Characteristics tag="cell type">
|
| 1391 |
+
peripheral blood mononuclear cells (PBMC)
|
| 1392 |
+
</Characteristics>
|
| 1393 |
+
<Molecule>genomic DNA</Molecule>
|
| 1394 |
+
<Extract-Protocol>
|
| 1395 |
+
genomic DNA was extracted and purified from PBMC samples using Qiagen DNeasy Blood & Tissue Kit according to manufacturer instructions
|
| 1396 |
+
</Extract-Protocol>
|
| 1397 |
+
<Label>Cy3, Cy5</Label>
|
| 1398 |
+
<Label-Protocol>
|
| 1399 |
+
Standard Illumina Protocol
|
| 1400 |
+
</Label-Protocol>
|
| 1401 |
+
</Channel>
|
| 1402 |
+
<Hybridization-Protocol>
|
| 1403 |
+
bisulphite converted DNA was hybridised to Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol
|
| 1404 |
+
</Hybridization-Protocol>
|
| 1405 |
+
<Scan-Protocol>
|
| 1406 |
+
Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
|
| 1407 |
+
</Scan-Protocol>
|
| 1408 |
+
<Description>
|
| 1409 |
+
PBMC genomic DNA from HC subject 8
|
| 1410 |
+
</Description>
|
| 1411 |
+
<Data-Processing>
|
| 1412 |
+
Illumina Genome Studio; Matrix signal intensities contains unmethylated and methylated signal intensities; Matrix processed contains non-normalized average beta values.
|
| 1413 |
+
</Data-Processing>
|
| 1414 |
+
<Platform-Ref ref="GPL21145" />
|
| 1415 |
+
<Contact-Ref ref="contrib1" />
|
| 1416 |
+
<Supplementary-Data type="unknown">
|
| 1417 |
+
NONE
|
| 1418 |
+
</Supplementary-Data>
|
| 1419 |
+
<Data-Table>
|
| 1420 |
+
<Column position="1">
|
| 1421 |
+
<Name>ID_REF</Name>
|
| 1422 |
+
</Column>
|
| 1423 |
+
<Column position="2">
|
| 1424 |
+
<Name>VALUE</Name>
|
| 1425 |
+
<Description>Average Beta</Description>
|
| 1426 |
+
</Column>
|
| 1427 |
+
<Column position="3">
|
| 1428 |
+
<Name>Detection Pval</Name>
|
| 1429 |
+
</Column>
|
| 1430 |
+
<External-Data rows="866895">
|
| 1431 |
+
GSM3024945-tbl-1.txt
|
| 1432 |
+
</External-Data>
|
| 1433 |
+
</Data-Table>
|
| 1434 |
+
</Sample>
|
| 1435 |
+
|
| 1436 |
+
<Sample iid="GSM3024946">
|
| 1437 |
+
<Status database="GEO">
|
| 1438 |
+
<Submission-Date>2018-02-27</Submission-Date>
|
| 1439 |
+
<Release-Date>2018-07-23</Release-Date>
|
| 1440 |
+
<Last-Update-Date>2018-07-23</Last-Update-Date>
|
| 1441 |
+
</Status>
|
| 1442 |
+
<Title>PBMC genomic DNA ME/CFS 12</Title>
|
| 1443 |
+
<Accession database="GEO">GSM3024946</Accession>
|
| 1444 |
+
<Type>genomic</Type>
|
| 1445 |
+
<Channel-Count>1</Channel-Count>
|
| 1446 |
+
<Channel position="1">
|
| 1447 |
+
<Source>ME/CFS PBMC</Source>
|
| 1448 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 1449 |
+
<Characteristics tag="gender">
|
| 1450 |
+
female
|
| 1451 |
+
</Characteristics>
|
| 1452 |
+
<Characteristics tag="subject id">
|
| 1453 |
+
ME/CFS subject 12
|
| 1454 |
+
</Characteristics>
|
| 1455 |
+
<Characteristics tag="disease state">
|
| 1456 |
+
Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS)
|
| 1457 |
+
</Characteristics>
|
| 1458 |
+
<Characteristics tag="cell type">
|
| 1459 |
+
peripheral blood mononuclear cells (PBMC)
|
| 1460 |
+
</Characteristics>
|
| 1461 |
+
<Molecule>genomic DNA</Molecule>
|
| 1462 |
+
<Extract-Protocol>
|
| 1463 |
+
genomic DNA was extracted and purified from PBMC samples using Qiagen DNeasy Blood & Tissue Kit according to manufacturer instructions
|
| 1464 |
+
</Extract-Protocol>
|
| 1465 |
+
<Label>Cy3, Cy5</Label>
|
| 1466 |
+
<Label-Protocol>
|
| 1467 |
+
Standard Illumina Protocol
|
| 1468 |
+
</Label-Protocol>
|
| 1469 |
+
</Channel>
|
| 1470 |
+
<Hybridization-Protocol>
|
| 1471 |
+
bisulphite converted DNA was hybridised to Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol
|
| 1472 |
+
</Hybridization-Protocol>
|
| 1473 |
+
<Scan-Protocol>
|
| 1474 |
+
Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
|
| 1475 |
+
</Scan-Protocol>
|
| 1476 |
+
<Description>
|
| 1477 |
+
PBMC genomic DNA from ME/CFS subject 12
|
| 1478 |
+
</Description>
|
| 1479 |
+
<Data-Processing>
|
| 1480 |
+
Illumina Genome Studio; Matrix signal intensities contains unmethylated and methylated signal intensities; Matrix processed contains non-normalized average beta values.
|
| 1481 |
+
</Data-Processing>
|
| 1482 |
+
<Platform-Ref ref="GPL21145" />
|
| 1483 |
+
<Contact-Ref ref="contrib1" />
|
| 1484 |
+
<Supplementary-Data type="unknown">
|
| 1485 |
+
NONE
|
| 1486 |
+
</Supplementary-Data>
|
| 1487 |
+
<Data-Table>
|
| 1488 |
+
<Column position="1">
|
| 1489 |
+
<Name>ID_REF</Name>
|
| 1490 |
+
</Column>
|
| 1491 |
+
<Column position="2">
|
| 1492 |
+
<Name>VALUE</Name>
|
| 1493 |
+
<Description>Average Beta</Description>
|
| 1494 |
+
</Column>
|
| 1495 |
+
<Column position="3">
|
| 1496 |
+
<Name>Detection Pval</Name>
|
| 1497 |
+
</Column>
|
| 1498 |
+
<External-Data rows="866895">
|
| 1499 |
+
GSM3024946-tbl-1.txt
|
| 1500 |
+
</External-Data>
|
| 1501 |
+
</Data-Table>
|
| 1502 |
+
</Sample>
|
| 1503 |
+
|
| 1504 |
+
<Sample iid="GSM3024947">
|
| 1505 |
+
<Status database="GEO">
|
| 1506 |
+
<Submission-Date>2018-02-27</Submission-Date>
|
| 1507 |
+
<Release-Date>2018-07-23</Release-Date>
|
| 1508 |
+
<Last-Update-Date>2018-07-23</Last-Update-Date>
|
| 1509 |
+
</Status>
|
| 1510 |
+
<Title>PBMC genomic DNA Healthy Control (HC) 9</Title>
|
| 1511 |
+
<Accession database="GEO">GSM3024947</Accession>
|
| 1512 |
+
<Type>genomic</Type>
|
| 1513 |
+
<Channel-Count>1</Channel-Count>
|
| 1514 |
+
<Channel position="1">
|
| 1515 |
+
<Source>HC PBMC</Source>
|
| 1516 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 1517 |
+
<Characteristics tag="gender">
|
| 1518 |
+
female
|
| 1519 |
+
</Characteristics>
|
| 1520 |
+
<Characteristics tag="subject id">
|
| 1521 |
+
HC subject 9
|
| 1522 |
+
</Characteristics>
|
| 1523 |
+
<Characteristics tag="disease state">
|
| 1524 |
+
Healthy Control (HC)
|
| 1525 |
+
</Characteristics>
|
| 1526 |
+
<Characteristics tag="cell type">
|
| 1527 |
+
peripheral blood mononuclear cells (PBMC)
|
| 1528 |
+
</Characteristics>
|
| 1529 |
+
<Molecule>genomic DNA</Molecule>
|
| 1530 |
+
<Extract-Protocol>
|
| 1531 |
+
genomic DNA was extracted and purified from PBMC samples using Qiagen DNeasy Blood & Tissue Kit according to manufacturer instructions
|
| 1532 |
+
</Extract-Protocol>
|
| 1533 |
+
<Label>Cy3, Cy5</Label>
|
| 1534 |
+
<Label-Protocol>
|
| 1535 |
+
Standard Illumina Protocol
|
| 1536 |
+
</Label-Protocol>
|
| 1537 |
+
</Channel>
|
| 1538 |
+
<Hybridization-Protocol>
|
| 1539 |
+
bisulphite converted DNA was hybridised to Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol
|
| 1540 |
+
</Hybridization-Protocol>
|
| 1541 |
+
<Scan-Protocol>
|
| 1542 |
+
Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
|
| 1543 |
+
</Scan-Protocol>
|
| 1544 |
+
<Description>
|
| 1545 |
+
PBMC genomic DNA from HC subject 9
|
| 1546 |
+
</Description>
|
| 1547 |
+
<Data-Processing>
|
| 1548 |
+
Illumina Genome Studio; Matrix signal intensities contains unmethylated and methylated signal intensities; Matrix processed contains non-normalized average beta values.
|
| 1549 |
+
</Data-Processing>
|
| 1550 |
+
<Platform-Ref ref="GPL21145" />
|
| 1551 |
+
<Contact-Ref ref="contrib1" />
|
| 1552 |
+
<Supplementary-Data type="unknown">
|
| 1553 |
+
NONE
|
| 1554 |
+
</Supplementary-Data>
|
| 1555 |
+
<Data-Table>
|
| 1556 |
+
<Column position="1">
|
| 1557 |
+
<Name>ID_REF</Name>
|
| 1558 |
+
</Column>
|
| 1559 |
+
<Column position="2">
|
| 1560 |
+
<Name>VALUE</Name>
|
| 1561 |
+
<Description>Average Beta</Description>
|
| 1562 |
+
</Column>
|
| 1563 |
+
<Column position="3">
|
| 1564 |
+
<Name>Detection Pval</Name>
|
| 1565 |
+
</Column>
|
| 1566 |
+
<External-Data rows="866895">
|
| 1567 |
+
GSM3024947-tbl-1.txt
|
| 1568 |
+
</External-Data>
|
| 1569 |
+
</Data-Table>
|
| 1570 |
+
</Sample>
|
| 1571 |
+
|
| 1572 |
+
<Sample iid="GSM3024948">
|
| 1573 |
+
<Status database="GEO">
|
| 1574 |
+
<Submission-Date>2018-02-27</Submission-Date>
|
| 1575 |
+
<Release-Date>2018-07-23</Release-Date>
|
| 1576 |
+
<Last-Update-Date>2018-07-23</Last-Update-Date>
|
| 1577 |
+
</Status>
|
| 1578 |
+
<Title>PBMC genomic DNA ME/CFS 13</Title>
|
| 1579 |
+
<Accession database="GEO">GSM3024948</Accession>
|
| 1580 |
+
<Type>genomic</Type>
|
| 1581 |
+
<Channel-Count>1</Channel-Count>
|
| 1582 |
+
<Channel position="1">
|
| 1583 |
+
<Source>ME/CFS PBMC</Source>
|
| 1584 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 1585 |
+
<Characteristics tag="gender">
|
| 1586 |
+
female
|
| 1587 |
+
</Characteristics>
|
| 1588 |
+
<Characteristics tag="subject id">
|
| 1589 |
+
ME/CFS subject 13
|
| 1590 |
+
</Characteristics>
|
| 1591 |
+
<Characteristics tag="disease state">
|
| 1592 |
+
Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS)
|
| 1593 |
+
</Characteristics>
|
| 1594 |
+
<Characteristics tag="cell type">
|
| 1595 |
+
peripheral blood mononuclear cells (PBMC)
|
| 1596 |
+
</Characteristics>
|
| 1597 |
+
<Molecule>genomic DNA</Molecule>
|
| 1598 |
+
<Extract-Protocol>
|
| 1599 |
+
genomic DNA was extracted and purified from PBMC samples using Qiagen DNeasy Blood & Tissue Kit according to manufacturer instructions
|
| 1600 |
+
</Extract-Protocol>
|
| 1601 |
+
<Label>Cy3, Cy5</Label>
|
| 1602 |
+
<Label-Protocol>
|
| 1603 |
+
Standard Illumina Protocol
|
| 1604 |
+
</Label-Protocol>
|
| 1605 |
+
</Channel>
|
| 1606 |
+
<Hybridization-Protocol>
|
| 1607 |
+
bisulphite converted DNA was hybridised to Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol
|
| 1608 |
+
</Hybridization-Protocol>
|
| 1609 |
+
<Scan-Protocol>
|
| 1610 |
+
Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
|
| 1611 |
+
</Scan-Protocol>
|
| 1612 |
+
<Description>
|
| 1613 |
+
PBMC genomic DNA from ME/CFS subject 13
|
| 1614 |
+
</Description>
|
| 1615 |
+
<Data-Processing>
|
| 1616 |
+
Illumina Genome Studio; Matrix signal intensities contains unmethylated and methylated signal intensities; Matrix processed contains non-normalized average beta values.
|
| 1617 |
+
</Data-Processing>
|
| 1618 |
+
<Platform-Ref ref="GPL21145" />
|
| 1619 |
+
<Contact-Ref ref="contrib1" />
|
| 1620 |
+
<Supplementary-Data type="unknown">
|
| 1621 |
+
NONE
|
| 1622 |
+
</Supplementary-Data>
|
| 1623 |
+
<Data-Table>
|
| 1624 |
+
<Column position="1">
|
| 1625 |
+
<Name>ID_REF</Name>
|
| 1626 |
+
</Column>
|
| 1627 |
+
<Column position="2">
|
| 1628 |
+
<Name>VALUE</Name>
|
| 1629 |
+
<Description>Average Beta</Description>
|
| 1630 |
+
</Column>
|
| 1631 |
+
<Column position="3">
|
| 1632 |
+
<Name>Detection Pval</Name>
|
| 1633 |
+
</Column>
|
| 1634 |
+
<External-Data rows="866895">
|
| 1635 |
+
GSM3024948-tbl-1.txt
|
| 1636 |
+
</External-Data>
|
| 1637 |
+
</Data-Table>
|
| 1638 |
+
</Sample>
|
| 1639 |
+
|
| 1640 |
+
<Sample iid="GSM3024949">
|
| 1641 |
+
<Status database="GEO">
|
| 1642 |
+
<Submission-Date>2018-02-27</Submission-Date>
|
| 1643 |
+
<Release-Date>2018-07-23</Release-Date>
|
| 1644 |
+
<Last-Update-Date>2018-07-23</Last-Update-Date>
|
| 1645 |
+
</Status>
|
| 1646 |
+
<Title>PBMC genomic DNA Healthy Control (HC) 10</Title>
|
| 1647 |
+
<Accession database="GEO">GSM3024949</Accession>
|
| 1648 |
+
<Type>genomic</Type>
|
| 1649 |
+
<Channel-Count>1</Channel-Count>
|
| 1650 |
+
<Channel position="1">
|
| 1651 |
+
<Source>HC PBMC</Source>
|
| 1652 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 1653 |
+
<Characteristics tag="gender">
|
| 1654 |
+
female
|
| 1655 |
+
</Characteristics>
|
| 1656 |
+
<Characteristics tag="subject id">
|
| 1657 |
+
HC subject 10
|
| 1658 |
+
</Characteristics>
|
| 1659 |
+
<Characteristics tag="disease state">
|
| 1660 |
+
Healthy Control (HC)
|
| 1661 |
+
</Characteristics>
|
| 1662 |
+
<Characteristics tag="cell type">
|
| 1663 |
+
peripheral blood mononuclear cells (PBMC)
|
| 1664 |
+
</Characteristics>
|
| 1665 |
+
<Molecule>genomic DNA</Molecule>
|
| 1666 |
+
<Extract-Protocol>
|
| 1667 |
+
genomic DNA was extracted and purified from PBMC samples using Qiagen DNeasy Blood & Tissue Kit according to manufacturer instructions
|
| 1668 |
+
</Extract-Protocol>
|
| 1669 |
+
<Label>Cy3, Cy5</Label>
|
| 1670 |
+
<Label-Protocol>
|
| 1671 |
+
Standard Illumina Protocol
|
| 1672 |
+
</Label-Protocol>
|
| 1673 |
+
</Channel>
|
| 1674 |
+
<Hybridization-Protocol>
|
| 1675 |
+
bisulphite converted DNA was hybridised to Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol
|
| 1676 |
+
</Hybridization-Protocol>
|
| 1677 |
+
<Scan-Protocol>
|
| 1678 |
+
Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
|
| 1679 |
+
</Scan-Protocol>
|
| 1680 |
+
<Description>
|
| 1681 |
+
PBMC genomic DNA from HC subject 10
|
| 1682 |
+
</Description>
|
| 1683 |
+
<Data-Processing>
|
| 1684 |
+
Illumina Genome Studio; Matrix signal intensities contains unmethylated and methylated signal intensities; Matrix processed contains non-normalized average beta values.
|
| 1685 |
+
</Data-Processing>
|
| 1686 |
+
<Platform-Ref ref="GPL21145" />
|
| 1687 |
+
<Contact-Ref ref="contrib1" />
|
| 1688 |
+
<Supplementary-Data type="unknown">
|
| 1689 |
+
NONE
|
| 1690 |
+
</Supplementary-Data>
|
| 1691 |
+
<Data-Table>
|
| 1692 |
+
<Column position="1">
|
| 1693 |
+
<Name>ID_REF</Name>
|
| 1694 |
+
</Column>
|
| 1695 |
+
<Column position="2">
|
| 1696 |
+
<Name>VALUE</Name>
|
| 1697 |
+
<Description>Average Beta</Description>
|
| 1698 |
+
</Column>
|
| 1699 |
+
<Column position="3">
|
| 1700 |
+
<Name>Detection Pval</Name>
|
| 1701 |
+
</Column>
|
| 1702 |
+
<External-Data rows="866895">
|
| 1703 |
+
GSM3024949-tbl-1.txt
|
| 1704 |
+
</External-Data>
|
| 1705 |
+
</Data-Table>
|
| 1706 |
+
</Sample>
|
| 1707 |
+
|
| 1708 |
+
<Sample iid="GSM3024950">
|
| 1709 |
+
<Status database="GEO">
|
| 1710 |
+
<Submission-Date>2018-02-27</Submission-Date>
|
| 1711 |
+
<Release-Date>2018-07-23</Release-Date>
|
| 1712 |
+
<Last-Update-Date>2018-07-23</Last-Update-Date>
|
| 1713 |
+
</Status>
|
| 1714 |
+
<Title>PBMC genomic DNA Healthy Control (HC) 11</Title>
|
| 1715 |
+
<Accession database="GEO">GSM3024950</Accession>
|
| 1716 |
+
<Type>genomic</Type>
|
| 1717 |
+
<Channel-Count>1</Channel-Count>
|
| 1718 |
+
<Channel position="1">
|
| 1719 |
+
<Source>HC PBMC</Source>
|
| 1720 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 1721 |
+
<Characteristics tag="gender">
|
| 1722 |
+
female
|
| 1723 |
+
</Characteristics>
|
| 1724 |
+
<Characteristics tag="subject id">
|
| 1725 |
+
HC subject 11
|
| 1726 |
+
</Characteristics>
|
| 1727 |
+
<Characteristics tag="disease state">
|
| 1728 |
+
Healthy Control (HC)
|
| 1729 |
+
</Characteristics>
|
| 1730 |
+
<Characteristics tag="cell type">
|
| 1731 |
+
peripheral blood mononuclear cells (PBMC)
|
| 1732 |
+
</Characteristics>
|
| 1733 |
+
<Molecule>genomic DNA</Molecule>
|
| 1734 |
+
<Extract-Protocol>
|
| 1735 |
+
genomic DNA was extracted and purified from PBMC samples using Qiagen DNeasy Blood & Tissue Kit according to manufacturer instructions
|
| 1736 |
+
</Extract-Protocol>
|
| 1737 |
+
<Label>Cy3, Cy5</Label>
|
| 1738 |
+
<Label-Protocol>
|
| 1739 |
+
Standard Illumina Protocol
|
| 1740 |
+
</Label-Protocol>
|
| 1741 |
+
</Channel>
|
| 1742 |
+
<Hybridization-Protocol>
|
| 1743 |
+
bisulphite converted DNA was hybridised to Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol
|
| 1744 |
+
</Hybridization-Protocol>
|
| 1745 |
+
<Scan-Protocol>
|
| 1746 |
+
Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
|
| 1747 |
+
</Scan-Protocol>
|
| 1748 |
+
<Description>
|
| 1749 |
+
PBMC genomic DNA from HC subject 11
|
| 1750 |
+
</Description>
|
| 1751 |
+
<Data-Processing>
|
| 1752 |
+
Illumina Genome Studio; Matrix signal intensities contains unmethylated and methylated signal intensities; Matrix processed contains non-normalized average beta values.
|
| 1753 |
+
</Data-Processing>
|
| 1754 |
+
<Platform-Ref ref="GPL21145" />
|
| 1755 |
+
<Contact-Ref ref="contrib1" />
|
| 1756 |
+
<Supplementary-Data type="unknown">
|
| 1757 |
+
NONE
|
| 1758 |
+
</Supplementary-Data>
|
| 1759 |
+
<Data-Table>
|
| 1760 |
+
<Column position="1">
|
| 1761 |
+
<Name>ID_REF</Name>
|
| 1762 |
+
</Column>
|
| 1763 |
+
<Column position="2">
|
| 1764 |
+
<Name>VALUE</Name>
|
| 1765 |
+
<Description>Average Beta</Description>
|
| 1766 |
+
</Column>
|
| 1767 |
+
<Column position="3">
|
| 1768 |
+
<Name>Detection Pval</Name>
|
| 1769 |
+
</Column>
|
| 1770 |
+
<External-Data rows="866895">
|
| 1771 |
+
GSM3024950-tbl-1.txt
|
| 1772 |
+
</External-Data>
|
| 1773 |
+
</Data-Table>
|
| 1774 |
+
</Sample>
|
| 1775 |
+
|
| 1776 |
+
<Sample iid="GSM3024951">
|
| 1777 |
+
<Status database="GEO">
|
| 1778 |
+
<Submission-Date>2018-02-27</Submission-Date>
|
| 1779 |
+
<Release-Date>2018-07-23</Release-Date>
|
| 1780 |
+
<Last-Update-Date>2018-07-23</Last-Update-Date>
|
| 1781 |
+
</Status>
|
| 1782 |
+
<Title>PBMC genomic DNA Healthy Control (HC) 12</Title>
|
| 1783 |
+
<Accession database="GEO">GSM3024951</Accession>
|
| 1784 |
+
<Type>genomic</Type>
|
| 1785 |
+
<Channel-Count>1</Channel-Count>
|
| 1786 |
+
<Channel position="1">
|
| 1787 |
+
<Source>HC PBMC</Source>
|
| 1788 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 1789 |
+
<Characteristics tag="gender">
|
| 1790 |
+
female
|
| 1791 |
+
</Characteristics>
|
| 1792 |
+
<Characteristics tag="subject id">
|
| 1793 |
+
HC subject 12
|
| 1794 |
+
</Characteristics>
|
| 1795 |
+
<Characteristics tag="disease state">
|
| 1796 |
+
Healthy Control (HC)
|
| 1797 |
+
</Characteristics>
|
| 1798 |
+
<Characteristics tag="cell type">
|
| 1799 |
+
peripheral blood mononuclear cells (PBMC)
|
| 1800 |
+
</Characteristics>
|
| 1801 |
+
<Molecule>genomic DNA</Molecule>
|
| 1802 |
+
<Extract-Protocol>
|
| 1803 |
+
genomic DNA was extracted and purified from PBMC samples using Qiagen DNeasy Blood & Tissue Kit according to manufacturer instructions
|
| 1804 |
+
</Extract-Protocol>
|
| 1805 |
+
<Label>Cy3, Cy5</Label>
|
| 1806 |
+
<Label-Protocol>
|
| 1807 |
+
Standard Illumina Protocol
|
| 1808 |
+
</Label-Protocol>
|
| 1809 |
+
</Channel>
|
| 1810 |
+
<Hybridization-Protocol>
|
| 1811 |
+
bisulphite converted DNA was hybridised to Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol
|
| 1812 |
+
</Hybridization-Protocol>
|
| 1813 |
+
<Scan-Protocol>
|
| 1814 |
+
Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
|
| 1815 |
+
</Scan-Protocol>
|
| 1816 |
+
<Description>
|
| 1817 |
+
PBMC genomic DNA from HC subject 12
|
| 1818 |
+
</Description>
|
| 1819 |
+
<Data-Processing>
|
| 1820 |
+
Illumina Genome Studio; Matrix signal intensities contains unmethylated and methylated signal intensities; Matrix processed contains non-normalized average beta values.
|
| 1821 |
+
</Data-Processing>
|
| 1822 |
+
<Platform-Ref ref="GPL21145" />
|
| 1823 |
+
<Contact-Ref ref="contrib1" />
|
| 1824 |
+
<Supplementary-Data type="unknown">
|
| 1825 |
+
NONE
|
| 1826 |
+
</Supplementary-Data>
|
| 1827 |
+
<Data-Table>
|
| 1828 |
+
<Column position="1">
|
| 1829 |
+
<Name>ID_REF</Name>
|
| 1830 |
+
</Column>
|
| 1831 |
+
<Column position="2">
|
| 1832 |
+
<Name>VALUE</Name>
|
| 1833 |
+
<Description>Average Beta</Description>
|
| 1834 |
+
</Column>
|
| 1835 |
+
<Column position="3">
|
| 1836 |
+
<Name>Detection Pval</Name>
|
| 1837 |
+
</Column>
|
| 1838 |
+
<External-Data rows="866895">
|
| 1839 |
+
GSM3024951-tbl-1.txt
|
| 1840 |
+
</External-Data>
|
| 1841 |
+
</Data-Table>
|
| 1842 |
+
</Sample>
|
| 1843 |
+
|
| 1844 |
+
<Series iid="GSE111183">
|
| 1845 |
+
<Status database="GEO">
|
| 1846 |
+
<Submission-Date>2018-02-27</Submission-Date>
|
| 1847 |
+
<Release-Date>2018-07-23</Release-Date>
|
| 1848 |
+
<Last-Update-Date>2019-01-20</Last-Update-Date>
|
| 1849 |
+
</Status>
|
| 1850 |
+
<Title>Identification of Myalgic Encephalomyelitis/Chronic Fatigue Syndrome-associated DNA methylation patterns</Title>
|
| 1851 |
+
<Accession database="GEO">GSE111183</Accession>
|
| 1852 |
+
<Pubmed-ID>30036399</Pubmed-ID>
|
| 1853 |
+
<Summary>
|
| 1854 |
+
Background: Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) is a complex condition that involves multiple organ systems and is characterized by an abrupt or delayed onset of persistent/relapsing symptomatology such as debilitating fatigue, immune dysfunction, neurological problems, and other symptoms not curable for at least 6 months. Disruption of DNA methylation patterns has been tied to various immune and neurological diseases; however, the status of this epigenetic mark in ME/CFS remains uncertain. This study aimed at identifying changes in the DNA methylation patterns that are causative of changes in the regulation of gene expression in ME/CSF patients. Such changes may be also used for diagnostic purposes and be indicative of potential therapeutic targets.
|
| 1855 |
+
Methods: Peripheral blood mononuclear cells (PBMCs) from 13 ME/CFS patients and 12 healthy controls (HC) were used to extract genomic DNA and measure global DNA methylation, and the methylation status at 850,000 CpG sites was assessed using Illumina MethylationEPIC microarrays.
|
| 1856 |
+
Results: Global DNA methylation levels of ME/CFS patients were similar to those of HC. However, microarray-based genome-wide technology allowed detection of 17,296 differentially methylated CpG sites in 6,368 genes across promoters, gene regulatory elements and within coding regions of genes. Analysis of DNA methylation in promoter regions found 307 differentially methylated promoters (DMP); genes associated with DMP participate in at least 15 different pathways mostly related to cell signaling with a strong immune component.
|
| 1857 |
+
Conclusions: This is the first study that has explored genome-wide epigenetic changes associated with ME/CFS using the new MethylationEPIC microarrays covering about 850,000 CpG sites. Our results are consistent with dysregulation of the immune system in ME/CFS and suggest a role of this epigenetic modification on the DNA pathobiology of ME/CFS.
|
| 1858 |
+
</Summary>
|
| 1859 |
+
<Overall-Design>
|
| 1860 |
+
Genomic DNA from 25 peripheral blood mononuclear cells (PBMC) samples (13 ME/CFS, 12 controls) were bisulfite-converted and hybridised to the Illumina MethylationEPIC microarrays. GenomeStudio idat files were generated and the data was analyzed using the RnBeads R package.
|
| 1861 |
+
</Overall-Design>
|
| 1862 |
+
<Type>Methylation profiling by array</Type>
|
| 1863 |
+
<Contributor-Ref ref="contrib3" position="1" />
|
| 1864 |
+
<Contributor-Ref ref="contrib4" position="2" />
|
| 1865 |
+
<Contributor-Ref ref="contrib5" position="3" />
|
| 1866 |
+
<Contributor-Ref ref="contrib6" position="4" />
|
| 1867 |
+
<Contributor-Ref ref="contrib7" position="5" />
|
| 1868 |
+
<Contributor-Ref ref="contrib8" position="6" />
|
| 1869 |
+
<Contributor-Ref ref="contrib9" position="7" />
|
| 1870 |
+
<Contributor-Ref ref="contrib1" position="8" />
|
| 1871 |
+
<Contact-Ref ref="contrib1" />
|
| 1872 |
+
<Sample-Ref ref="GSM3024927" />
|
| 1873 |
+
<Sample-Ref ref="GSM3024928" />
|
| 1874 |
+
<Sample-Ref ref="GSM3024929" />
|
| 1875 |
+
<Sample-Ref ref="GSM3024930" />
|
| 1876 |
+
<Sample-Ref ref="GSM3024931" />
|
| 1877 |
+
<Sample-Ref ref="GSM3024932" />
|
| 1878 |
+
<Sample-Ref ref="GSM3024933" />
|
| 1879 |
+
<Sample-Ref ref="GSM3024934" />
|
| 1880 |
+
<Sample-Ref ref="GSM3024935" />
|
| 1881 |
+
<Sample-Ref ref="GSM3024936" />
|
| 1882 |
+
<Sample-Ref ref="GSM3024937" />
|
| 1883 |
+
<Sample-Ref ref="GSM3024938" />
|
| 1884 |
+
<Sample-Ref ref="GSM3024939" />
|
| 1885 |
+
<Sample-Ref ref="GSM3024940" />
|
| 1886 |
+
<Sample-Ref ref="GSM3024941" />
|
| 1887 |
+
<Sample-Ref ref="GSM3024942" />
|
| 1888 |
+
<Sample-Ref ref="GSM3024943" />
|
| 1889 |
+
<Sample-Ref ref="GSM3024944" />
|
| 1890 |
+
<Sample-Ref ref="GSM3024945" />
|
| 1891 |
+
<Sample-Ref ref="GSM3024946" />
|
| 1892 |
+
<Sample-Ref ref="GSM3024947" />
|
| 1893 |
+
<Sample-Ref ref="GSM3024948" />
|
| 1894 |
+
<Sample-Ref ref="GSM3024949" />
|
| 1895 |
+
<Sample-Ref ref="GSM3024950" />
|
| 1896 |
+
<Sample-Ref ref="GSM3024951" />
|
| 1897 |
+
<Supplementary-Data type="TAR">
|
| 1898 |
+
ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE111nnn/GSE111183/suppl/GSE111183_RAW.tar
|
| 1899 |
+
</Supplementary-Data>
|
| 1900 |
+
<Supplementary-Data type="TXT">
|
| 1901 |
+
ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE111nnn/GSE111183/suppl/GSE111183_signal_intensities.txt.gz
|
| 1902 |
+
</Supplementary-Data>
|
| 1903 |
+
<Relation type="BioProject" target="https://www.ncbi.nlm.nih.gov/bioproject/PRJNA436126" />
|
| 1904 |
+
</Series>
|
| 1905 |
+
|
| 1906 |
+
</MINiML>
|
ME/GSE153667/GSE153667_RAW/GSM4649028_Control2_CpG.txt
ADDED
|
The diff for this file is too large to render.
See raw diff
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|
ME/GSE153667/GSE153667_RAW/GSM4649033_Control7_CpG.txt
ADDED
|
The diff for this file is too large to render.
See raw diff
|
|
|
ME/GSE153667/GSE153667_RAW/GSM4649045_Patient9_CpG.txt
ADDED
|
The diff for this file is too large to render.
See raw diff
|
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|
ME/GSE153667/meta/._GSE153667_family.soft
ADDED
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Binary file (4.1 kB). View file
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ME/GSE153667/meta/._GSE153667_family.xml
ADDED
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Binary file (4.1 kB). View file
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ME/GSE153667/meta/._GSE153667_series_matrix.txt
ADDED
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Binary file (4.1 kB). View file
|
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ME/GSE153667/meta/GSE153667_family.soft
ADDED
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@@ -0,0 +1,853 @@
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| 1 |
+
^DATABASE = GeoMiame
|
| 2 |
+
!Database_name = Gene Expression Omnibus (GEO)
|
| 3 |
+
!Database_institute = NCBI NLM NIH
|
| 4 |
+
!Database_web_link = http://www.ncbi.nlm.nih.gov/geo
|
| 5 |
+
!Database_email = geo@ncbi.nlm.nih.gov
|
| 6 |
+
^SERIES = GSE153667
|
| 7 |
+
!Series_title = Changes in the Epigenetic Landscape of Myalgic Encephalomyelitis/Chronic Fatigue Syndrome Reflect Systemic Dysfunctions
|
| 8 |
+
!Series_geo_accession = GSE153667
|
| 9 |
+
!Series_status = Public on Jul 02 2020
|
| 10 |
+
!Series_submission_date = Jul 01 2020
|
| 11 |
+
!Series_last_update_date = Nov 09 2020
|
| 12 |
+
!Series_pubmed_id = 33148325
|
| 13 |
+
!Series_summary = Purpose: ME/CFS is a lifelong debilitating disease that affects approximately 1% of the global population. Previous studies have identified dysfunctional activity in metabolic, immune and neurological pathways. The goal of this study is to identify ME/CFS specific variations in DNA methylation to determine whether the patient specific epigenetic patterns provide insight into the disease pathophysiology.
|
| 14 |
+
!Series_summary = Methods: DNA was extracted from the PBMCs of 10 ME/CFS patients and age/gender matched controls. After performing RRBS the sequence was aligned to hg19 genome using Bismark. The data was analyzed using first an ANOVA F test through DMAP in order to determine variation between the patient and control groups across 40-220bp fragments of the genome. Additional analysis was performed following a MethylKit pipeline, which analyzed the variation on a single CpG basis using a Fishers test.
|
| 15 |
+
!Series_summary = Results: From a total of 146,575 DMAP fragments we identified 76 differentially methylated fragments (P <0.05, Diff meth +/- 15%). A total of 31 were associated with gene regions (intronic/exonic). MethylKit analysis also identified a total of 394 differentially methylated cytosines (FDR corrected P <0.05, Diff meth +/- 15%) from a total of 196,172 individual analyzed cytosines, 91 of the statistically significant cytosines fell within gene regions. Comparison of both methylomes and regions where both the DMAP fragments and multiple MethylKit cytosines fell highlighted areas of the genome containing regulatory elements associated with metabolic and immune activity. Gene body pathway enrichment additionally identified immune metabolic and neurological related functions.
|
| 16 |
+
!Series_summary = Conclusions: Our study represents the first investigation of ME/CFS patients using reduced representation bisulfite sequencing. We identified a number of major differences between patients that distinguished them from healthy controls. Our results identified a number of differentially methylated regulatory elements and gene bodies that highlight the disturbed pathophysiology in ME/CFS. In particular the large number of enriched neurotransmitter and neuropeptide reactome pathways highlighted a disturbed neurological pathophysiology in patients.
|
| 17 |
+
!Series_overall_design = RRBS Analysis of 10 ME/CFS patients vs. Controls
|
| 18 |
+
!Series_type = Methylation profiling by high throughput sequencing
|
| 19 |
+
!Series_contributor = Amber,,Helliwell
|
| 20 |
+
!Series_contributor = Warren,,Tate
|
| 21 |
+
!Series_contributor = Aniruddha,,Chatterjee
|
| 22 |
+
!Series_contributor = Peter,,Stockwell
|
| 23 |
+
!Series_contributor = Eiren,,Sweetman
|
| 24 |
+
!Series_contributor = Tina,,Edgar
|
| 25 |
+
!Series_sample_id = GSM4649027
|
| 26 |
+
!Series_sample_id = GSM4649028
|
| 27 |
+
!Series_sample_id = GSM4649029
|
| 28 |
+
!Series_sample_id = GSM4649030
|
| 29 |
+
!Series_sample_id = GSM4649031
|
| 30 |
+
!Series_sample_id = GSM4649032
|
| 31 |
+
!Series_sample_id = GSM4649033
|
| 32 |
+
!Series_sample_id = GSM4649034
|
| 33 |
+
!Series_sample_id = GSM4649035
|
| 34 |
+
!Series_sample_id = GSM4649036
|
| 35 |
+
!Series_sample_id = GSM4649037
|
| 36 |
+
!Series_sample_id = GSM4649038
|
| 37 |
+
!Series_sample_id = GSM4649039
|
| 38 |
+
!Series_sample_id = GSM4649040
|
| 39 |
+
!Series_sample_id = GSM4649041
|
| 40 |
+
!Series_sample_id = GSM4649042
|
| 41 |
+
!Series_sample_id = GSM4649043
|
| 42 |
+
!Series_sample_id = GSM4649044
|
| 43 |
+
!Series_sample_id = GSM4649045
|
| 44 |
+
!Series_sample_id = GSM4649046
|
| 45 |
+
!Series_contact_name = Amber,,Helliwell
|
| 46 |
+
!Series_contact_department = Biochemistry Department
|
| 47 |
+
!Series_contact_institute = University of Otago
|
| 48 |
+
!Series_contact_address = 710 Cumberland Road
|
| 49 |
+
!Series_contact_city = Dunedin
|
| 50 |
+
!Series_contact_zip/postal_code = 9016
|
| 51 |
+
!Series_contact_country = New Zealand
|
| 52 |
+
!Series_supplementary_file = ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE153nnn/GSE153667/suppl/GSE153667_DMAP_matrix.csv.gz
|
| 53 |
+
!Series_supplementary_file = ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE153nnn/GSE153667/suppl/GSE153667_GeneMatrix.xlsx
|
| 54 |
+
!Series_supplementary_file = ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE153nnn/GSE153667/suppl/GSE153667_Meth_Matrix.csv.gz
|
| 55 |
+
!Series_supplementary_file = ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE153nnn/GSE153667/suppl/GSE153667_RAW.tar
|
| 56 |
+
!Series_platform_id = GPL16791
|
| 57 |
+
!Series_platform_taxid = 9606
|
| 58 |
+
!Series_sample_taxid = 9606
|
| 59 |
+
!Series_relation = BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA643579
|
| 60 |
+
!Series_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP269624
|
| 61 |
+
^PLATFORM = GPL16791
|
| 62 |
+
!Platform_title = Illumina HiSeq 2500 (Homo sapiens)
|
| 63 |
+
!Platform_geo_accession = GPL16791
|
| 64 |
+
!Platform_status = Public on Mar 14 2013
|
| 65 |
+
!Platform_submission_date = Mar 14 2013
|
| 66 |
+
!Platform_last_update_date = Mar 27 2019
|
| 67 |
+
!Platform_technology = high-throughput sequencing
|
| 68 |
+
!Platform_distribution = virtual
|
| 69 |
+
!Platform_organism = Homo sapiens
|
| 70 |
+
!Platform_taxid = 9606
|
| 71 |
+
!Platform_contact_name = ,,GEO
|
| 72 |
+
!Platform_contact_country = USA
|
| 73 |
+
!Platform_data_row_count = 0
|
| 74 |
+
^SAMPLE = GSM4649027
|
| 75 |
+
!Sample_title = Control1
|
| 76 |
+
!Sample_geo_accession = GSM4649027
|
| 77 |
+
!Sample_status = Public on Jul 02 2020
|
| 78 |
+
!Sample_submission_date = Jul 01 2020
|
| 79 |
+
!Sample_last_update_date = Jul 02 2020
|
| 80 |
+
!Sample_type = SRA
|
| 81 |
+
!Sample_channel_count = 1
|
| 82 |
+
!Sample_source_name_ch1 = Peripheral Blood Mononuclear Cells
|
| 83 |
+
!Sample_organism_ch1 = Homo sapiens
|
| 84 |
+
!Sample_taxid_ch1 = 9606
|
| 85 |
+
!Sample_characteristics_ch1 = disease state: Control
|
| 86 |
+
!Sample_molecule_ch1 = genomic DNA
|
| 87 |
+
!Sample_extract_protocol_ch1 = DNA was extracted from 200ul of PBMCs
|
| 88 |
+
!Sample_extract_protocol_ch1 = MSPI digestion (purify), end repair (purify), A-tialing and adaptor ligation (purify), PCR amplification (purify), Gel size selection and gel extraction (purify)
|
| 89 |
+
!Sample_data_processing = reads were adaptor trimmed using bismark that used a file of adaptor sequences and trimmed three bases back from any detected adaptor to delete the C invorporated and rejecting any reads that were trimmed to less than 10bp
|
| 90 |
+
!Sample_data_processing = reads were aligned to the hg19 genome using bismark with the following specifications: a tolerance for one non-bisulfite mismatch per read, the default minimum alignment score (L,O, -02), and with ignore - quals in order to calculate the mismatch penalty by considering the quality value at the mismatched position to be the highest possible
|
| 91 |
+
!Sample_data_processing = bam files generated by Bismark alignment were then processed using DMAP to compare control vs. patients with the following specifications: ANOVA F test on fragments 40-220bp in length, with the fragment requireing at lest 2 CpGs to have 10 or more sequence reads. The differential methylation file was then annotated with protein coding gene information using the DMAP command identgeneloc. DMAPmatrix.csv file contains this data.
|
| 92 |
+
!Sample_data_processing = the bam files were additionally analysed following a MethylKit based pipeline where first the data was filtered for low read coverage (less than 10 times coverage) and normalised basde on mean coverage distribution before comparing pooled patient and control groups using a Fisher's test. Methmatrix.csv file contains this data
|
| 93 |
+
!Sample_data_processing = Genome_build: hg19
|
| 94 |
+
!Sample_data_processing = Supplementary_files_format_and_content: Individual .txt files for each sample containing C and T frequency per base and coverage. Matrix (csv file) containing methylation percentages for each sample used in the control vs patient analysis for the MethylKit single CpG pipeline.
|
| 95 |
+
!Sample_data_processing = Supplementary_files_format_and_content: A matrix containing the DMAP output data (individual sample percentages, significance values, associated genomic features, fragment length, CpG per fragment). .
|
| 96 |
+
!Sample_platform_id = GPL16791
|
| 97 |
+
!Sample_contact_name = Amber,,Helliwell
|
| 98 |
+
!Sample_contact_department = Biochemistry Department
|
| 99 |
+
!Sample_contact_institute = University of Otago
|
| 100 |
+
!Sample_contact_address = 710 Cumberland Road
|
| 101 |
+
!Sample_contact_city = Dunedin
|
| 102 |
+
!Sample_contact_zip/postal_code = 9016
|
| 103 |
+
!Sample_contact_country = New Zealand
|
| 104 |
+
!Sample_instrument_model = Illumina HiSeq 2500
|
| 105 |
+
!Sample_library_selection = Reduced Representation
|
| 106 |
+
!Sample_library_source = genomic
|
| 107 |
+
!Sample_library_strategy = Bisulfite-Seq
|
| 108 |
+
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN15420272
|
| 109 |
+
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8651460
|
| 110 |
+
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4649nnn/GSM4649027/suppl/GSM4649027_Control1_CpG.txt.gz
|
| 111 |
+
!Sample_series_id = GSE153667
|
| 112 |
+
!Sample_data_row_count = 0
|
| 113 |
+
^SAMPLE = GSM4649028
|
| 114 |
+
!Sample_title = Control2
|
| 115 |
+
!Sample_geo_accession = GSM4649028
|
| 116 |
+
!Sample_status = Public on Jul 02 2020
|
| 117 |
+
!Sample_submission_date = Jul 01 2020
|
| 118 |
+
!Sample_last_update_date = Jul 02 2020
|
| 119 |
+
!Sample_type = SRA
|
| 120 |
+
!Sample_channel_count = 1
|
| 121 |
+
!Sample_source_name_ch1 = Peripheral Blood Mononuclear Cells
|
| 122 |
+
!Sample_organism_ch1 = Homo sapiens
|
| 123 |
+
!Sample_taxid_ch1 = 9606
|
| 124 |
+
!Sample_characteristics_ch1 = disease state: Control
|
| 125 |
+
!Sample_molecule_ch1 = genomic DNA
|
| 126 |
+
!Sample_extract_protocol_ch1 = DNA was extracted from 200ul of PBMCs
|
| 127 |
+
!Sample_extract_protocol_ch1 = MSPI digestion (purify), end repair (purify), A-tialing and adaptor ligation (purify), PCR amplification (purify), Gel size selection and gel extraction (purify)
|
| 128 |
+
!Sample_data_processing = reads were adaptor trimmed using bismark that used a file of adaptor sequences and trimmed three bases back from any detected adaptor to delete the C invorporated and rejecting any reads that were trimmed to less than 10bp
|
| 129 |
+
!Sample_data_processing = reads were aligned to the hg19 genome using bismark with the following specifications: a tolerance for one non-bisulfite mismatch per read, the default minimum alignment score (L,O, -02), and with ignore - quals in order to calculate the mismatch penalty by considering the quality value at the mismatched position to be the highest possible
|
| 130 |
+
!Sample_data_processing = bam files generated by Bismark alignment were then processed using DMAP to compare control vs. patients with the following specifications: ANOVA F test on fragments 40-220bp in length, with the fragment requireing at lest 2 CpGs to have 10 or more sequence reads. The differential methylation file was then annotated with protein coding gene information using the DMAP command identgeneloc. DMAPmatrix.csv file contains this data.
|
| 131 |
+
!Sample_data_processing = the bam files were additionally analysed following a MethylKit based pipeline where first the data was filtered for low read coverage (less than 10 times coverage) and normalised basde on mean coverage distribution before comparing pooled patient and control groups using a Fisher's test. Methmatrix.csv file contains this data
|
| 132 |
+
!Sample_data_processing = Genome_build: hg19
|
| 133 |
+
!Sample_data_processing = Supplementary_files_format_and_content: Individual .txt files for each sample containing C and T frequency per base and coverage. Matrix (csv file) containing methylation percentages for each sample used in the control vs patient analysis for the MethylKit single CpG pipeline.
|
| 134 |
+
!Sample_data_processing = Supplementary_files_format_and_content: A matrix containing the DMAP output data (individual sample percentages, significance values, associated genomic features, fragment length, CpG per fragment). .
|
| 135 |
+
!Sample_platform_id = GPL16791
|
| 136 |
+
!Sample_contact_name = Amber,,Helliwell
|
| 137 |
+
!Sample_contact_department = Biochemistry Department
|
| 138 |
+
!Sample_contact_institute = University of Otago
|
| 139 |
+
!Sample_contact_address = 710 Cumberland Road
|
| 140 |
+
!Sample_contact_city = Dunedin
|
| 141 |
+
!Sample_contact_zip/postal_code = 9016
|
| 142 |
+
!Sample_contact_country = New Zealand
|
| 143 |
+
!Sample_instrument_model = Illumina HiSeq 2500
|
| 144 |
+
!Sample_library_selection = Reduced Representation
|
| 145 |
+
!Sample_library_source = genomic
|
| 146 |
+
!Sample_library_strategy = Bisulfite-Seq
|
| 147 |
+
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN15420271
|
| 148 |
+
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8651461
|
| 149 |
+
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4649nnn/GSM4649028/suppl/GSM4649028_Control2_CpG.txt.gz
|
| 150 |
+
!Sample_series_id = GSE153667
|
| 151 |
+
!Sample_data_row_count = 0
|
| 152 |
+
^SAMPLE = GSM4649029
|
| 153 |
+
!Sample_title = Control3
|
| 154 |
+
!Sample_geo_accession = GSM4649029
|
| 155 |
+
!Sample_status = Public on Jul 02 2020
|
| 156 |
+
!Sample_submission_date = Jul 01 2020
|
| 157 |
+
!Sample_last_update_date = Jul 02 2020
|
| 158 |
+
!Sample_type = SRA
|
| 159 |
+
!Sample_channel_count = 1
|
| 160 |
+
!Sample_source_name_ch1 = Peripheral Blood Mononuclear Cells
|
| 161 |
+
!Sample_organism_ch1 = Homo sapiens
|
| 162 |
+
!Sample_taxid_ch1 = 9606
|
| 163 |
+
!Sample_characteristics_ch1 = disease state: Control
|
| 164 |
+
!Sample_molecule_ch1 = genomic DNA
|
| 165 |
+
!Sample_extract_protocol_ch1 = DNA was extracted from 200ul of PBMCs
|
| 166 |
+
!Sample_extract_protocol_ch1 = MSPI digestion (purify), end repair (purify), A-tialing and adaptor ligation (purify), PCR amplification (purify), Gel size selection and gel extraction (purify)
|
| 167 |
+
!Sample_data_processing = reads were adaptor trimmed using bismark that used a file of adaptor sequences and trimmed three bases back from any detected adaptor to delete the C invorporated and rejecting any reads that were trimmed to less than 10bp
|
| 168 |
+
!Sample_data_processing = reads were aligned to the hg19 genome using bismark with the following specifications: a tolerance for one non-bisulfite mismatch per read, the default minimum alignment score (L,O, -02), and with ignore - quals in order to calculate the mismatch penalty by considering the quality value at the mismatched position to be the highest possible
|
| 169 |
+
!Sample_data_processing = bam files generated by Bismark alignment were then processed using DMAP to compare control vs. patients with the following specifications: ANOVA F test on fragments 40-220bp in length, with the fragment requireing at lest 2 CpGs to have 10 or more sequence reads. The differential methylation file was then annotated with protein coding gene information using the DMAP command identgeneloc. DMAPmatrix.csv file contains this data.
|
| 170 |
+
!Sample_data_processing = the bam files were additionally analysed following a MethylKit based pipeline where first the data was filtered for low read coverage (less than 10 times coverage) and normalised basde on mean coverage distribution before comparing pooled patient and control groups using a Fisher's test. Methmatrix.csv file contains this data
|
| 171 |
+
!Sample_data_processing = Genome_build: hg19
|
| 172 |
+
!Sample_data_processing = Supplementary_files_format_and_content: Individual .txt files for each sample containing C and T frequency per base and coverage. Matrix (csv file) containing methylation percentages for each sample used in the control vs patient analysis for the MethylKit single CpG pipeline.
|
| 173 |
+
!Sample_data_processing = Supplementary_files_format_and_content: A matrix containing the DMAP output data (individual sample percentages, significance values, associated genomic features, fragment length, CpG per fragment). .
|
| 174 |
+
!Sample_platform_id = GPL16791
|
| 175 |
+
!Sample_contact_name = Amber,,Helliwell
|
| 176 |
+
!Sample_contact_department = Biochemistry Department
|
| 177 |
+
!Sample_contact_institute = University of Otago
|
| 178 |
+
!Sample_contact_address = 710 Cumberland Road
|
| 179 |
+
!Sample_contact_city = Dunedin
|
| 180 |
+
!Sample_contact_zip/postal_code = 9016
|
| 181 |
+
!Sample_contact_country = New Zealand
|
| 182 |
+
!Sample_instrument_model = Illumina HiSeq 2500
|
| 183 |
+
!Sample_library_selection = Reduced Representation
|
| 184 |
+
!Sample_library_source = genomic
|
| 185 |
+
!Sample_library_strategy = Bisulfite-Seq
|
| 186 |
+
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN15420270
|
| 187 |
+
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8651462
|
| 188 |
+
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4649nnn/GSM4649029/suppl/GSM4649029_Control3_CpG.txt.gz
|
| 189 |
+
!Sample_series_id = GSE153667
|
| 190 |
+
!Sample_data_row_count = 0
|
| 191 |
+
^SAMPLE = GSM4649030
|
| 192 |
+
!Sample_title = Control4
|
| 193 |
+
!Sample_geo_accession = GSM4649030
|
| 194 |
+
!Sample_status = Public on Jul 02 2020
|
| 195 |
+
!Sample_submission_date = Jul 01 2020
|
| 196 |
+
!Sample_last_update_date = Jul 02 2020
|
| 197 |
+
!Sample_type = SRA
|
| 198 |
+
!Sample_channel_count = 1
|
| 199 |
+
!Sample_source_name_ch1 = Peripheral Blood Mononuclear Cells
|
| 200 |
+
!Sample_organism_ch1 = Homo sapiens
|
| 201 |
+
!Sample_taxid_ch1 = 9606
|
| 202 |
+
!Sample_characteristics_ch1 = disease state: Control
|
| 203 |
+
!Sample_molecule_ch1 = genomic DNA
|
| 204 |
+
!Sample_extract_protocol_ch1 = DNA was extracted from 200ul of PBMCs
|
| 205 |
+
!Sample_extract_protocol_ch1 = MSPI digestion (purify), end repair (purify), A-tialing and adaptor ligation (purify), PCR amplification (purify), Gel size selection and gel extraction (purify)
|
| 206 |
+
!Sample_data_processing = reads were adaptor trimmed using bismark that used a file of adaptor sequences and trimmed three bases back from any detected adaptor to delete the C invorporated and rejecting any reads that were trimmed to less than 10bp
|
| 207 |
+
!Sample_data_processing = reads were aligned to the hg19 genome using bismark with the following specifications: a tolerance for one non-bisulfite mismatch per read, the default minimum alignment score (L,O, -02), and with ignore - quals in order to calculate the mismatch penalty by considering the quality value at the mismatched position to be the highest possible
|
| 208 |
+
!Sample_data_processing = bam files generated by Bismark alignment were then processed using DMAP to compare control vs. patients with the following specifications: ANOVA F test on fragments 40-220bp in length, with the fragment requireing at lest 2 CpGs to have 10 or more sequence reads. The differential methylation file was then annotated with protein coding gene information using the DMAP command identgeneloc. DMAPmatrix.csv file contains this data.
|
| 209 |
+
!Sample_data_processing = the bam files were additionally analysed following a MethylKit based pipeline where first the data was filtered for low read coverage (less than 10 times coverage) and normalised basde on mean coverage distribution before comparing pooled patient and control groups using a Fisher's test. Methmatrix.csv file contains this data
|
| 210 |
+
!Sample_data_processing = Genome_build: hg19
|
| 211 |
+
!Sample_data_processing = Supplementary_files_format_and_content: Individual .txt files for each sample containing C and T frequency per base and coverage. Matrix (csv file) containing methylation percentages for each sample used in the control vs patient analysis for the MethylKit single CpG pipeline.
|
| 212 |
+
!Sample_data_processing = Supplementary_files_format_and_content: A matrix containing the DMAP output data (individual sample percentages, significance values, associated genomic features, fragment length, CpG per fragment). .
|
| 213 |
+
!Sample_platform_id = GPL16791
|
| 214 |
+
!Sample_contact_name = Amber,,Helliwell
|
| 215 |
+
!Sample_contact_department = Biochemistry Department
|
| 216 |
+
!Sample_contact_institute = University of Otago
|
| 217 |
+
!Sample_contact_address = 710 Cumberland Road
|
| 218 |
+
!Sample_contact_city = Dunedin
|
| 219 |
+
!Sample_contact_zip/postal_code = 9016
|
| 220 |
+
!Sample_contact_country = New Zealand
|
| 221 |
+
!Sample_instrument_model = Illumina HiSeq 2500
|
| 222 |
+
!Sample_library_selection = Reduced Representation
|
| 223 |
+
!Sample_library_source = genomic
|
| 224 |
+
!Sample_library_strategy = Bisulfite-Seq
|
| 225 |
+
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN15420269
|
| 226 |
+
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8651463
|
| 227 |
+
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4649nnn/GSM4649030/suppl/GSM4649030_Control4_CpG.txt.gz
|
| 228 |
+
!Sample_series_id = GSE153667
|
| 229 |
+
!Sample_data_row_count = 0
|
| 230 |
+
^SAMPLE = GSM4649031
|
| 231 |
+
!Sample_title = Control5
|
| 232 |
+
!Sample_geo_accession = GSM4649031
|
| 233 |
+
!Sample_status = Public on Jul 02 2020
|
| 234 |
+
!Sample_submission_date = Jul 01 2020
|
| 235 |
+
!Sample_last_update_date = Jul 02 2020
|
| 236 |
+
!Sample_type = SRA
|
| 237 |
+
!Sample_channel_count = 1
|
| 238 |
+
!Sample_source_name_ch1 = Peripheral Blood Mononuclear Cells
|
| 239 |
+
!Sample_organism_ch1 = Homo sapiens
|
| 240 |
+
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!Sample_extract_protocol_ch1 = MSPI digestion (purify), end repair (purify), A-tialing and adaptor ligation (purify), PCR amplification (purify), Gel size selection and gel extraction (purify)
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| 245 |
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!Sample_data_processing = reads were adaptor trimmed using bismark that used a file of adaptor sequences and trimmed three bases back from any detected adaptor to delete the C invorporated and rejecting any reads that were trimmed to less than 10bp
|
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!Sample_data_processing = reads were aligned to the hg19 genome using bismark with the following specifications: a tolerance for one non-bisulfite mismatch per read, the default minimum alignment score (L,O, -02), and with ignore - quals in order to calculate the mismatch penalty by considering the quality value at the mismatched position to be the highest possible
|
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!Sample_data_processing = bam files generated by Bismark alignment were then processed using DMAP to compare control vs. patients with the following specifications: ANOVA F test on fragments 40-220bp in length, with the fragment requireing at lest 2 CpGs to have 10 or more sequence reads. The differential methylation file was then annotated with protein coding gene information using the DMAP command identgeneloc. DMAPmatrix.csv file contains this data.
|
| 248 |
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!Sample_data_processing = the bam files were additionally analysed following a MethylKit based pipeline where first the data was filtered for low read coverage (less than 10 times coverage) and normalised basde on mean coverage distribution before comparing pooled patient and control groups using a Fisher's test. Methmatrix.csv file contains this data
|
| 249 |
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!Sample_data_processing = Genome_build: hg19
|
| 250 |
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!Sample_data_processing = Supplementary_files_format_and_content: Individual .txt files for each sample containing C and T frequency per base and coverage. Matrix (csv file) containing methylation percentages for each sample used in the control vs patient analysis for the MethylKit single CpG pipeline.
|
| 251 |
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!Sample_data_processing = Supplementary_files_format_and_content: A matrix containing the DMAP output data (individual sample percentages, significance values, associated genomic features, fragment length, CpG per fragment). .
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| 252 |
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!Sample_platform_id = GPL16791
|
| 253 |
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!Sample_contact_name = Amber,,Helliwell
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| 254 |
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!Sample_contact_department = Biochemistry Department
|
| 255 |
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!Sample_contact_institute = University of Otago
|
| 256 |
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!Sample_contact_address = 710 Cumberland Road
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| 257 |
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!Sample_contact_city = Dunedin
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!Sample_contact_zip/postal_code = 9016
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!Sample_instrument_model = Illumina HiSeq 2500
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|
| 263 |
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!Sample_library_strategy = Bisulfite-Seq
|
| 264 |
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!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN15420268
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| 265 |
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!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8651464
|
| 266 |
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!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4649nnn/GSM4649031/suppl/GSM4649031_Control5_CpG.txt.gz
|
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^SAMPLE = GSM4649032
|
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!Sample_title = Control6
|
| 271 |
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|
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!Sample_status = Public on Jul 02 2020
|
| 273 |
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!Sample_last_update_date = Jul 02 2020
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| 275 |
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| 280 |
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| 283 |
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!Sample_extract_protocol_ch1 = MSPI digestion (purify), end repair (purify), A-tialing and adaptor ligation (purify), PCR amplification (purify), Gel size selection and gel extraction (purify)
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!Sample_data_processing = reads were adaptor trimmed using bismark that used a file of adaptor sequences and trimmed three bases back from any detected adaptor to delete the C invorporated and rejecting any reads that were trimmed to less than 10bp
|
| 285 |
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!Sample_data_processing = reads were aligned to the hg19 genome using bismark with the following specifications: a tolerance for one non-bisulfite mismatch per read, the default minimum alignment score (L,O, -02), and with ignore - quals in order to calculate the mismatch penalty by considering the quality value at the mismatched position to be the highest possible
|
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!Sample_data_processing = bam files generated by Bismark alignment were then processed using DMAP to compare control vs. patients with the following specifications: ANOVA F test on fragments 40-220bp in length, with the fragment requireing at lest 2 CpGs to have 10 or more sequence reads. The differential methylation file was then annotated with protein coding gene information using the DMAP command identgeneloc. DMAPmatrix.csv file contains this data.
|
| 287 |
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!Sample_data_processing = the bam files were additionally analysed following a MethylKit based pipeline where first the data was filtered for low read coverage (less than 10 times coverage) and normalised basde on mean coverage distribution before comparing pooled patient and control groups using a Fisher's test. Methmatrix.csv file contains this data
|
| 288 |
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!Sample_data_processing = Genome_build: hg19
|
| 289 |
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!Sample_data_processing = Supplementary_files_format_and_content: Individual .txt files for each sample containing C and T frequency per base and coverage. Matrix (csv file) containing methylation percentages for each sample used in the control vs patient analysis for the MethylKit single CpG pipeline.
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| 290 |
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!Sample_data_processing = Supplementary_files_format_and_content: A matrix containing the DMAP output data (individual sample percentages, significance values, associated genomic features, fragment length, CpG per fragment). .
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!Sample_platform_id = GPL16791
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| 292 |
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!Sample_contact_name = Amber,,Helliwell
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| 293 |
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!Sample_contact_department = Biochemistry Department
|
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!Sample_contact_institute = University of Otago
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| 295 |
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!Sample_contact_address = 710 Cumberland Road
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!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN15420267
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!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8651465
|
| 305 |
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!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4649nnn/GSM4649032/suppl/GSM4649032_Control6_CpG.txt.gz
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^SAMPLE = GSM4649033
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!Sample_extract_protocol_ch1 = MSPI digestion (purify), end repair (purify), A-tialing and adaptor ligation (purify), PCR amplification (purify), Gel size selection and gel extraction (purify)
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!Sample_data_processing = reads were adaptor trimmed using bismark that used a file of adaptor sequences and trimmed three bases back from any detected adaptor to delete the C invorporated and rejecting any reads that were trimmed to less than 10bp
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| 324 |
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!Sample_data_processing = reads were aligned to the hg19 genome using bismark with the following specifications: a tolerance for one non-bisulfite mismatch per read, the default minimum alignment score (L,O, -02), and with ignore - quals in order to calculate the mismatch penalty by considering the quality value at the mismatched position to be the highest possible
|
| 325 |
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!Sample_data_processing = bam files generated by Bismark alignment were then processed using DMAP to compare control vs. patients with the following specifications: ANOVA F test on fragments 40-220bp in length, with the fragment requireing at lest 2 CpGs to have 10 or more sequence reads. The differential methylation file was then annotated with protein coding gene information using the DMAP command identgeneloc. DMAPmatrix.csv file contains this data.
|
| 326 |
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!Sample_data_processing = the bam files were additionally analysed following a MethylKit based pipeline where first the data was filtered for low read coverage (less than 10 times coverage) and normalised basde on mean coverage distribution before comparing pooled patient and control groups using a Fisher's test. Methmatrix.csv file contains this data
|
| 327 |
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!Sample_data_processing = Genome_build: hg19
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!Sample_data_processing = Supplementary_files_format_and_content: Individual .txt files for each sample containing C and T frequency per base and coverage. Matrix (csv file) containing methylation percentages for each sample used in the control vs patient analysis for the MethylKit single CpG pipeline.
|
| 329 |
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!Sample_data_processing = Supplementary_files_format_and_content: A matrix containing the DMAP output data (individual sample percentages, significance values, associated genomic features, fragment length, CpG per fragment). .
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| 330 |
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!Sample_platform_id = GPL16791
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!Sample_contact_name = Amber,,Helliwell
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| 332 |
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!Sample_contact_department = Biochemistry Department
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!Sample_contact_institute = University of Otago
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!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN15420266
|
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!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8651466
|
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!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4649nnn/GSM4649033/suppl/GSM4649033_Control7_CpG.txt.gz
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^SAMPLE = GSM4649034
|
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!Sample_title = Control8
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!Sample_status = Public on Jul 02 2020
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!Sample_submission_date = Jul 01 2020
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| 360 |
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| 361 |
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!Sample_extract_protocol_ch1 = MSPI digestion (purify), end repair (purify), A-tialing and adaptor ligation (purify), PCR amplification (purify), Gel size selection and gel extraction (purify)
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| 362 |
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!Sample_data_processing = reads were adaptor trimmed using bismark that used a file of adaptor sequences and trimmed three bases back from any detected adaptor to delete the C invorporated and rejecting any reads that were trimmed to less than 10bp
|
| 363 |
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!Sample_data_processing = reads were aligned to the hg19 genome using bismark with the following specifications: a tolerance for one non-bisulfite mismatch per read, the default minimum alignment score (L,O, -02), and with ignore - quals in order to calculate the mismatch penalty by considering the quality value at the mismatched position to be the highest possible
|
| 364 |
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!Sample_data_processing = bam files generated by Bismark alignment were then processed using DMAP to compare control vs. patients with the following specifications: ANOVA F test on fragments 40-220bp in length, with the fragment requireing at lest 2 CpGs to have 10 or more sequence reads. The differential methylation file was then annotated with protein coding gene information using the DMAP command identgeneloc. DMAPmatrix.csv file contains this data.
|
| 365 |
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!Sample_data_processing = the bam files were additionally analysed following a MethylKit based pipeline where first the data was filtered for low read coverage (less than 10 times coverage) and normalised basde on mean coverage distribution before comparing pooled patient and control groups using a Fisher's test. Methmatrix.csv file contains this data
|
| 366 |
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!Sample_data_processing = Genome_build: hg19
|
| 367 |
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!Sample_data_processing = Supplementary_files_format_and_content: Individual .txt files for each sample containing C and T frequency per base and coverage. Matrix (csv file) containing methylation percentages for each sample used in the control vs patient analysis for the MethylKit single CpG pipeline.
|
| 368 |
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!Sample_data_processing = Supplementary_files_format_and_content: A matrix containing the DMAP output data (individual sample percentages, significance values, associated genomic features, fragment length, CpG per fragment). .
|
| 369 |
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!Sample_platform_id = GPL16791
|
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!Sample_contact_name = Amber,,Helliwell
|
| 371 |
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!Sample_contact_department = Biochemistry Department
|
| 372 |
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!Sample_contact_institute = University of Otago
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!Sample_contact_address = 710 Cumberland Road
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| 374 |
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!Sample_contact_city = Dunedin
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!Sample_contact_zip/postal_code = 9016
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!Sample_contact_country = New Zealand
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!Sample_library_source = genomic
|
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!Sample_library_strategy = Bisulfite-Seq
|
| 381 |
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!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN15420265
|
| 382 |
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!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8651467
|
| 383 |
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!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4649nnn/GSM4649034/suppl/GSM4649034_Control8_CpG.txt.gz
|
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!Sample_series_id = GSE153667
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| 386 |
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^SAMPLE = GSM4649035
|
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!Sample_title = Control9
|
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!Sample_geo_accession = GSM4649035
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!Sample_status = Public on Jul 02 2020
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!Sample_submission_date = Jul 01 2020
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!Sample_last_update_date = Jul 02 2020
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!Sample_molecule_ch1 = genomic DNA
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!Sample_extract_protocol_ch1 = MSPI digestion (purify), end repair (purify), A-tialing and adaptor ligation (purify), PCR amplification (purify), Gel size selection and gel extraction (purify)
|
| 401 |
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!Sample_data_processing = reads were adaptor trimmed using bismark that used a file of adaptor sequences and trimmed three bases back from any detected adaptor to delete the C invorporated and rejecting any reads that were trimmed to less than 10bp
|
| 402 |
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!Sample_data_processing = reads were aligned to the hg19 genome using bismark with the following specifications: a tolerance for one non-bisulfite mismatch per read, the default minimum alignment score (L,O, -02), and with ignore - quals in order to calculate the mismatch penalty by considering the quality value at the mismatched position to be the highest possible
|
| 403 |
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!Sample_data_processing = bam files generated by Bismark alignment were then processed using DMAP to compare control vs. patients with the following specifications: ANOVA F test on fragments 40-220bp in length, with the fragment requireing at lest 2 CpGs to have 10 or more sequence reads. The differential methylation file was then annotated with protein coding gene information using the DMAP command identgeneloc. DMAPmatrix.csv file contains this data.
|
| 404 |
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!Sample_data_processing = the bam files were additionally analysed following a MethylKit based pipeline where first the data was filtered for low read coverage (less than 10 times coverage) and normalised basde on mean coverage distribution before comparing pooled patient and control groups using a Fisher's test. Methmatrix.csv file contains this data
|
| 405 |
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!Sample_data_processing = Genome_build: hg19
|
| 406 |
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!Sample_data_processing = Supplementary_files_format_and_content: Individual .txt files for each sample containing C and T frequency per base and coverage. Matrix (csv file) containing methylation percentages for each sample used in the control vs patient analysis for the MethylKit single CpG pipeline.
|
| 407 |
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!Sample_data_processing = Supplementary_files_format_and_content: A matrix containing the DMAP output data (individual sample percentages, significance values, associated genomic features, fragment length, CpG per fragment). .
|
| 408 |
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!Sample_platform_id = GPL16791
|
| 409 |
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!Sample_contact_name = Amber,,Helliwell
|
| 410 |
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!Sample_contact_department = Biochemistry Department
|
| 411 |
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!Sample_contact_institute = University of Otago
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| 412 |
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!Sample_contact_address = 710 Cumberland Road
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!Sample_contact_city = Dunedin
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!Sample_contact_zip/postal_code = 9016
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!Sample_contact_country = New Zealand
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|
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!Sample_library_source = genomic
|
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!Sample_library_strategy = Bisulfite-Seq
|
| 420 |
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!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN15420264
|
| 421 |
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!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8651468
|
| 422 |
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!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4649nnn/GSM4649035/suppl/GSM4649035_Control9_CpG.txt.gz
|
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!Sample_series_id = GSE153667
|
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| 425 |
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^SAMPLE = GSM4649036
|
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!Sample_title = Control10
|
| 427 |
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!Sample_geo_accession = GSM4649036
|
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!Sample_status = Public on Jul 02 2020
|
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!Sample_submission_date = Jul 01 2020
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!Sample_last_update_date = Jul 02 2020
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!Sample_extract_protocol_ch1 = MSPI digestion (purify), end repair (purify), A-tialing and adaptor ligation (purify), PCR amplification (purify), Gel size selection and gel extraction (purify)
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!Sample_data_processing = reads were adaptor trimmed using bismark that used a file of adaptor sequences and trimmed three bases back from any detected adaptor to delete the C invorporated and rejecting any reads that were trimmed to less than 10bp
|
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!Sample_data_processing = reads were aligned to the hg19 genome using bismark with the following specifications: a tolerance for one non-bisulfite mismatch per read, the default minimum alignment score (L,O, -02), and with ignore - quals in order to calculate the mismatch penalty by considering the quality value at the mismatched position to be the highest possible
|
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!Sample_data_processing = bam files generated by Bismark alignment were then processed using DMAP to compare control vs. patients with the following specifications: ANOVA F test on fragments 40-220bp in length, with the fragment requireing at lest 2 CpGs to have 10 or more sequence reads. The differential methylation file was then annotated with protein coding gene information using the DMAP command identgeneloc. DMAPmatrix.csv file contains this data.
|
| 443 |
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!Sample_data_processing = the bam files were additionally analysed following a MethylKit based pipeline where first the data was filtered for low read coverage (less than 10 times coverage) and normalised basde on mean coverage distribution before comparing pooled patient and control groups using a Fisher's test. Methmatrix.csv file contains this data
|
| 444 |
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!Sample_data_processing = Genome_build: hg19
|
| 445 |
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!Sample_data_processing = Supplementary_files_format_and_content: Individual .txt files for each sample containing C and T frequency per base and coverage. Matrix (csv file) containing methylation percentages for each sample used in the control vs patient analysis for the MethylKit single CpG pipeline.
|
| 446 |
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!Sample_data_processing = Supplementary_files_format_and_content: A matrix containing the DMAP output data (individual sample percentages, significance values, associated genomic features, fragment length, CpG per fragment). .
|
| 447 |
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!Sample_platform_id = GPL16791
|
| 448 |
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!Sample_contact_name = Amber,,Helliwell
|
| 449 |
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!Sample_contact_department = Biochemistry Department
|
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!Sample_contact_institute = University of Otago
|
| 451 |
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!Sample_contact_address = 710 Cumberland Road
|
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!Sample_contact_city = Dunedin
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!Sample_contact_zip/postal_code = 9016
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!Sample_contact_country = New Zealand
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!Sample_instrument_model = Illumina HiSeq 2500
|
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!Sample_library_selection = Reduced Representation
|
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!Sample_library_source = genomic
|
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!Sample_library_strategy = Bisulfite-Seq
|
| 459 |
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!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN15420263
|
| 460 |
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!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8651469
|
| 461 |
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!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4649nnn/GSM4649036/suppl/GSM4649036_Control10_CpG.txt.gz
|
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!Sample_series_id = GSE153667
|
| 463 |
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!Sample_data_row_count = 0
|
| 464 |
+
^SAMPLE = GSM4649037
|
| 465 |
+
!Sample_title = Patient1
|
| 466 |
+
!Sample_geo_accession = GSM4649037
|
| 467 |
+
!Sample_status = Public on Jul 02 2020
|
| 468 |
+
!Sample_submission_date = Jul 01 2020
|
| 469 |
+
!Sample_last_update_date = Jul 02 2020
|
| 470 |
+
!Sample_type = SRA
|
| 471 |
+
!Sample_channel_count = 1
|
| 472 |
+
!Sample_source_name_ch1 = Peripheral Blood Mononuclear Cells
|
| 473 |
+
!Sample_organism_ch1 = Homo sapiens
|
| 474 |
+
!Sample_taxid_ch1 = 9606
|
| 475 |
+
!Sample_characteristics_ch1 = disease state: Patient
|
| 476 |
+
!Sample_molecule_ch1 = genomic DNA
|
| 477 |
+
!Sample_extract_protocol_ch1 = DNA was extracted from 200ul of PBMCs
|
| 478 |
+
!Sample_extract_protocol_ch1 = MSPI digestion (purify), end repair (purify), A-tialing and adaptor ligation (purify), PCR amplification (purify), Gel size selection and gel extraction (purify)
|
| 479 |
+
!Sample_data_processing = reads were adaptor trimmed using bismark that used a file of adaptor sequences and trimmed three bases back from any detected adaptor to delete the C invorporated and rejecting any reads that were trimmed to less than 10bp
|
| 480 |
+
!Sample_data_processing = reads were aligned to the hg19 genome using bismark with the following specifications: a tolerance for one non-bisulfite mismatch per read, the default minimum alignment score (L,O, -02), and with ignore - quals in order to calculate the mismatch penalty by considering the quality value at the mismatched position to be the highest possible
|
| 481 |
+
!Sample_data_processing = bam files generated by Bismark alignment were then processed using DMAP to compare control vs. patients with the following specifications: ANOVA F test on fragments 40-220bp in length, with the fragment requireing at lest 2 CpGs to have 10 or more sequence reads. The differential methylation file was then annotated with protein coding gene information using the DMAP command identgeneloc. DMAPmatrix.csv file contains this data.
|
| 482 |
+
!Sample_data_processing = the bam files were additionally analysed following a MethylKit based pipeline where first the data was filtered for low read coverage (less than 10 times coverage) and normalised basde on mean coverage distribution before comparing pooled patient and control groups using a Fisher's test. Methmatrix.csv file contains this data
|
| 483 |
+
!Sample_data_processing = Genome_build: hg19
|
| 484 |
+
!Sample_data_processing = Supplementary_files_format_and_content: Individual .txt files for each sample containing C and T frequency per base and coverage. Matrix (csv file) containing methylation percentages for each sample used in the control vs patient analysis for the MethylKit single CpG pipeline.
|
| 485 |
+
!Sample_data_processing = Supplementary_files_format_and_content: A matrix containing the DMAP output data (individual sample percentages, significance values, associated genomic features, fragment length, CpG per fragment). .
|
| 486 |
+
!Sample_platform_id = GPL16791
|
| 487 |
+
!Sample_contact_name = Amber,,Helliwell
|
| 488 |
+
!Sample_contact_department = Biochemistry Department
|
| 489 |
+
!Sample_contact_institute = University of Otago
|
| 490 |
+
!Sample_contact_address = 710 Cumberland Road
|
| 491 |
+
!Sample_contact_city = Dunedin
|
| 492 |
+
!Sample_contact_zip/postal_code = 9016
|
| 493 |
+
!Sample_contact_country = New Zealand
|
| 494 |
+
!Sample_instrument_model = Illumina HiSeq 2500
|
| 495 |
+
!Sample_library_selection = Reduced Representation
|
| 496 |
+
!Sample_library_source = genomic
|
| 497 |
+
!Sample_library_strategy = Bisulfite-Seq
|
| 498 |
+
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN15420262
|
| 499 |
+
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8651470
|
| 500 |
+
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4649nnn/GSM4649037/suppl/GSM4649037_Patient1_CpG.txt.gz
|
| 501 |
+
!Sample_series_id = GSE153667
|
| 502 |
+
!Sample_data_row_count = 0
|
| 503 |
+
^SAMPLE = GSM4649038
|
| 504 |
+
!Sample_title = Patient2
|
| 505 |
+
!Sample_geo_accession = GSM4649038
|
| 506 |
+
!Sample_status = Public on Jul 02 2020
|
| 507 |
+
!Sample_submission_date = Jul 01 2020
|
| 508 |
+
!Sample_last_update_date = Jul 02 2020
|
| 509 |
+
!Sample_type = SRA
|
| 510 |
+
!Sample_channel_count = 1
|
| 511 |
+
!Sample_source_name_ch1 = Peripheral Blood Mononuclear Cells
|
| 512 |
+
!Sample_organism_ch1 = Homo sapiens
|
| 513 |
+
!Sample_taxid_ch1 = 9606
|
| 514 |
+
!Sample_characteristics_ch1 = disease state: Patient
|
| 515 |
+
!Sample_molecule_ch1 = genomic DNA
|
| 516 |
+
!Sample_extract_protocol_ch1 = DNA was extracted from 200ul of PBMCs
|
| 517 |
+
!Sample_extract_protocol_ch1 = MSPI digestion (purify), end repair (purify), A-tialing and adaptor ligation (purify), PCR amplification (purify), Gel size selection and gel extraction (purify)
|
| 518 |
+
!Sample_data_processing = reads were adaptor trimmed using bismark that used a file of adaptor sequences and trimmed three bases back from any detected adaptor to delete the C invorporated and rejecting any reads that were trimmed to less than 10bp
|
| 519 |
+
!Sample_data_processing = reads were aligned to the hg19 genome using bismark with the following specifications: a tolerance for one non-bisulfite mismatch per read, the default minimum alignment score (L,O, -02), and with ignore - quals in order to calculate the mismatch penalty by considering the quality value at the mismatched position to be the highest possible
|
| 520 |
+
!Sample_data_processing = bam files generated by Bismark alignment were then processed using DMAP to compare control vs. patients with the following specifications: ANOVA F test on fragments 40-220bp in length, with the fragment requireing at lest 2 CpGs to have 10 or more sequence reads. The differential methylation file was then annotated with protein coding gene information using the DMAP command identgeneloc. DMAPmatrix.csv file contains this data.
|
| 521 |
+
!Sample_data_processing = the bam files were additionally analysed following a MethylKit based pipeline where first the data was filtered for low read coverage (less than 10 times coverage) and normalised basde on mean coverage distribution before comparing pooled patient and control groups using a Fisher's test. Methmatrix.csv file contains this data
|
| 522 |
+
!Sample_data_processing = Genome_build: hg19
|
| 523 |
+
!Sample_data_processing = Supplementary_files_format_and_content: Individual .txt files for each sample containing C and T frequency per base and coverage. Matrix (csv file) containing methylation percentages for each sample used in the control vs patient analysis for the MethylKit single CpG pipeline.
|
| 524 |
+
!Sample_data_processing = Supplementary_files_format_and_content: A matrix containing the DMAP output data (individual sample percentages, significance values, associated genomic features, fragment length, CpG per fragment). .
|
| 525 |
+
!Sample_platform_id = GPL16791
|
| 526 |
+
!Sample_contact_name = Amber,,Helliwell
|
| 527 |
+
!Sample_contact_department = Biochemistry Department
|
| 528 |
+
!Sample_contact_institute = University of Otago
|
| 529 |
+
!Sample_contact_address = 710 Cumberland Road
|
| 530 |
+
!Sample_contact_city = Dunedin
|
| 531 |
+
!Sample_contact_zip/postal_code = 9016
|
| 532 |
+
!Sample_contact_country = New Zealand
|
| 533 |
+
!Sample_instrument_model = Illumina HiSeq 2500
|
| 534 |
+
!Sample_library_selection = Reduced Representation
|
| 535 |
+
!Sample_library_source = genomic
|
| 536 |
+
!Sample_library_strategy = Bisulfite-Seq
|
| 537 |
+
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN15420261
|
| 538 |
+
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8651471
|
| 539 |
+
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4649nnn/GSM4649038/suppl/GSM4649038_Patient2_CpG.txt.gz
|
| 540 |
+
!Sample_series_id = GSE153667
|
| 541 |
+
!Sample_data_row_count = 0
|
| 542 |
+
^SAMPLE = GSM4649039
|
| 543 |
+
!Sample_title = Patient3
|
| 544 |
+
!Sample_geo_accession = GSM4649039
|
| 545 |
+
!Sample_status = Public on Jul 02 2020
|
| 546 |
+
!Sample_submission_date = Jul 01 2020
|
| 547 |
+
!Sample_last_update_date = Jul 02 2020
|
| 548 |
+
!Sample_type = SRA
|
| 549 |
+
!Sample_channel_count = 1
|
| 550 |
+
!Sample_source_name_ch1 = Peripheral Blood Mononuclear Cells
|
| 551 |
+
!Sample_organism_ch1 = Homo sapiens
|
| 552 |
+
!Sample_taxid_ch1 = 9606
|
| 553 |
+
!Sample_characteristics_ch1 = disease state: Patient
|
| 554 |
+
!Sample_molecule_ch1 = genomic DNA
|
| 555 |
+
!Sample_extract_protocol_ch1 = DNA was extracted from 200ul of PBMCs
|
| 556 |
+
!Sample_extract_protocol_ch1 = MSPI digestion (purify), end repair (purify), A-tialing and adaptor ligation (purify), PCR amplification (purify), Gel size selection and gel extraction (purify)
|
| 557 |
+
!Sample_data_processing = reads were adaptor trimmed using bismark that used a file of adaptor sequences and trimmed three bases back from any detected adaptor to delete the C invorporated and rejecting any reads that were trimmed to less than 10bp
|
| 558 |
+
!Sample_data_processing = reads were aligned to the hg19 genome using bismark with the following specifications: a tolerance for one non-bisulfite mismatch per read, the default minimum alignment score (L,O, -02), and with ignore - quals in order to calculate the mismatch penalty by considering the quality value at the mismatched position to be the highest possible
|
| 559 |
+
!Sample_data_processing = bam files generated by Bismark alignment were then processed using DMAP to compare control vs. patients with the following specifications: ANOVA F test on fragments 40-220bp in length, with the fragment requireing at lest 2 CpGs to have 10 or more sequence reads. The differential methylation file was then annotated with protein coding gene information using the DMAP command identgeneloc. DMAPmatrix.csv file contains this data.
|
| 560 |
+
!Sample_data_processing = the bam files were additionally analysed following a MethylKit based pipeline where first the data was filtered for low read coverage (less than 10 times coverage) and normalised basde on mean coverage distribution before comparing pooled patient and control groups using a Fisher's test. Methmatrix.csv file contains this data
|
| 561 |
+
!Sample_data_processing = Genome_build: hg19
|
| 562 |
+
!Sample_data_processing = Supplementary_files_format_and_content: Individual .txt files for each sample containing C and T frequency per base and coverage. Matrix (csv file) containing methylation percentages for each sample used in the control vs patient analysis for the MethylKit single CpG pipeline.
|
| 563 |
+
!Sample_data_processing = Supplementary_files_format_and_content: A matrix containing the DMAP output data (individual sample percentages, significance values, associated genomic features, fragment length, CpG per fragment). .
|
| 564 |
+
!Sample_platform_id = GPL16791
|
| 565 |
+
!Sample_contact_name = Amber,,Helliwell
|
| 566 |
+
!Sample_contact_department = Biochemistry Department
|
| 567 |
+
!Sample_contact_institute = University of Otago
|
| 568 |
+
!Sample_contact_address = 710 Cumberland Road
|
| 569 |
+
!Sample_contact_city = Dunedin
|
| 570 |
+
!Sample_contact_zip/postal_code = 9016
|
| 571 |
+
!Sample_contact_country = New Zealand
|
| 572 |
+
!Sample_instrument_model = Illumina HiSeq 2500
|
| 573 |
+
!Sample_library_selection = Reduced Representation
|
| 574 |
+
!Sample_library_source = genomic
|
| 575 |
+
!Sample_library_strategy = Bisulfite-Seq
|
| 576 |
+
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN15420260
|
| 577 |
+
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8651472
|
| 578 |
+
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4649nnn/GSM4649039/suppl/GSM4649039_Patient3_CpG.txt.gz
|
| 579 |
+
!Sample_series_id = GSE153667
|
| 580 |
+
!Sample_data_row_count = 0
|
| 581 |
+
^SAMPLE = GSM4649040
|
| 582 |
+
!Sample_title = Patient4
|
| 583 |
+
!Sample_geo_accession = GSM4649040
|
| 584 |
+
!Sample_status = Public on Jul 02 2020
|
| 585 |
+
!Sample_submission_date = Jul 01 2020
|
| 586 |
+
!Sample_last_update_date = Jul 02 2020
|
| 587 |
+
!Sample_type = SRA
|
| 588 |
+
!Sample_channel_count = 1
|
| 589 |
+
!Sample_source_name_ch1 = Peripheral Blood Mononuclear Cells
|
| 590 |
+
!Sample_organism_ch1 = Homo sapiens
|
| 591 |
+
!Sample_taxid_ch1 = 9606
|
| 592 |
+
!Sample_characteristics_ch1 = disease state: Patient
|
| 593 |
+
!Sample_molecule_ch1 = genomic DNA
|
| 594 |
+
!Sample_extract_protocol_ch1 = DNA was extracted from 200ul of PBMCs
|
| 595 |
+
!Sample_extract_protocol_ch1 = MSPI digestion (purify), end repair (purify), A-tialing and adaptor ligation (purify), PCR amplification (purify), Gel size selection and gel extraction (purify)
|
| 596 |
+
!Sample_data_processing = reads were adaptor trimmed using bismark that used a file of adaptor sequences and trimmed three bases back from any detected adaptor to delete the C invorporated and rejecting any reads that were trimmed to less than 10bp
|
| 597 |
+
!Sample_data_processing = reads were aligned to the hg19 genome using bismark with the following specifications: a tolerance for one non-bisulfite mismatch per read, the default minimum alignment score (L,O, -02), and with ignore - quals in order to calculate the mismatch penalty by considering the quality value at the mismatched position to be the highest possible
|
| 598 |
+
!Sample_data_processing = bam files generated by Bismark alignment were then processed using DMAP to compare control vs. patients with the following specifications: ANOVA F test on fragments 40-220bp in length, with the fragment requireing at lest 2 CpGs to have 10 or more sequence reads. The differential methylation file was then annotated with protein coding gene information using the DMAP command identgeneloc. DMAPmatrix.csv file contains this data.
|
| 599 |
+
!Sample_data_processing = the bam files were additionally analysed following a MethylKit based pipeline where first the data was filtered for low read coverage (less than 10 times coverage) and normalised basde on mean coverage distribution before comparing pooled patient and control groups using a Fisher's test. Methmatrix.csv file contains this data
|
| 600 |
+
!Sample_data_processing = Genome_build: hg19
|
| 601 |
+
!Sample_data_processing = Supplementary_files_format_and_content: Individual .txt files for each sample containing C and T frequency per base and coverage. Matrix (csv file) containing methylation percentages for each sample used in the control vs patient analysis for the MethylKit single CpG pipeline.
|
| 602 |
+
!Sample_data_processing = Supplementary_files_format_and_content: A matrix containing the DMAP output data (individual sample percentages, significance values, associated genomic features, fragment length, CpG per fragment). .
|
| 603 |
+
!Sample_platform_id = GPL16791
|
| 604 |
+
!Sample_contact_name = Amber,,Helliwell
|
| 605 |
+
!Sample_contact_department = Biochemistry Department
|
| 606 |
+
!Sample_contact_institute = University of Otago
|
| 607 |
+
!Sample_contact_address = 710 Cumberland Road
|
| 608 |
+
!Sample_contact_city = Dunedin
|
| 609 |
+
!Sample_contact_zip/postal_code = 9016
|
| 610 |
+
!Sample_contact_country = New Zealand
|
| 611 |
+
!Sample_instrument_model = Illumina HiSeq 2500
|
| 612 |
+
!Sample_library_selection = Reduced Representation
|
| 613 |
+
!Sample_library_source = genomic
|
| 614 |
+
!Sample_library_strategy = Bisulfite-Seq
|
| 615 |
+
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN15420259
|
| 616 |
+
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8651473
|
| 617 |
+
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4649nnn/GSM4649040/suppl/GSM4649040_Patient4_CpG.txt.gz
|
| 618 |
+
!Sample_series_id = GSE153667
|
| 619 |
+
!Sample_data_row_count = 0
|
| 620 |
+
^SAMPLE = GSM4649041
|
| 621 |
+
!Sample_title = Patient5
|
| 622 |
+
!Sample_geo_accession = GSM4649041
|
| 623 |
+
!Sample_status = Public on Jul 02 2020
|
| 624 |
+
!Sample_submission_date = Jul 01 2020
|
| 625 |
+
!Sample_last_update_date = Jul 02 2020
|
| 626 |
+
!Sample_type = SRA
|
| 627 |
+
!Sample_channel_count = 1
|
| 628 |
+
!Sample_source_name_ch1 = Peripheral Blood Mononuclear Cells
|
| 629 |
+
!Sample_organism_ch1 = Homo sapiens
|
| 630 |
+
!Sample_taxid_ch1 = 9606
|
| 631 |
+
!Sample_characteristics_ch1 = disease state: Patient
|
| 632 |
+
!Sample_molecule_ch1 = genomic DNA
|
| 633 |
+
!Sample_extract_protocol_ch1 = DNA was extracted from 200ul of PBMCs
|
| 634 |
+
!Sample_extract_protocol_ch1 = MSPI digestion (purify), end repair (purify), A-tialing and adaptor ligation (purify), PCR amplification (purify), Gel size selection and gel extraction (purify)
|
| 635 |
+
!Sample_data_processing = reads were adaptor trimmed using bismark that used a file of adaptor sequences and trimmed three bases back from any detected adaptor to delete the C invorporated and rejecting any reads that were trimmed to less than 10bp
|
| 636 |
+
!Sample_data_processing = reads were aligned to the hg19 genome using bismark with the following specifications: a tolerance for one non-bisulfite mismatch per read, the default minimum alignment score (L,O, -02), and with ignore - quals in order to calculate the mismatch penalty by considering the quality value at the mismatched position to be the highest possible
|
| 637 |
+
!Sample_data_processing = bam files generated by Bismark alignment were then processed using DMAP to compare control vs. patients with the following specifications: ANOVA F test on fragments 40-220bp in length, with the fragment requireing at lest 2 CpGs to have 10 or more sequence reads. The differential methylation file was then annotated with protein coding gene information using the DMAP command identgeneloc. DMAPmatrix.csv file contains this data.
|
| 638 |
+
!Sample_data_processing = the bam files were additionally analysed following a MethylKit based pipeline where first the data was filtered for low read coverage (less than 10 times coverage) and normalised basde on mean coverage distribution before comparing pooled patient and control groups using a Fisher's test. Methmatrix.csv file contains this data
|
| 639 |
+
!Sample_data_processing = Genome_build: hg19
|
| 640 |
+
!Sample_data_processing = Supplementary_files_format_and_content: Individual .txt files for each sample containing C and T frequency per base and coverage. Matrix (csv file) containing methylation percentages for each sample used in the control vs patient analysis for the MethylKit single CpG pipeline.
|
| 641 |
+
!Sample_data_processing = Supplementary_files_format_and_content: A matrix containing the DMAP output data (individual sample percentages, significance values, associated genomic features, fragment length, CpG per fragment). .
|
| 642 |
+
!Sample_platform_id = GPL16791
|
| 643 |
+
!Sample_contact_name = Amber,,Helliwell
|
| 644 |
+
!Sample_contact_department = Biochemistry Department
|
| 645 |
+
!Sample_contact_institute = University of Otago
|
| 646 |
+
!Sample_contact_address = 710 Cumberland Road
|
| 647 |
+
!Sample_contact_city = Dunedin
|
| 648 |
+
!Sample_contact_zip/postal_code = 9016
|
| 649 |
+
!Sample_contact_country = New Zealand
|
| 650 |
+
!Sample_instrument_model = Illumina HiSeq 2500
|
| 651 |
+
!Sample_library_selection = Reduced Representation
|
| 652 |
+
!Sample_library_source = genomic
|
| 653 |
+
!Sample_library_strategy = Bisulfite-Seq
|
| 654 |
+
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN15420258
|
| 655 |
+
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8651474
|
| 656 |
+
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4649nnn/GSM4649041/suppl/GSM4649041_Patient5_CpG.txt.gz
|
| 657 |
+
!Sample_series_id = GSE153667
|
| 658 |
+
!Sample_data_row_count = 0
|
| 659 |
+
^SAMPLE = GSM4649042
|
| 660 |
+
!Sample_title = Patient6
|
| 661 |
+
!Sample_geo_accession = GSM4649042
|
| 662 |
+
!Sample_status = Public on Jul 02 2020
|
| 663 |
+
!Sample_submission_date = Jul 01 2020
|
| 664 |
+
!Sample_last_update_date = Jul 02 2020
|
| 665 |
+
!Sample_type = SRA
|
| 666 |
+
!Sample_channel_count = 1
|
| 667 |
+
!Sample_source_name_ch1 = Peripheral Blood Mononuclear Cells
|
| 668 |
+
!Sample_organism_ch1 = Homo sapiens
|
| 669 |
+
!Sample_taxid_ch1 = 9606
|
| 670 |
+
!Sample_characteristics_ch1 = disease state: Patient
|
| 671 |
+
!Sample_molecule_ch1 = genomic DNA
|
| 672 |
+
!Sample_extract_protocol_ch1 = DNA was extracted from 200ul of PBMCs
|
| 673 |
+
!Sample_extract_protocol_ch1 = MSPI digestion (purify), end repair (purify), A-tialing and adaptor ligation (purify), PCR amplification (purify), Gel size selection and gel extraction (purify)
|
| 674 |
+
!Sample_data_processing = reads were adaptor trimmed using bismark that used a file of adaptor sequences and trimmed three bases back from any detected adaptor to delete the C invorporated and rejecting any reads that were trimmed to less than 10bp
|
| 675 |
+
!Sample_data_processing = reads were aligned to the hg19 genome using bismark with the following specifications: a tolerance for one non-bisulfite mismatch per read, the default minimum alignment score (L,O, -02), and with ignore - quals in order to calculate the mismatch penalty by considering the quality value at the mismatched position to be the highest possible
|
| 676 |
+
!Sample_data_processing = bam files generated by Bismark alignment were then processed using DMAP to compare control vs. patients with the following specifications: ANOVA F test on fragments 40-220bp in length, with the fragment requireing at lest 2 CpGs to have 10 or more sequence reads. The differential methylation file was then annotated with protein coding gene information using the DMAP command identgeneloc. DMAPmatrix.csv file contains this data.
|
| 677 |
+
!Sample_data_processing = the bam files were additionally analysed following a MethylKit based pipeline where first the data was filtered for low read coverage (less than 10 times coverage) and normalised basde on mean coverage distribution before comparing pooled patient and control groups using a Fisher's test. Methmatrix.csv file contains this data
|
| 678 |
+
!Sample_data_processing = Genome_build: hg19
|
| 679 |
+
!Sample_data_processing = Supplementary_files_format_and_content: Individual .txt files for each sample containing C and T frequency per base and coverage. Matrix (csv file) containing methylation percentages for each sample used in the control vs patient analysis for the MethylKit single CpG pipeline.
|
| 680 |
+
!Sample_data_processing = Supplementary_files_format_and_content: A matrix containing the DMAP output data (individual sample percentages, significance values, associated genomic features, fragment length, CpG per fragment). .
|
| 681 |
+
!Sample_platform_id = GPL16791
|
| 682 |
+
!Sample_contact_name = Amber,,Helliwell
|
| 683 |
+
!Sample_contact_department = Biochemistry Department
|
| 684 |
+
!Sample_contact_institute = University of Otago
|
| 685 |
+
!Sample_contact_address = 710 Cumberland Road
|
| 686 |
+
!Sample_contact_city = Dunedin
|
| 687 |
+
!Sample_contact_zip/postal_code = 9016
|
| 688 |
+
!Sample_contact_country = New Zealand
|
| 689 |
+
!Sample_instrument_model = Illumina HiSeq 2500
|
| 690 |
+
!Sample_library_selection = Reduced Representation
|
| 691 |
+
!Sample_library_source = genomic
|
| 692 |
+
!Sample_library_strategy = Bisulfite-Seq
|
| 693 |
+
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN15420257
|
| 694 |
+
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8651475
|
| 695 |
+
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4649nnn/GSM4649042/suppl/GSM4649042_Patient6_CpG.txt.gz
|
| 696 |
+
!Sample_series_id = GSE153667
|
| 697 |
+
!Sample_data_row_count = 0
|
| 698 |
+
^SAMPLE = GSM4649043
|
| 699 |
+
!Sample_title = Patient7
|
| 700 |
+
!Sample_geo_accession = GSM4649043
|
| 701 |
+
!Sample_status = Public on Jul 02 2020
|
| 702 |
+
!Sample_submission_date = Jul 01 2020
|
| 703 |
+
!Sample_last_update_date = Jul 02 2020
|
| 704 |
+
!Sample_type = SRA
|
| 705 |
+
!Sample_channel_count = 1
|
| 706 |
+
!Sample_source_name_ch1 = Peripheral Blood Mononuclear Cells
|
| 707 |
+
!Sample_organism_ch1 = Homo sapiens
|
| 708 |
+
!Sample_taxid_ch1 = 9606
|
| 709 |
+
!Sample_characteristics_ch1 = disease state: Patient
|
| 710 |
+
!Sample_molecule_ch1 = genomic DNA
|
| 711 |
+
!Sample_extract_protocol_ch1 = DNA was extracted from 200ul of PBMCs
|
| 712 |
+
!Sample_extract_protocol_ch1 = MSPI digestion (purify), end repair (purify), A-tialing and adaptor ligation (purify), PCR amplification (purify), Gel size selection and gel extraction (purify)
|
| 713 |
+
!Sample_data_processing = reads were adaptor trimmed using bismark that used a file of adaptor sequences and trimmed three bases back from any detected adaptor to delete the C invorporated and rejecting any reads that were trimmed to less than 10bp
|
| 714 |
+
!Sample_data_processing = reads were aligned to the hg19 genome using bismark with the following specifications: a tolerance for one non-bisulfite mismatch per read, the default minimum alignment score (L,O, -02), and with ignore - quals in order to calculate the mismatch penalty by considering the quality value at the mismatched position to be the highest possible
|
| 715 |
+
!Sample_data_processing = bam files generated by Bismark alignment were then processed using DMAP to compare control vs. patients with the following specifications: ANOVA F test on fragments 40-220bp in length, with the fragment requireing at lest 2 CpGs to have 10 or more sequence reads. The differential methylation file was then annotated with protein coding gene information using the DMAP command identgeneloc. DMAPmatrix.csv file contains this data.
|
| 716 |
+
!Sample_data_processing = the bam files were additionally analysed following a MethylKit based pipeline where first the data was filtered for low read coverage (less than 10 times coverage) and normalised basde on mean coverage distribution before comparing pooled patient and control groups using a Fisher's test. Methmatrix.csv file contains this data
|
| 717 |
+
!Sample_data_processing = Genome_build: hg19
|
| 718 |
+
!Sample_data_processing = Supplementary_files_format_and_content: Individual .txt files for each sample containing C and T frequency per base and coverage. Matrix (csv file) containing methylation percentages for each sample used in the control vs patient analysis for the MethylKit single CpG pipeline.
|
| 719 |
+
!Sample_data_processing = Supplementary_files_format_and_content: A matrix containing the DMAP output data (individual sample percentages, significance values, associated genomic features, fragment length, CpG per fragment). .
|
| 720 |
+
!Sample_platform_id = GPL16791
|
| 721 |
+
!Sample_contact_name = Amber,,Helliwell
|
| 722 |
+
!Sample_contact_department = Biochemistry Department
|
| 723 |
+
!Sample_contact_institute = University of Otago
|
| 724 |
+
!Sample_contact_address = 710 Cumberland Road
|
| 725 |
+
!Sample_contact_city = Dunedin
|
| 726 |
+
!Sample_contact_zip/postal_code = 9016
|
| 727 |
+
!Sample_contact_country = New Zealand
|
| 728 |
+
!Sample_instrument_model = Illumina HiSeq 2500
|
| 729 |
+
!Sample_library_selection = Reduced Representation
|
| 730 |
+
!Sample_library_source = genomic
|
| 731 |
+
!Sample_library_strategy = Bisulfite-Seq
|
| 732 |
+
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN15420256
|
| 733 |
+
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8651476
|
| 734 |
+
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4649nnn/GSM4649043/suppl/GSM4649043_Patient7_CpG.txt.gz
|
| 735 |
+
!Sample_series_id = GSE153667
|
| 736 |
+
!Sample_data_row_count = 0
|
| 737 |
+
^SAMPLE = GSM4649044
|
| 738 |
+
!Sample_title = Patient8
|
| 739 |
+
!Sample_geo_accession = GSM4649044
|
| 740 |
+
!Sample_status = Public on Jul 02 2020
|
| 741 |
+
!Sample_submission_date = Jul 01 2020
|
| 742 |
+
!Sample_last_update_date = Jul 02 2020
|
| 743 |
+
!Sample_type = SRA
|
| 744 |
+
!Sample_channel_count = 1
|
| 745 |
+
!Sample_source_name_ch1 = Peripheral Blood Mononuclear Cells
|
| 746 |
+
!Sample_organism_ch1 = Homo sapiens
|
| 747 |
+
!Sample_taxid_ch1 = 9606
|
| 748 |
+
!Sample_characteristics_ch1 = disease state: Patient
|
| 749 |
+
!Sample_molecule_ch1 = genomic DNA
|
| 750 |
+
!Sample_extract_protocol_ch1 = DNA was extracted from 200ul of PBMCs
|
| 751 |
+
!Sample_extract_protocol_ch1 = MSPI digestion (purify), end repair (purify), A-tialing and adaptor ligation (purify), PCR amplification (purify), Gel size selection and gel extraction (purify)
|
| 752 |
+
!Sample_data_processing = reads were adaptor trimmed using bismark that used a file of adaptor sequences and trimmed three bases back from any detected adaptor to delete the C invorporated and rejecting any reads that were trimmed to less than 10bp
|
| 753 |
+
!Sample_data_processing = reads were aligned to the hg19 genome using bismark with the following specifications: a tolerance for one non-bisulfite mismatch per read, the default minimum alignment score (L,O, -02), and with ignore - quals in order to calculate the mismatch penalty by considering the quality value at the mismatched position to be the highest possible
|
| 754 |
+
!Sample_data_processing = bam files generated by Bismark alignment were then processed using DMAP to compare control vs. patients with the following specifications: ANOVA F test on fragments 40-220bp in length, with the fragment requireing at lest 2 CpGs to have 10 or more sequence reads. The differential methylation file was then annotated with protein coding gene information using the DMAP command identgeneloc. DMAPmatrix.csv file contains this data.
|
| 755 |
+
!Sample_data_processing = the bam files were additionally analysed following a MethylKit based pipeline where first the data was filtered for low read coverage (less than 10 times coverage) and normalised basde on mean coverage distribution before comparing pooled patient and control groups using a Fisher's test. Methmatrix.csv file contains this data
|
| 756 |
+
!Sample_data_processing = Genome_build: hg19
|
| 757 |
+
!Sample_data_processing = Supplementary_files_format_and_content: Individual .txt files for each sample containing C and T frequency per base and coverage. Matrix (csv file) containing methylation percentages for each sample used in the control vs patient analysis for the MethylKit single CpG pipeline.
|
| 758 |
+
!Sample_data_processing = Supplementary_files_format_and_content: A matrix containing the DMAP output data (individual sample percentages, significance values, associated genomic features, fragment length, CpG per fragment). .
|
| 759 |
+
!Sample_platform_id = GPL16791
|
| 760 |
+
!Sample_contact_name = Amber,,Helliwell
|
| 761 |
+
!Sample_contact_department = Biochemistry Department
|
| 762 |
+
!Sample_contact_institute = University of Otago
|
| 763 |
+
!Sample_contact_address = 710 Cumberland Road
|
| 764 |
+
!Sample_contact_city = Dunedin
|
| 765 |
+
!Sample_contact_zip/postal_code = 9016
|
| 766 |
+
!Sample_contact_country = New Zealand
|
| 767 |
+
!Sample_instrument_model = Illumina HiSeq 2500
|
| 768 |
+
!Sample_library_selection = Reduced Representation
|
| 769 |
+
!Sample_library_source = genomic
|
| 770 |
+
!Sample_library_strategy = Bisulfite-Seq
|
| 771 |
+
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN15420255
|
| 772 |
+
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8651477
|
| 773 |
+
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4649nnn/GSM4649044/suppl/GSM4649044_Patient8_CpG.txt.gz
|
| 774 |
+
!Sample_series_id = GSE153667
|
| 775 |
+
!Sample_data_row_count = 0
|
| 776 |
+
^SAMPLE = GSM4649045
|
| 777 |
+
!Sample_title = Patient9
|
| 778 |
+
!Sample_geo_accession = GSM4649045
|
| 779 |
+
!Sample_status = Public on Jul 02 2020
|
| 780 |
+
!Sample_submission_date = Jul 01 2020
|
| 781 |
+
!Sample_last_update_date = Jul 02 2020
|
| 782 |
+
!Sample_type = SRA
|
| 783 |
+
!Sample_channel_count = 1
|
| 784 |
+
!Sample_source_name_ch1 = Peripheral Blood Mononuclear Cells
|
| 785 |
+
!Sample_organism_ch1 = Homo sapiens
|
| 786 |
+
!Sample_taxid_ch1 = 9606
|
| 787 |
+
!Sample_characteristics_ch1 = disease state: Patient
|
| 788 |
+
!Sample_molecule_ch1 = genomic DNA
|
| 789 |
+
!Sample_extract_protocol_ch1 = DNA was extracted from 200ul of PBMCs
|
| 790 |
+
!Sample_extract_protocol_ch1 = MSPI digestion (purify), end repair (purify), A-tialing and adaptor ligation (purify), PCR amplification (purify), Gel size selection and gel extraction (purify)
|
| 791 |
+
!Sample_data_processing = reads were adaptor trimmed using bismark that used a file of adaptor sequences and trimmed three bases back from any detected adaptor to delete the C invorporated and rejecting any reads that were trimmed to less than 10bp
|
| 792 |
+
!Sample_data_processing = reads were aligned to the hg19 genome using bismark with the following specifications: a tolerance for one non-bisulfite mismatch per read, the default minimum alignment score (L,O, -02), and with ignore - quals in order to calculate the mismatch penalty by considering the quality value at the mismatched position to be the highest possible
|
| 793 |
+
!Sample_data_processing = bam files generated by Bismark alignment were then processed using DMAP to compare control vs. patients with the following specifications: ANOVA F test on fragments 40-220bp in length, with the fragment requireing at lest 2 CpGs to have 10 or more sequence reads. The differential methylation file was then annotated with protein coding gene information using the DMAP command identgeneloc. DMAPmatrix.csv file contains this data.
|
| 794 |
+
!Sample_data_processing = the bam files were additionally analysed following a MethylKit based pipeline where first the data was filtered for low read coverage (less than 10 times coverage) and normalised basde on mean coverage distribution before comparing pooled patient and control groups using a Fisher's test. Methmatrix.csv file contains this data
|
| 795 |
+
!Sample_data_processing = Genome_build: hg19
|
| 796 |
+
!Sample_data_processing = Supplementary_files_format_and_content: Individual .txt files for each sample containing C and T frequency per base and coverage. Matrix (csv file) containing methylation percentages for each sample used in the control vs patient analysis for the MethylKit single CpG pipeline.
|
| 797 |
+
!Sample_data_processing = Supplementary_files_format_and_content: A matrix containing the DMAP output data (individual sample percentages, significance values, associated genomic features, fragment length, CpG per fragment). .
|
| 798 |
+
!Sample_platform_id = GPL16791
|
| 799 |
+
!Sample_contact_name = Amber,,Helliwell
|
| 800 |
+
!Sample_contact_department = Biochemistry Department
|
| 801 |
+
!Sample_contact_institute = University of Otago
|
| 802 |
+
!Sample_contact_address = 710 Cumberland Road
|
| 803 |
+
!Sample_contact_city = Dunedin
|
| 804 |
+
!Sample_contact_zip/postal_code = 9016
|
| 805 |
+
!Sample_contact_country = New Zealand
|
| 806 |
+
!Sample_instrument_model = Illumina HiSeq 2500
|
| 807 |
+
!Sample_library_selection = Reduced Representation
|
| 808 |
+
!Sample_library_source = genomic
|
| 809 |
+
!Sample_library_strategy = Bisulfite-Seq
|
| 810 |
+
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN15420254
|
| 811 |
+
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8651478
|
| 812 |
+
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4649nnn/GSM4649045/suppl/GSM4649045_Patient9_CpG.txt.gz
|
| 813 |
+
!Sample_series_id = GSE153667
|
| 814 |
+
!Sample_data_row_count = 0
|
| 815 |
+
^SAMPLE = GSM4649046
|
| 816 |
+
!Sample_title = Patient10
|
| 817 |
+
!Sample_geo_accession = GSM4649046
|
| 818 |
+
!Sample_status = Public on Jul 02 2020
|
| 819 |
+
!Sample_submission_date = Jul 01 2020
|
| 820 |
+
!Sample_last_update_date = Jul 02 2020
|
| 821 |
+
!Sample_type = SRA
|
| 822 |
+
!Sample_channel_count = 1
|
| 823 |
+
!Sample_source_name_ch1 = Peripheral Blood Mononuclear Cells
|
| 824 |
+
!Sample_organism_ch1 = Homo sapiens
|
| 825 |
+
!Sample_taxid_ch1 = 9606
|
| 826 |
+
!Sample_characteristics_ch1 = disease state: Patient
|
| 827 |
+
!Sample_molecule_ch1 = genomic DNA
|
| 828 |
+
!Sample_extract_protocol_ch1 = DNA was extracted from 200ul of PBMCs
|
| 829 |
+
!Sample_extract_protocol_ch1 = MSPI digestion (purify), end repair (purify), A-tialing and adaptor ligation (purify), PCR amplification (purify), Gel size selection and gel extraction (purify)
|
| 830 |
+
!Sample_data_processing = reads were adaptor trimmed using bismark that used a file of adaptor sequences and trimmed three bases back from any detected adaptor to delete the C invorporated and rejecting any reads that were trimmed to less than 10bp
|
| 831 |
+
!Sample_data_processing = reads were aligned to the hg19 genome using bismark with the following specifications: a tolerance for one non-bisulfite mismatch per read, the default minimum alignment score (L,O, -02), and with ignore - quals in order to calculate the mismatch penalty by considering the quality value at the mismatched position to be the highest possible
|
| 832 |
+
!Sample_data_processing = bam files generated by Bismark alignment were then processed using DMAP to compare control vs. patients with the following specifications: ANOVA F test on fragments 40-220bp in length, with the fragment requireing at lest 2 CpGs to have 10 or more sequence reads. The differential methylation file was then annotated with protein coding gene information using the DMAP command identgeneloc. DMAPmatrix.csv file contains this data.
|
| 833 |
+
!Sample_data_processing = the bam files were additionally analysed following a MethylKit based pipeline where first the data was filtered for low read coverage (less than 10 times coverage) and normalised basde on mean coverage distribution before comparing pooled patient and control groups using a Fisher's test. Methmatrix.csv file contains this data
|
| 834 |
+
!Sample_data_processing = Genome_build: hg19
|
| 835 |
+
!Sample_data_processing = Supplementary_files_format_and_content: Individual .txt files for each sample containing C and T frequency per base and coverage. Matrix (csv file) containing methylation percentages for each sample used in the control vs patient analysis for the MethylKit single CpG pipeline.
|
| 836 |
+
!Sample_data_processing = Supplementary_files_format_and_content: A matrix containing the DMAP output data (individual sample percentages, significance values, associated genomic features, fragment length, CpG per fragment). .
|
| 837 |
+
!Sample_platform_id = GPL16791
|
| 838 |
+
!Sample_contact_name = Amber,,Helliwell
|
| 839 |
+
!Sample_contact_department = Biochemistry Department
|
| 840 |
+
!Sample_contact_institute = University of Otago
|
| 841 |
+
!Sample_contact_address = 710 Cumberland Road
|
| 842 |
+
!Sample_contact_city = Dunedin
|
| 843 |
+
!Sample_contact_zip/postal_code = 9016
|
| 844 |
+
!Sample_contact_country = New Zealand
|
| 845 |
+
!Sample_instrument_model = Illumina HiSeq 2500
|
| 846 |
+
!Sample_library_selection = Reduced Representation
|
| 847 |
+
!Sample_library_source = genomic
|
| 848 |
+
!Sample_library_strategy = Bisulfite-Seq
|
| 849 |
+
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN15420253
|
| 850 |
+
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8651479
|
| 851 |
+
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4649nnn/GSM4649046/suppl/GSM4649046_Patient10_CpG.txt.gz
|
| 852 |
+
!Sample_series_id = GSE153667
|
| 853 |
+
!Sample_data_row_count = 0
|
ME/GSE153667/meta/GSE153667_family.xml
ADDED
|
@@ -0,0 +1,1056 @@
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|
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|
|
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|
|
|
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|
|
|
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|
|
|
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|
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|
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|
|
|
|
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|
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|
|
|
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|
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|
|
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|
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|
| 1 |
+
<?xml version="1.0" encoding="UTF-8" standalone="no"?>
|
| 2 |
+
|
| 3 |
+
<MINiML
|
| 4 |
+
xmlns="http://www.ncbi.nlm.nih.gov/geo/info/MINiML"
|
| 5 |
+
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
|
| 6 |
+
xsi:schemaLocation="http://www.ncbi.nlm.nih.gov/geo/info/MINiML http://www.ncbi.nlm.nih.gov/geo/info/MINiML.xsd"
|
| 7 |
+
version="0.5.0" >
|
| 8 |
+
|
| 9 |
+
<Contributor iid="contrib1">
|
| 10 |
+
<Person><First>Amber</First><Last>Helliwell</Last></Person>
|
| 11 |
+
<Department>Biochemistry Department</Department>
|
| 12 |
+
<Organization>University of Otago</Organization>
|
| 13 |
+
<Address>
|
| 14 |
+
<Line>710 Cumberland Road</Line>
|
| 15 |
+
<City>Dunedin</City>
|
| 16 |
+
<Postal-Code>9016</Postal-Code>
|
| 17 |
+
<Country>New Zealand</Country>
|
| 18 |
+
</Address>
|
| 19 |
+
</Contributor>
|
| 20 |
+
|
| 21 |
+
<Contributor iid="contrib2">
|
| 22 |
+
<Organization>GEO</Organization>
|
| 23 |
+
<Address>
|
| 24 |
+
<City></City>
|
| 25 |
+
<Country>USA</Country>
|
| 26 |
+
</Address>
|
| 27 |
+
</Contributor>
|
| 28 |
+
|
| 29 |
+
<Contributor iid="contrib3">
|
| 30 |
+
<Person><First>Warren</First><Last>Tate</Last></Person>
|
| 31 |
+
</Contributor>
|
| 32 |
+
|
| 33 |
+
<Contributor iid="contrib4">
|
| 34 |
+
<Person><First>Aniruddha</First><Last>Chatterjee</Last></Person>
|
| 35 |
+
</Contributor>
|
| 36 |
+
|
| 37 |
+
<Contributor iid="contrib5">
|
| 38 |
+
<Person><First>Peter</First><Last>Stockwell</Last></Person>
|
| 39 |
+
</Contributor>
|
| 40 |
+
|
| 41 |
+
<Contributor iid="contrib6">
|
| 42 |
+
<Person><First>Eiren</First><Last>Sweetman</Last></Person>
|
| 43 |
+
</Contributor>
|
| 44 |
+
|
| 45 |
+
<Contributor iid="contrib7">
|
| 46 |
+
<Person><First>Tina</First><Last>Edgar</Last></Person>
|
| 47 |
+
</Contributor>
|
| 48 |
+
|
| 49 |
+
<Database iid="GEO">
|
| 50 |
+
<Name>Gene Expression Omnibus (GEO)</Name>
|
| 51 |
+
<Public-ID>GEO</Public-ID>
|
| 52 |
+
<Organization>NCBI NLM NIH</Organization>
|
| 53 |
+
<Web-Link>http://www.ncbi.nlm.nih.gov/geo</Web-Link>
|
| 54 |
+
<Email>geo@ncbi.nlm.nih.gov</Email>
|
| 55 |
+
</Database>
|
| 56 |
+
|
| 57 |
+
<Platform iid="GPL16791">
|
| 58 |
+
<Status database="GEO">
|
| 59 |
+
<Submission-Date>2013-03-14</Submission-Date>
|
| 60 |
+
<Release-Date>2013-03-14</Release-Date>
|
| 61 |
+
<Last-Update-Date>2019-03-27</Last-Update-Date>
|
| 62 |
+
</Status>
|
| 63 |
+
<Title>Illumina HiSeq 2500 (Homo sapiens)</Title>
|
| 64 |
+
<Accession database="GEO">GPL16791</Accession>
|
| 65 |
+
<Technology>high-throughput sequencing</Technology>
|
| 66 |
+
<Distribution>virtual</Distribution>
|
| 67 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 68 |
+
<Manufacturer></Manufacturer>
|
| 69 |
+
<Manufacture-Protocol>
|
| 70 |
+
</Manufacture-Protocol>
|
| 71 |
+
<Contact-Ref ref="contrib2" />
|
| 72 |
+
</Platform>
|
| 73 |
+
|
| 74 |
+
<Sample iid="GSM4649027">
|
| 75 |
+
<Status database="GEO">
|
| 76 |
+
<Submission-Date>2020-07-01</Submission-Date>
|
| 77 |
+
<Release-Date>2020-07-02</Release-Date>
|
| 78 |
+
<Last-Update-Date>2020-07-02</Last-Update-Date>
|
| 79 |
+
</Status>
|
| 80 |
+
<Title>Control1</Title>
|
| 81 |
+
<Accession database="GEO">GSM4649027</Accession>
|
| 82 |
+
<Type>SRA</Type>
|
| 83 |
+
<Channel-Count>1</Channel-Count>
|
| 84 |
+
<Channel position="1">
|
| 85 |
+
<Source>Peripheral Blood Mononuclear Cells</Source>
|
| 86 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 87 |
+
<Characteristics tag="disease state">
|
| 88 |
+
Control
|
| 89 |
+
</Characteristics>
|
| 90 |
+
<Molecule>genomic DNA</Molecule>
|
| 91 |
+
<Extract-Protocol>
|
| 92 |
+
DNA was extracted from 200ul of PBMCs
|
| 93 |
+
MSPI digestion (purify), end repair (purify), A-tialing and adaptor ligation (purify), PCR amplification (purify), Gel size selection and gel extraction (purify)
|
| 94 |
+
</Extract-Protocol>
|
| 95 |
+
</Channel>
|
| 96 |
+
<Data-Processing>
|
| 97 |
+
reads were adaptor trimmed using bismark that used a file of adaptor sequences and trimmed three bases back from any detected adaptor to delete the C invorporated and rejecting any reads that were trimmed to less than 10bp
|
| 98 |
+
reads were aligned to the hg19 genome using bismark with the following specifications: a tolerance for one non-bisulfite mismatch per read, the default minimum alignment score (L,O, -02), and with ignore - quals in order to calculate the mismatch penalty by considering the quality value at the mismatched position to be the highest possible
|
| 99 |
+
bam files generated by Bismark alignment were then processed using DMAP to compare control vs. patients with the following specifications: ANOVA F test on fragments 40-220bp in length, with the fragment requireing at lest 2 CpGs to have 10 or more sequence reads. The differential methylation file was then annotated with protein coding gene information using the DMAP command identgeneloc. DMAPmatrix.csv file contains this data.
|
| 100 |
+
the bam files were additionally analysed following a MethylKit based pipeline where first the data was filtered for low read coverage (less than 10 times coverage) and normalised basde on mean coverage distribution before comparing pooled patient and control groups using a Fisher's test. Methmatrix.csv file contains this data
|
| 101 |
+
Genome_build: hg19
|
| 102 |
+
Supplementary_files_format_and_content: Individual .txt files for each sample containing C and T frequency per base and coverage. Matrix (csv file) containing methylation percentages for each sample used in the control vs patient analysis for the MethylKit single CpG pipeline.
|
| 103 |
+
Supplementary_files_format_and_content: A matrix containing the DMAP output data (individual sample percentages, significance values, associated genomic features, fragment length, CpG per fragment). .
|
| 104 |
+
</Data-Processing>
|
| 105 |
+
<Platform-Ref ref="GPL16791" />
|
| 106 |
+
<Library-Strategy>Bisulfite-Seq</Library-Strategy>
|
| 107 |
+
<Library-Source>genomic</Library-Source>
|
| 108 |
+
<Library-Selection>Reduced Representation</Library-Selection>
|
| 109 |
+
<Instrument-Model>
|
| 110 |
+
<Predefined>Illumina HiSeq 2500</Predefined>
|
| 111 |
+
</Instrument-Model>
|
| 112 |
+
<Contact-Ref ref="contrib1" />
|
| 113 |
+
<Supplementary-Data type="TXT">
|
| 114 |
+
ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4649nnn/GSM4649027/suppl/GSM4649027_Control1_CpG.txt.gz
|
| 115 |
+
</Supplementary-Data>
|
| 116 |
+
<Relation type="BioSample" target="https://www.ncbi.nlm.nih.gov/biosample/SAMN15420272" />
|
| 117 |
+
<Relation type="SRA" target="https://www.ncbi.nlm.nih.gov/sra?term=SRX8651460" />
|
| 118 |
+
</Sample>
|
| 119 |
+
|
| 120 |
+
<Sample iid="GSM4649028">
|
| 121 |
+
<Status database="GEO">
|
| 122 |
+
<Submission-Date>2020-07-01</Submission-Date>
|
| 123 |
+
<Release-Date>2020-07-02</Release-Date>
|
| 124 |
+
<Last-Update-Date>2020-07-02</Last-Update-Date>
|
| 125 |
+
</Status>
|
| 126 |
+
<Title>Control2</Title>
|
| 127 |
+
<Accession database="GEO">GSM4649028</Accession>
|
| 128 |
+
<Type>SRA</Type>
|
| 129 |
+
<Channel-Count>1</Channel-Count>
|
| 130 |
+
<Channel position="1">
|
| 131 |
+
<Source>Peripheral Blood Mononuclear Cells</Source>
|
| 132 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 133 |
+
<Characteristics tag="disease state">
|
| 134 |
+
Control
|
| 135 |
+
</Characteristics>
|
| 136 |
+
<Molecule>genomic DNA</Molecule>
|
| 137 |
+
<Extract-Protocol>
|
| 138 |
+
DNA was extracted from 200ul of PBMCs
|
| 139 |
+
MSPI digestion (purify), end repair (purify), A-tialing and adaptor ligation (purify), PCR amplification (purify), Gel size selection and gel extraction (purify)
|
| 140 |
+
</Extract-Protocol>
|
| 141 |
+
</Channel>
|
| 142 |
+
<Data-Processing>
|
| 143 |
+
reads were adaptor trimmed using bismark that used a file of adaptor sequences and trimmed three bases back from any detected adaptor to delete the C invorporated and rejecting any reads that were trimmed to less than 10bp
|
| 144 |
+
reads were aligned to the hg19 genome using bismark with the following specifications: a tolerance for one non-bisulfite mismatch per read, the default minimum alignment score (L,O, -02), and with ignore - quals in order to calculate the mismatch penalty by considering the quality value at the mismatched position to be the highest possible
|
| 145 |
+
bam files generated by Bismark alignment were then processed using DMAP to compare control vs. patients with the following specifications: ANOVA F test on fragments 40-220bp in length, with the fragment requireing at lest 2 CpGs to have 10 or more sequence reads. The differential methylation file was then annotated with protein coding gene information using the DMAP command identgeneloc. DMAPmatrix.csv file contains this data.
|
| 146 |
+
the bam files were additionally analysed following a MethylKit based pipeline where first the data was filtered for low read coverage (less than 10 times coverage) and normalised basde on mean coverage distribution before comparing pooled patient and control groups using a Fisher's test. Methmatrix.csv file contains this data
|
| 147 |
+
Genome_build: hg19
|
| 148 |
+
Supplementary_files_format_and_content: Individual .txt files for each sample containing C and T frequency per base and coverage. Matrix (csv file) containing methylation percentages for each sample used in the control vs patient analysis for the MethylKit single CpG pipeline.
|
| 149 |
+
Supplementary_files_format_and_content: A matrix containing the DMAP output data (individual sample percentages, significance values, associated genomic features, fragment length, CpG per fragment). .
|
| 150 |
+
</Data-Processing>
|
| 151 |
+
<Platform-Ref ref="GPL16791" />
|
| 152 |
+
<Library-Strategy>Bisulfite-Seq</Library-Strategy>
|
| 153 |
+
<Library-Source>genomic</Library-Source>
|
| 154 |
+
<Library-Selection>Reduced Representation</Library-Selection>
|
| 155 |
+
<Instrument-Model>
|
| 156 |
+
<Predefined>Illumina HiSeq 2500</Predefined>
|
| 157 |
+
</Instrument-Model>
|
| 158 |
+
<Contact-Ref ref="contrib1" />
|
| 159 |
+
<Supplementary-Data type="TXT">
|
| 160 |
+
ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4649nnn/GSM4649028/suppl/GSM4649028_Control2_CpG.txt.gz
|
| 161 |
+
</Supplementary-Data>
|
| 162 |
+
<Relation type="BioSample" target="https://www.ncbi.nlm.nih.gov/biosample/SAMN15420271" />
|
| 163 |
+
<Relation type="SRA" target="https://www.ncbi.nlm.nih.gov/sra?term=SRX8651461" />
|
| 164 |
+
</Sample>
|
| 165 |
+
|
| 166 |
+
<Sample iid="GSM4649029">
|
| 167 |
+
<Status database="GEO">
|
| 168 |
+
<Submission-Date>2020-07-01</Submission-Date>
|
| 169 |
+
<Release-Date>2020-07-02</Release-Date>
|
| 170 |
+
<Last-Update-Date>2020-07-02</Last-Update-Date>
|
| 171 |
+
</Status>
|
| 172 |
+
<Title>Control3</Title>
|
| 173 |
+
<Accession database="GEO">GSM4649029</Accession>
|
| 174 |
+
<Type>SRA</Type>
|
| 175 |
+
<Channel-Count>1</Channel-Count>
|
| 176 |
+
<Channel position="1">
|
| 177 |
+
<Source>Peripheral Blood Mononuclear Cells</Source>
|
| 178 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 179 |
+
<Characteristics tag="disease state">
|
| 180 |
+
Control
|
| 181 |
+
</Characteristics>
|
| 182 |
+
<Molecule>genomic DNA</Molecule>
|
| 183 |
+
<Extract-Protocol>
|
| 184 |
+
DNA was extracted from 200ul of PBMCs
|
| 185 |
+
MSPI digestion (purify), end repair (purify), A-tialing and adaptor ligation (purify), PCR amplification (purify), Gel size selection and gel extraction (purify)
|
| 186 |
+
</Extract-Protocol>
|
| 187 |
+
</Channel>
|
| 188 |
+
<Data-Processing>
|
| 189 |
+
reads were adaptor trimmed using bismark that used a file of adaptor sequences and trimmed three bases back from any detected adaptor to delete the C invorporated and rejecting any reads that were trimmed to less than 10bp
|
| 190 |
+
reads were aligned to the hg19 genome using bismark with the following specifications: a tolerance for one non-bisulfite mismatch per read, the default minimum alignment score (L,O, -02), and with ignore - quals in order to calculate the mismatch penalty by considering the quality value at the mismatched position to be the highest possible
|
| 191 |
+
bam files generated by Bismark alignment were then processed using DMAP to compare control vs. patients with the following specifications: ANOVA F test on fragments 40-220bp in length, with the fragment requireing at lest 2 CpGs to have 10 or more sequence reads. The differential methylation file was then annotated with protein coding gene information using the DMAP command identgeneloc. DMAPmatrix.csv file contains this data.
|
| 192 |
+
the bam files were additionally analysed following a MethylKit based pipeline where first the data was filtered for low read coverage (less than 10 times coverage) and normalised basde on mean coverage distribution before comparing pooled patient and control groups using a Fisher's test. Methmatrix.csv file contains this data
|
| 193 |
+
Genome_build: hg19
|
| 194 |
+
Supplementary_files_format_and_content: Individual .txt files for each sample containing C and T frequency per base and coverage. Matrix (csv file) containing methylation percentages for each sample used in the control vs patient analysis for the MethylKit single CpG pipeline.
|
| 195 |
+
Supplementary_files_format_and_content: A matrix containing the DMAP output data (individual sample percentages, significance values, associated genomic features, fragment length, CpG per fragment). .
|
| 196 |
+
</Data-Processing>
|
| 197 |
+
<Platform-Ref ref="GPL16791" />
|
| 198 |
+
<Library-Strategy>Bisulfite-Seq</Library-Strategy>
|
| 199 |
+
<Library-Source>genomic</Library-Source>
|
| 200 |
+
<Library-Selection>Reduced Representation</Library-Selection>
|
| 201 |
+
<Instrument-Model>
|
| 202 |
+
<Predefined>Illumina HiSeq 2500</Predefined>
|
| 203 |
+
</Instrument-Model>
|
| 204 |
+
<Contact-Ref ref="contrib1" />
|
| 205 |
+
<Supplementary-Data type="TXT">
|
| 206 |
+
ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4649nnn/GSM4649029/suppl/GSM4649029_Control3_CpG.txt.gz
|
| 207 |
+
</Supplementary-Data>
|
| 208 |
+
<Relation type="BioSample" target="https://www.ncbi.nlm.nih.gov/biosample/SAMN15420270" />
|
| 209 |
+
<Relation type="SRA" target="https://www.ncbi.nlm.nih.gov/sra?term=SRX8651462" />
|
| 210 |
+
</Sample>
|
| 211 |
+
|
| 212 |
+
<Sample iid="GSM4649030">
|
| 213 |
+
<Status database="GEO">
|
| 214 |
+
<Submission-Date>2020-07-01</Submission-Date>
|
| 215 |
+
<Release-Date>2020-07-02</Release-Date>
|
| 216 |
+
<Last-Update-Date>2020-07-02</Last-Update-Date>
|
| 217 |
+
</Status>
|
| 218 |
+
<Title>Control4</Title>
|
| 219 |
+
<Accession database="GEO">GSM4649030</Accession>
|
| 220 |
+
<Type>SRA</Type>
|
| 221 |
+
<Channel-Count>1</Channel-Count>
|
| 222 |
+
<Channel position="1">
|
| 223 |
+
<Source>Peripheral Blood Mononuclear Cells</Source>
|
| 224 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 225 |
+
<Characteristics tag="disease state">
|
| 226 |
+
Control
|
| 227 |
+
</Characteristics>
|
| 228 |
+
<Molecule>genomic DNA</Molecule>
|
| 229 |
+
<Extract-Protocol>
|
| 230 |
+
DNA was extracted from 200ul of PBMCs
|
| 231 |
+
MSPI digestion (purify), end repair (purify), A-tialing and adaptor ligation (purify), PCR amplification (purify), Gel size selection and gel extraction (purify)
|
| 232 |
+
</Extract-Protocol>
|
| 233 |
+
</Channel>
|
| 234 |
+
<Data-Processing>
|
| 235 |
+
reads were adaptor trimmed using bismark that used a file of adaptor sequences and trimmed three bases back from any detected adaptor to delete the C invorporated and rejecting any reads that were trimmed to less than 10bp
|
| 236 |
+
reads were aligned to the hg19 genome using bismark with the following specifications: a tolerance for one non-bisulfite mismatch per read, the default minimum alignment score (L,O, -02), and with ignore - quals in order to calculate the mismatch penalty by considering the quality value at the mismatched position to be the highest possible
|
| 237 |
+
bam files generated by Bismark alignment were then processed using DMAP to compare control vs. patients with the following specifications: ANOVA F test on fragments 40-220bp in length, with the fragment requireing at lest 2 CpGs to have 10 or more sequence reads. The differential methylation file was then annotated with protein coding gene information using the DMAP command identgeneloc. DMAPmatrix.csv file contains this data.
|
| 238 |
+
the bam files were additionally analysed following a MethylKit based pipeline where first the data was filtered for low read coverage (less than 10 times coverage) and normalised basde on mean coverage distribution before comparing pooled patient and control groups using a Fisher's test. Methmatrix.csv file contains this data
|
| 239 |
+
Genome_build: hg19
|
| 240 |
+
Supplementary_files_format_and_content: Individual .txt files for each sample containing C and T frequency per base and coverage. Matrix (csv file) containing methylation percentages for each sample used in the control vs patient analysis for the MethylKit single CpG pipeline.
|
| 241 |
+
Supplementary_files_format_and_content: A matrix containing the DMAP output data (individual sample percentages, significance values, associated genomic features, fragment length, CpG per fragment). .
|
| 242 |
+
</Data-Processing>
|
| 243 |
+
<Platform-Ref ref="GPL16791" />
|
| 244 |
+
<Library-Strategy>Bisulfite-Seq</Library-Strategy>
|
| 245 |
+
<Library-Source>genomic</Library-Source>
|
| 246 |
+
<Library-Selection>Reduced Representation</Library-Selection>
|
| 247 |
+
<Instrument-Model>
|
| 248 |
+
<Predefined>Illumina HiSeq 2500</Predefined>
|
| 249 |
+
</Instrument-Model>
|
| 250 |
+
<Contact-Ref ref="contrib1" />
|
| 251 |
+
<Supplementary-Data type="TXT">
|
| 252 |
+
ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4649nnn/GSM4649030/suppl/GSM4649030_Control4_CpG.txt.gz
|
| 253 |
+
</Supplementary-Data>
|
| 254 |
+
<Relation type="BioSample" target="https://www.ncbi.nlm.nih.gov/biosample/SAMN15420269" />
|
| 255 |
+
<Relation type="SRA" target="https://www.ncbi.nlm.nih.gov/sra?term=SRX8651463" />
|
| 256 |
+
</Sample>
|
| 257 |
+
|
| 258 |
+
<Sample iid="GSM4649031">
|
| 259 |
+
<Status database="GEO">
|
| 260 |
+
<Submission-Date>2020-07-01</Submission-Date>
|
| 261 |
+
<Release-Date>2020-07-02</Release-Date>
|
| 262 |
+
<Last-Update-Date>2020-07-02</Last-Update-Date>
|
| 263 |
+
</Status>
|
| 264 |
+
<Title>Control5</Title>
|
| 265 |
+
<Accession database="GEO">GSM4649031</Accession>
|
| 266 |
+
<Type>SRA</Type>
|
| 267 |
+
<Channel-Count>1</Channel-Count>
|
| 268 |
+
<Channel position="1">
|
| 269 |
+
<Source>Peripheral Blood Mononuclear Cells</Source>
|
| 270 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 271 |
+
<Characteristics tag="disease state">
|
| 272 |
+
Control
|
| 273 |
+
</Characteristics>
|
| 274 |
+
<Molecule>genomic DNA</Molecule>
|
| 275 |
+
<Extract-Protocol>
|
| 276 |
+
DNA was extracted from 200ul of PBMCs
|
| 277 |
+
MSPI digestion (purify), end repair (purify), A-tialing and adaptor ligation (purify), PCR amplification (purify), Gel size selection and gel extraction (purify)
|
| 278 |
+
</Extract-Protocol>
|
| 279 |
+
</Channel>
|
| 280 |
+
<Data-Processing>
|
| 281 |
+
reads were adaptor trimmed using bismark that used a file of adaptor sequences and trimmed three bases back from any detected adaptor to delete the C invorporated and rejecting any reads that were trimmed to less than 10bp
|
| 282 |
+
reads were aligned to the hg19 genome using bismark with the following specifications: a tolerance for one non-bisulfite mismatch per read, the default minimum alignment score (L,O, -02), and with ignore - quals in order to calculate the mismatch penalty by considering the quality value at the mismatched position to be the highest possible
|
| 283 |
+
bam files generated by Bismark alignment were then processed using DMAP to compare control vs. patients with the following specifications: ANOVA F test on fragments 40-220bp in length, with the fragment requireing at lest 2 CpGs to have 10 or more sequence reads. The differential methylation file was then annotated with protein coding gene information using the DMAP command identgeneloc. DMAPmatrix.csv file contains this data.
|
| 284 |
+
the bam files were additionally analysed following a MethylKit based pipeline where first the data was filtered for low read coverage (less than 10 times coverage) and normalised basde on mean coverage distribution before comparing pooled patient and control groups using a Fisher's test. Methmatrix.csv file contains this data
|
| 285 |
+
Genome_build: hg19
|
| 286 |
+
Supplementary_files_format_and_content: Individual .txt files for each sample containing C and T frequency per base and coverage. Matrix (csv file) containing methylation percentages for each sample used in the control vs patient analysis for the MethylKit single CpG pipeline.
|
| 287 |
+
Supplementary_files_format_and_content: A matrix containing the DMAP output data (individual sample percentages, significance values, associated genomic features, fragment length, CpG per fragment). .
|
| 288 |
+
</Data-Processing>
|
| 289 |
+
<Platform-Ref ref="GPL16791" />
|
| 290 |
+
<Library-Strategy>Bisulfite-Seq</Library-Strategy>
|
| 291 |
+
<Library-Source>genomic</Library-Source>
|
| 292 |
+
<Library-Selection>Reduced Representation</Library-Selection>
|
| 293 |
+
<Instrument-Model>
|
| 294 |
+
<Predefined>Illumina HiSeq 2500</Predefined>
|
| 295 |
+
</Instrument-Model>
|
| 296 |
+
<Contact-Ref ref="contrib1" />
|
| 297 |
+
<Supplementary-Data type="TXT">
|
| 298 |
+
ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4649nnn/GSM4649031/suppl/GSM4649031_Control5_CpG.txt.gz
|
| 299 |
+
</Supplementary-Data>
|
| 300 |
+
<Relation type="BioSample" target="https://www.ncbi.nlm.nih.gov/biosample/SAMN15420268" />
|
| 301 |
+
<Relation type="SRA" target="https://www.ncbi.nlm.nih.gov/sra?term=SRX8651464" />
|
| 302 |
+
</Sample>
|
| 303 |
+
|
| 304 |
+
<Sample iid="GSM4649032">
|
| 305 |
+
<Status database="GEO">
|
| 306 |
+
<Submission-Date>2020-07-01</Submission-Date>
|
| 307 |
+
<Release-Date>2020-07-02</Release-Date>
|
| 308 |
+
<Last-Update-Date>2020-07-02</Last-Update-Date>
|
| 309 |
+
</Status>
|
| 310 |
+
<Title>Control6</Title>
|
| 311 |
+
<Accession database="GEO">GSM4649032</Accession>
|
| 312 |
+
<Type>SRA</Type>
|
| 313 |
+
<Channel-Count>1</Channel-Count>
|
| 314 |
+
<Channel position="1">
|
| 315 |
+
<Source>Peripheral Blood Mononuclear Cells</Source>
|
| 316 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 317 |
+
<Characteristics tag="disease state">
|
| 318 |
+
Control
|
| 319 |
+
</Characteristics>
|
| 320 |
+
<Molecule>genomic DNA</Molecule>
|
| 321 |
+
<Extract-Protocol>
|
| 322 |
+
DNA was extracted from 200ul of PBMCs
|
| 323 |
+
MSPI digestion (purify), end repair (purify), A-tialing and adaptor ligation (purify), PCR amplification (purify), Gel size selection and gel extraction (purify)
|
| 324 |
+
</Extract-Protocol>
|
| 325 |
+
</Channel>
|
| 326 |
+
<Data-Processing>
|
| 327 |
+
reads were adaptor trimmed using bismark that used a file of adaptor sequences and trimmed three bases back from any detected adaptor to delete the C invorporated and rejecting any reads that were trimmed to less than 10bp
|
| 328 |
+
reads were aligned to the hg19 genome using bismark with the following specifications: a tolerance for one non-bisulfite mismatch per read, the default minimum alignment score (L,O, -02), and with ignore - quals in order to calculate the mismatch penalty by considering the quality value at the mismatched position to be the highest possible
|
| 329 |
+
bam files generated by Bismark alignment were then processed using DMAP to compare control vs. patients with the following specifications: ANOVA F test on fragments 40-220bp in length, with the fragment requireing at lest 2 CpGs to have 10 or more sequence reads. The differential methylation file was then annotated with protein coding gene information using the DMAP command identgeneloc. DMAPmatrix.csv file contains this data.
|
| 330 |
+
the bam files were additionally analysed following a MethylKit based pipeline where first the data was filtered for low read coverage (less than 10 times coverage) and normalised basde on mean coverage distribution before comparing pooled patient and control groups using a Fisher's test. Methmatrix.csv file contains this data
|
| 331 |
+
Genome_build: hg19
|
| 332 |
+
Supplementary_files_format_and_content: Individual .txt files for each sample containing C and T frequency per base and coverage. Matrix (csv file) containing methylation percentages for each sample used in the control vs patient analysis for the MethylKit single CpG pipeline.
|
| 333 |
+
Supplementary_files_format_and_content: A matrix containing the DMAP output data (individual sample percentages, significance values, associated genomic features, fragment length, CpG per fragment). .
|
| 334 |
+
</Data-Processing>
|
| 335 |
+
<Platform-Ref ref="GPL16791" />
|
| 336 |
+
<Library-Strategy>Bisulfite-Seq</Library-Strategy>
|
| 337 |
+
<Library-Source>genomic</Library-Source>
|
| 338 |
+
<Library-Selection>Reduced Representation</Library-Selection>
|
| 339 |
+
<Instrument-Model>
|
| 340 |
+
<Predefined>Illumina HiSeq 2500</Predefined>
|
| 341 |
+
</Instrument-Model>
|
| 342 |
+
<Contact-Ref ref="contrib1" />
|
| 343 |
+
<Supplementary-Data type="TXT">
|
| 344 |
+
ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4649nnn/GSM4649032/suppl/GSM4649032_Control6_CpG.txt.gz
|
| 345 |
+
</Supplementary-Data>
|
| 346 |
+
<Relation type="BioSample" target="https://www.ncbi.nlm.nih.gov/biosample/SAMN15420267" />
|
| 347 |
+
<Relation type="SRA" target="https://www.ncbi.nlm.nih.gov/sra?term=SRX8651465" />
|
| 348 |
+
</Sample>
|
| 349 |
+
|
| 350 |
+
<Sample iid="GSM4649033">
|
| 351 |
+
<Status database="GEO">
|
| 352 |
+
<Submission-Date>2020-07-01</Submission-Date>
|
| 353 |
+
<Release-Date>2020-07-02</Release-Date>
|
| 354 |
+
<Last-Update-Date>2020-07-02</Last-Update-Date>
|
| 355 |
+
</Status>
|
| 356 |
+
<Title>Control7</Title>
|
| 357 |
+
<Accession database="GEO">GSM4649033</Accession>
|
| 358 |
+
<Type>SRA</Type>
|
| 359 |
+
<Channel-Count>1</Channel-Count>
|
| 360 |
+
<Channel position="1">
|
| 361 |
+
<Source>Peripheral Blood Mononuclear Cells</Source>
|
| 362 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 363 |
+
<Characteristics tag="disease state">
|
| 364 |
+
Control
|
| 365 |
+
</Characteristics>
|
| 366 |
+
<Molecule>genomic DNA</Molecule>
|
| 367 |
+
<Extract-Protocol>
|
| 368 |
+
DNA was extracted from 200ul of PBMCs
|
| 369 |
+
MSPI digestion (purify), end repair (purify), A-tialing and adaptor ligation (purify), PCR amplification (purify), Gel size selection and gel extraction (purify)
|
| 370 |
+
</Extract-Protocol>
|
| 371 |
+
</Channel>
|
| 372 |
+
<Data-Processing>
|
| 373 |
+
reads were adaptor trimmed using bismark that used a file of adaptor sequences and trimmed three bases back from any detected adaptor to delete the C invorporated and rejecting any reads that were trimmed to less than 10bp
|
| 374 |
+
reads were aligned to the hg19 genome using bismark with the following specifications: a tolerance for one non-bisulfite mismatch per read, the default minimum alignment score (L,O, -02), and with ignore - quals in order to calculate the mismatch penalty by considering the quality value at the mismatched position to be the highest possible
|
| 375 |
+
bam files generated by Bismark alignment were then processed using DMAP to compare control vs. patients with the following specifications: ANOVA F test on fragments 40-220bp in length, with the fragment requireing at lest 2 CpGs to have 10 or more sequence reads. The differential methylation file was then annotated with protein coding gene information using the DMAP command identgeneloc. DMAPmatrix.csv file contains this data.
|
| 376 |
+
the bam files were additionally analysed following a MethylKit based pipeline where first the data was filtered for low read coverage (less than 10 times coverage) and normalised basde on mean coverage distribution before comparing pooled patient and control groups using a Fisher's test. Methmatrix.csv file contains this data
|
| 377 |
+
Genome_build: hg19
|
| 378 |
+
Supplementary_files_format_and_content: Individual .txt files for each sample containing C and T frequency per base and coverage. Matrix (csv file) containing methylation percentages for each sample used in the control vs patient analysis for the MethylKit single CpG pipeline.
|
| 379 |
+
Supplementary_files_format_and_content: A matrix containing the DMAP output data (individual sample percentages, significance values, associated genomic features, fragment length, CpG per fragment). .
|
| 380 |
+
</Data-Processing>
|
| 381 |
+
<Platform-Ref ref="GPL16791" />
|
| 382 |
+
<Library-Strategy>Bisulfite-Seq</Library-Strategy>
|
| 383 |
+
<Library-Source>genomic</Library-Source>
|
| 384 |
+
<Library-Selection>Reduced Representation</Library-Selection>
|
| 385 |
+
<Instrument-Model>
|
| 386 |
+
<Predefined>Illumina HiSeq 2500</Predefined>
|
| 387 |
+
</Instrument-Model>
|
| 388 |
+
<Contact-Ref ref="contrib1" />
|
| 389 |
+
<Supplementary-Data type="TXT">
|
| 390 |
+
ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4649nnn/GSM4649033/suppl/GSM4649033_Control7_CpG.txt.gz
|
| 391 |
+
</Supplementary-Data>
|
| 392 |
+
<Relation type="BioSample" target="https://www.ncbi.nlm.nih.gov/biosample/SAMN15420266" />
|
| 393 |
+
<Relation type="SRA" target="https://www.ncbi.nlm.nih.gov/sra?term=SRX8651466" />
|
| 394 |
+
</Sample>
|
| 395 |
+
|
| 396 |
+
<Sample iid="GSM4649034">
|
| 397 |
+
<Status database="GEO">
|
| 398 |
+
<Submission-Date>2020-07-01</Submission-Date>
|
| 399 |
+
<Release-Date>2020-07-02</Release-Date>
|
| 400 |
+
<Last-Update-Date>2020-07-02</Last-Update-Date>
|
| 401 |
+
</Status>
|
| 402 |
+
<Title>Control8</Title>
|
| 403 |
+
<Accession database="GEO">GSM4649034</Accession>
|
| 404 |
+
<Type>SRA</Type>
|
| 405 |
+
<Channel-Count>1</Channel-Count>
|
| 406 |
+
<Channel position="1">
|
| 407 |
+
<Source>Peripheral Blood Mononuclear Cells</Source>
|
| 408 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 409 |
+
<Characteristics tag="disease state">
|
| 410 |
+
Control
|
| 411 |
+
</Characteristics>
|
| 412 |
+
<Molecule>genomic DNA</Molecule>
|
| 413 |
+
<Extract-Protocol>
|
| 414 |
+
DNA was extracted from 200ul of PBMCs
|
| 415 |
+
MSPI digestion (purify), end repair (purify), A-tialing and adaptor ligation (purify), PCR amplification (purify), Gel size selection and gel extraction (purify)
|
| 416 |
+
</Extract-Protocol>
|
| 417 |
+
</Channel>
|
| 418 |
+
<Data-Processing>
|
| 419 |
+
reads were adaptor trimmed using bismark that used a file of adaptor sequences and trimmed three bases back from any detected adaptor to delete the C invorporated and rejecting any reads that were trimmed to less than 10bp
|
| 420 |
+
reads were aligned to the hg19 genome using bismark with the following specifications: a tolerance for one non-bisulfite mismatch per read, the default minimum alignment score (L,O, -02), and with ignore - quals in order to calculate the mismatch penalty by considering the quality value at the mismatched position to be the highest possible
|
| 421 |
+
bam files generated by Bismark alignment were then processed using DMAP to compare control vs. patients with the following specifications: ANOVA F test on fragments 40-220bp in length, with the fragment requireing at lest 2 CpGs to have 10 or more sequence reads. The differential methylation file was then annotated with protein coding gene information using the DMAP command identgeneloc. DMAPmatrix.csv file contains this data.
|
| 422 |
+
the bam files were additionally analysed following a MethylKit based pipeline where first the data was filtered for low read coverage (less than 10 times coverage) and normalised basde on mean coverage distribution before comparing pooled patient and control groups using a Fisher's test. Methmatrix.csv file contains this data
|
| 423 |
+
Genome_build: hg19
|
| 424 |
+
Supplementary_files_format_and_content: Individual .txt files for each sample containing C and T frequency per base and coverage. Matrix (csv file) containing methylation percentages for each sample used in the control vs patient analysis for the MethylKit single CpG pipeline.
|
| 425 |
+
Supplementary_files_format_and_content: A matrix containing the DMAP output data (individual sample percentages, significance values, associated genomic features, fragment length, CpG per fragment). .
|
| 426 |
+
</Data-Processing>
|
| 427 |
+
<Platform-Ref ref="GPL16791" />
|
| 428 |
+
<Library-Strategy>Bisulfite-Seq</Library-Strategy>
|
| 429 |
+
<Library-Source>genomic</Library-Source>
|
| 430 |
+
<Library-Selection>Reduced Representation</Library-Selection>
|
| 431 |
+
<Instrument-Model>
|
| 432 |
+
<Predefined>Illumina HiSeq 2500</Predefined>
|
| 433 |
+
</Instrument-Model>
|
| 434 |
+
<Contact-Ref ref="contrib1" />
|
| 435 |
+
<Supplementary-Data type="TXT">
|
| 436 |
+
ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4649nnn/GSM4649034/suppl/GSM4649034_Control8_CpG.txt.gz
|
| 437 |
+
</Supplementary-Data>
|
| 438 |
+
<Relation type="BioSample" target="https://www.ncbi.nlm.nih.gov/biosample/SAMN15420265" />
|
| 439 |
+
<Relation type="SRA" target="https://www.ncbi.nlm.nih.gov/sra?term=SRX8651467" />
|
| 440 |
+
</Sample>
|
| 441 |
+
|
| 442 |
+
<Sample iid="GSM4649035">
|
| 443 |
+
<Status database="GEO">
|
| 444 |
+
<Submission-Date>2020-07-01</Submission-Date>
|
| 445 |
+
<Release-Date>2020-07-02</Release-Date>
|
| 446 |
+
<Last-Update-Date>2020-07-02</Last-Update-Date>
|
| 447 |
+
</Status>
|
| 448 |
+
<Title>Control9</Title>
|
| 449 |
+
<Accession database="GEO">GSM4649035</Accession>
|
| 450 |
+
<Type>SRA</Type>
|
| 451 |
+
<Channel-Count>1</Channel-Count>
|
| 452 |
+
<Channel position="1">
|
| 453 |
+
<Source>Peripheral Blood Mononuclear Cells</Source>
|
| 454 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 455 |
+
<Characteristics tag="disease state">
|
| 456 |
+
Control
|
| 457 |
+
</Characteristics>
|
| 458 |
+
<Molecule>genomic DNA</Molecule>
|
| 459 |
+
<Extract-Protocol>
|
| 460 |
+
DNA was extracted from 200ul of PBMCs
|
| 461 |
+
MSPI digestion (purify), end repair (purify), A-tialing and adaptor ligation (purify), PCR amplification (purify), Gel size selection and gel extraction (purify)
|
| 462 |
+
</Extract-Protocol>
|
| 463 |
+
</Channel>
|
| 464 |
+
<Data-Processing>
|
| 465 |
+
reads were adaptor trimmed using bismark that used a file of adaptor sequences and trimmed three bases back from any detected adaptor to delete the C invorporated and rejecting any reads that were trimmed to less than 10bp
|
| 466 |
+
reads were aligned to the hg19 genome using bismark with the following specifications: a tolerance for one non-bisulfite mismatch per read, the default minimum alignment score (L,O, -02), and with ignore - quals in order to calculate the mismatch penalty by considering the quality value at the mismatched position to be the highest possible
|
| 467 |
+
bam files generated by Bismark alignment were then processed using DMAP to compare control vs. patients with the following specifications: ANOVA F test on fragments 40-220bp in length, with the fragment requireing at lest 2 CpGs to have 10 or more sequence reads. The differential methylation file was then annotated with protein coding gene information using the DMAP command identgeneloc. DMAPmatrix.csv file contains this data.
|
| 468 |
+
the bam files were additionally analysed following a MethylKit based pipeline where first the data was filtered for low read coverage (less than 10 times coverage) and normalised basde on mean coverage distribution before comparing pooled patient and control groups using a Fisher's test. Methmatrix.csv file contains this data
|
| 469 |
+
Genome_build: hg19
|
| 470 |
+
Supplementary_files_format_and_content: Individual .txt files for each sample containing C and T frequency per base and coverage. Matrix (csv file) containing methylation percentages for each sample used in the control vs patient analysis for the MethylKit single CpG pipeline.
|
| 471 |
+
Supplementary_files_format_and_content: A matrix containing the DMAP output data (individual sample percentages, significance values, associated genomic features, fragment length, CpG per fragment). .
|
| 472 |
+
</Data-Processing>
|
| 473 |
+
<Platform-Ref ref="GPL16791" />
|
| 474 |
+
<Library-Strategy>Bisulfite-Seq</Library-Strategy>
|
| 475 |
+
<Library-Source>genomic</Library-Source>
|
| 476 |
+
<Library-Selection>Reduced Representation</Library-Selection>
|
| 477 |
+
<Instrument-Model>
|
| 478 |
+
<Predefined>Illumina HiSeq 2500</Predefined>
|
| 479 |
+
</Instrument-Model>
|
| 480 |
+
<Contact-Ref ref="contrib1" />
|
| 481 |
+
<Supplementary-Data type="TXT">
|
| 482 |
+
ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4649nnn/GSM4649035/suppl/GSM4649035_Control9_CpG.txt.gz
|
| 483 |
+
</Supplementary-Data>
|
| 484 |
+
<Relation type="BioSample" target="https://www.ncbi.nlm.nih.gov/biosample/SAMN15420264" />
|
| 485 |
+
<Relation type="SRA" target="https://www.ncbi.nlm.nih.gov/sra?term=SRX8651468" />
|
| 486 |
+
</Sample>
|
| 487 |
+
|
| 488 |
+
<Sample iid="GSM4649036">
|
| 489 |
+
<Status database="GEO">
|
| 490 |
+
<Submission-Date>2020-07-01</Submission-Date>
|
| 491 |
+
<Release-Date>2020-07-02</Release-Date>
|
| 492 |
+
<Last-Update-Date>2020-07-02</Last-Update-Date>
|
| 493 |
+
</Status>
|
| 494 |
+
<Title>Control10</Title>
|
| 495 |
+
<Accession database="GEO">GSM4649036</Accession>
|
| 496 |
+
<Type>SRA</Type>
|
| 497 |
+
<Channel-Count>1</Channel-Count>
|
| 498 |
+
<Channel position="1">
|
| 499 |
+
<Source>Peripheral Blood Mononuclear Cells</Source>
|
| 500 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 501 |
+
<Characteristics tag="disease state">
|
| 502 |
+
Control
|
| 503 |
+
</Characteristics>
|
| 504 |
+
<Molecule>genomic DNA</Molecule>
|
| 505 |
+
<Extract-Protocol>
|
| 506 |
+
DNA was extracted from 200ul of PBMCs
|
| 507 |
+
MSPI digestion (purify), end repair (purify), A-tialing and adaptor ligation (purify), PCR amplification (purify), Gel size selection and gel extraction (purify)
|
| 508 |
+
</Extract-Protocol>
|
| 509 |
+
</Channel>
|
| 510 |
+
<Data-Processing>
|
| 511 |
+
reads were adaptor trimmed using bismark that used a file of adaptor sequences and trimmed three bases back from any detected adaptor to delete the C invorporated and rejecting any reads that were trimmed to less than 10bp
|
| 512 |
+
reads were aligned to the hg19 genome using bismark with the following specifications: a tolerance for one non-bisulfite mismatch per read, the default minimum alignment score (L,O, -02), and with ignore - quals in order to calculate the mismatch penalty by considering the quality value at the mismatched position to be the highest possible
|
| 513 |
+
bam files generated by Bismark alignment were then processed using DMAP to compare control vs. patients with the following specifications: ANOVA F test on fragments 40-220bp in length, with the fragment requireing at lest 2 CpGs to have 10 or more sequence reads. The differential methylation file was then annotated with protein coding gene information using the DMAP command identgeneloc. DMAPmatrix.csv file contains this data.
|
| 514 |
+
the bam files were additionally analysed following a MethylKit based pipeline where first the data was filtered for low read coverage (less than 10 times coverage) and normalised basde on mean coverage distribution before comparing pooled patient and control groups using a Fisher's test. Methmatrix.csv file contains this data
|
| 515 |
+
Genome_build: hg19
|
| 516 |
+
Supplementary_files_format_and_content: Individual .txt files for each sample containing C and T frequency per base and coverage. Matrix (csv file) containing methylation percentages for each sample used in the control vs patient analysis for the MethylKit single CpG pipeline.
|
| 517 |
+
Supplementary_files_format_and_content: A matrix containing the DMAP output data (individual sample percentages, significance values, associated genomic features, fragment length, CpG per fragment). .
|
| 518 |
+
</Data-Processing>
|
| 519 |
+
<Platform-Ref ref="GPL16791" />
|
| 520 |
+
<Library-Strategy>Bisulfite-Seq</Library-Strategy>
|
| 521 |
+
<Library-Source>genomic</Library-Source>
|
| 522 |
+
<Library-Selection>Reduced Representation</Library-Selection>
|
| 523 |
+
<Instrument-Model>
|
| 524 |
+
<Predefined>Illumina HiSeq 2500</Predefined>
|
| 525 |
+
</Instrument-Model>
|
| 526 |
+
<Contact-Ref ref="contrib1" />
|
| 527 |
+
<Supplementary-Data type="TXT">
|
| 528 |
+
ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4649nnn/GSM4649036/suppl/GSM4649036_Control10_CpG.txt.gz
|
| 529 |
+
</Supplementary-Data>
|
| 530 |
+
<Relation type="BioSample" target="https://www.ncbi.nlm.nih.gov/biosample/SAMN15420263" />
|
| 531 |
+
<Relation type="SRA" target="https://www.ncbi.nlm.nih.gov/sra?term=SRX8651469" />
|
| 532 |
+
</Sample>
|
| 533 |
+
|
| 534 |
+
<Sample iid="GSM4649037">
|
| 535 |
+
<Status database="GEO">
|
| 536 |
+
<Submission-Date>2020-07-01</Submission-Date>
|
| 537 |
+
<Release-Date>2020-07-02</Release-Date>
|
| 538 |
+
<Last-Update-Date>2020-07-02</Last-Update-Date>
|
| 539 |
+
</Status>
|
| 540 |
+
<Title>Patient1</Title>
|
| 541 |
+
<Accession database="GEO">GSM4649037</Accession>
|
| 542 |
+
<Type>SRA</Type>
|
| 543 |
+
<Channel-Count>1</Channel-Count>
|
| 544 |
+
<Channel position="1">
|
| 545 |
+
<Source>Peripheral Blood Mononuclear Cells</Source>
|
| 546 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 547 |
+
<Characteristics tag="disease state">
|
| 548 |
+
Patient
|
| 549 |
+
</Characteristics>
|
| 550 |
+
<Molecule>genomic DNA</Molecule>
|
| 551 |
+
<Extract-Protocol>
|
| 552 |
+
DNA was extracted from 200ul of PBMCs
|
| 553 |
+
MSPI digestion (purify), end repair (purify), A-tialing and adaptor ligation (purify), PCR amplification (purify), Gel size selection and gel extraction (purify)
|
| 554 |
+
</Extract-Protocol>
|
| 555 |
+
</Channel>
|
| 556 |
+
<Data-Processing>
|
| 557 |
+
reads were adaptor trimmed using bismark that used a file of adaptor sequences and trimmed three bases back from any detected adaptor to delete the C invorporated and rejecting any reads that were trimmed to less than 10bp
|
| 558 |
+
reads were aligned to the hg19 genome using bismark with the following specifications: a tolerance for one non-bisulfite mismatch per read, the default minimum alignment score (L,O, -02), and with ignore - quals in order to calculate the mismatch penalty by considering the quality value at the mismatched position to be the highest possible
|
| 559 |
+
bam files generated by Bismark alignment were then processed using DMAP to compare control vs. patients with the following specifications: ANOVA F test on fragments 40-220bp in length, with the fragment requireing at lest 2 CpGs to have 10 or more sequence reads. The differential methylation file was then annotated with protein coding gene information using the DMAP command identgeneloc. DMAPmatrix.csv file contains this data.
|
| 560 |
+
the bam files were additionally analysed following a MethylKit based pipeline where first the data was filtered for low read coverage (less than 10 times coverage) and normalised basde on mean coverage distribution before comparing pooled patient and control groups using a Fisher's test. Methmatrix.csv file contains this data
|
| 561 |
+
Genome_build: hg19
|
| 562 |
+
Supplementary_files_format_and_content: Individual .txt files for each sample containing C and T frequency per base and coverage. Matrix (csv file) containing methylation percentages for each sample used in the control vs patient analysis for the MethylKit single CpG pipeline.
|
| 563 |
+
Supplementary_files_format_and_content: A matrix containing the DMAP output data (individual sample percentages, significance values, associated genomic features, fragment length, CpG per fragment). .
|
| 564 |
+
</Data-Processing>
|
| 565 |
+
<Platform-Ref ref="GPL16791" />
|
| 566 |
+
<Library-Strategy>Bisulfite-Seq</Library-Strategy>
|
| 567 |
+
<Library-Source>genomic</Library-Source>
|
| 568 |
+
<Library-Selection>Reduced Representation</Library-Selection>
|
| 569 |
+
<Instrument-Model>
|
| 570 |
+
<Predefined>Illumina HiSeq 2500</Predefined>
|
| 571 |
+
</Instrument-Model>
|
| 572 |
+
<Contact-Ref ref="contrib1" />
|
| 573 |
+
<Supplementary-Data type="TXT">
|
| 574 |
+
ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4649nnn/GSM4649037/suppl/GSM4649037_Patient1_CpG.txt.gz
|
| 575 |
+
</Supplementary-Data>
|
| 576 |
+
<Relation type="BioSample" target="https://www.ncbi.nlm.nih.gov/biosample/SAMN15420262" />
|
| 577 |
+
<Relation type="SRA" target="https://www.ncbi.nlm.nih.gov/sra?term=SRX8651470" />
|
| 578 |
+
</Sample>
|
| 579 |
+
|
| 580 |
+
<Sample iid="GSM4649038">
|
| 581 |
+
<Status database="GEO">
|
| 582 |
+
<Submission-Date>2020-07-01</Submission-Date>
|
| 583 |
+
<Release-Date>2020-07-02</Release-Date>
|
| 584 |
+
<Last-Update-Date>2020-07-02</Last-Update-Date>
|
| 585 |
+
</Status>
|
| 586 |
+
<Title>Patient2</Title>
|
| 587 |
+
<Accession database="GEO">GSM4649038</Accession>
|
| 588 |
+
<Type>SRA</Type>
|
| 589 |
+
<Channel-Count>1</Channel-Count>
|
| 590 |
+
<Channel position="1">
|
| 591 |
+
<Source>Peripheral Blood Mononuclear Cells</Source>
|
| 592 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 593 |
+
<Characteristics tag="disease state">
|
| 594 |
+
Patient
|
| 595 |
+
</Characteristics>
|
| 596 |
+
<Molecule>genomic DNA</Molecule>
|
| 597 |
+
<Extract-Protocol>
|
| 598 |
+
DNA was extracted from 200ul of PBMCs
|
| 599 |
+
MSPI digestion (purify), end repair (purify), A-tialing and adaptor ligation (purify), PCR amplification (purify), Gel size selection and gel extraction (purify)
|
| 600 |
+
</Extract-Protocol>
|
| 601 |
+
</Channel>
|
| 602 |
+
<Data-Processing>
|
| 603 |
+
reads were adaptor trimmed using bismark that used a file of adaptor sequences and trimmed three bases back from any detected adaptor to delete the C invorporated and rejecting any reads that were trimmed to less than 10bp
|
| 604 |
+
reads were aligned to the hg19 genome using bismark with the following specifications: a tolerance for one non-bisulfite mismatch per read, the default minimum alignment score (L,O, -02), and with ignore - quals in order to calculate the mismatch penalty by considering the quality value at the mismatched position to be the highest possible
|
| 605 |
+
bam files generated by Bismark alignment were then processed using DMAP to compare control vs. patients with the following specifications: ANOVA F test on fragments 40-220bp in length, with the fragment requireing at lest 2 CpGs to have 10 or more sequence reads. The differential methylation file was then annotated with protein coding gene information using the DMAP command identgeneloc. DMAPmatrix.csv file contains this data.
|
| 606 |
+
the bam files were additionally analysed following a MethylKit based pipeline where first the data was filtered for low read coverage (less than 10 times coverage) and normalised basde on mean coverage distribution before comparing pooled patient and control groups using a Fisher's test. Methmatrix.csv file contains this data
|
| 607 |
+
Genome_build: hg19
|
| 608 |
+
Supplementary_files_format_and_content: Individual .txt files for each sample containing C and T frequency per base and coverage. Matrix (csv file) containing methylation percentages for each sample used in the control vs patient analysis for the MethylKit single CpG pipeline.
|
| 609 |
+
Supplementary_files_format_and_content: A matrix containing the DMAP output data (individual sample percentages, significance values, associated genomic features, fragment length, CpG per fragment). .
|
| 610 |
+
</Data-Processing>
|
| 611 |
+
<Platform-Ref ref="GPL16791" />
|
| 612 |
+
<Library-Strategy>Bisulfite-Seq</Library-Strategy>
|
| 613 |
+
<Library-Source>genomic</Library-Source>
|
| 614 |
+
<Library-Selection>Reduced Representation</Library-Selection>
|
| 615 |
+
<Instrument-Model>
|
| 616 |
+
<Predefined>Illumina HiSeq 2500</Predefined>
|
| 617 |
+
</Instrument-Model>
|
| 618 |
+
<Contact-Ref ref="contrib1" />
|
| 619 |
+
<Supplementary-Data type="TXT">
|
| 620 |
+
ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4649nnn/GSM4649038/suppl/GSM4649038_Patient2_CpG.txt.gz
|
| 621 |
+
</Supplementary-Data>
|
| 622 |
+
<Relation type="BioSample" target="https://www.ncbi.nlm.nih.gov/biosample/SAMN15420261" />
|
| 623 |
+
<Relation type="SRA" target="https://www.ncbi.nlm.nih.gov/sra?term=SRX8651471" />
|
| 624 |
+
</Sample>
|
| 625 |
+
|
| 626 |
+
<Sample iid="GSM4649039">
|
| 627 |
+
<Status database="GEO">
|
| 628 |
+
<Submission-Date>2020-07-01</Submission-Date>
|
| 629 |
+
<Release-Date>2020-07-02</Release-Date>
|
| 630 |
+
<Last-Update-Date>2020-07-02</Last-Update-Date>
|
| 631 |
+
</Status>
|
| 632 |
+
<Title>Patient3</Title>
|
| 633 |
+
<Accession database="GEO">GSM4649039</Accession>
|
| 634 |
+
<Type>SRA</Type>
|
| 635 |
+
<Channel-Count>1</Channel-Count>
|
| 636 |
+
<Channel position="1">
|
| 637 |
+
<Source>Peripheral Blood Mononuclear Cells</Source>
|
| 638 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 639 |
+
<Characteristics tag="disease state">
|
| 640 |
+
Patient
|
| 641 |
+
</Characteristics>
|
| 642 |
+
<Molecule>genomic DNA</Molecule>
|
| 643 |
+
<Extract-Protocol>
|
| 644 |
+
DNA was extracted from 200ul of PBMCs
|
| 645 |
+
MSPI digestion (purify), end repair (purify), A-tialing and adaptor ligation (purify), PCR amplification (purify), Gel size selection and gel extraction (purify)
|
| 646 |
+
</Extract-Protocol>
|
| 647 |
+
</Channel>
|
| 648 |
+
<Data-Processing>
|
| 649 |
+
reads were adaptor trimmed using bismark that used a file of adaptor sequences and trimmed three bases back from any detected adaptor to delete the C invorporated and rejecting any reads that were trimmed to less than 10bp
|
| 650 |
+
reads were aligned to the hg19 genome using bismark with the following specifications: a tolerance for one non-bisulfite mismatch per read, the default minimum alignment score (L,O, -02), and with ignore - quals in order to calculate the mismatch penalty by considering the quality value at the mismatched position to be the highest possible
|
| 651 |
+
bam files generated by Bismark alignment were then processed using DMAP to compare control vs. patients with the following specifications: ANOVA F test on fragments 40-220bp in length, with the fragment requireing at lest 2 CpGs to have 10 or more sequence reads. The differential methylation file was then annotated with protein coding gene information using the DMAP command identgeneloc. DMAPmatrix.csv file contains this data.
|
| 652 |
+
the bam files were additionally analysed following a MethylKit based pipeline where first the data was filtered for low read coverage (less than 10 times coverage) and normalised basde on mean coverage distribution before comparing pooled patient and control groups using a Fisher's test. Methmatrix.csv file contains this data
|
| 653 |
+
Genome_build: hg19
|
| 654 |
+
Supplementary_files_format_and_content: Individual .txt files for each sample containing C and T frequency per base and coverage. Matrix (csv file) containing methylation percentages for each sample used in the control vs patient analysis for the MethylKit single CpG pipeline.
|
| 655 |
+
Supplementary_files_format_and_content: A matrix containing the DMAP output data (individual sample percentages, significance values, associated genomic features, fragment length, CpG per fragment). .
|
| 656 |
+
</Data-Processing>
|
| 657 |
+
<Platform-Ref ref="GPL16791" />
|
| 658 |
+
<Library-Strategy>Bisulfite-Seq</Library-Strategy>
|
| 659 |
+
<Library-Source>genomic</Library-Source>
|
| 660 |
+
<Library-Selection>Reduced Representation</Library-Selection>
|
| 661 |
+
<Instrument-Model>
|
| 662 |
+
<Predefined>Illumina HiSeq 2500</Predefined>
|
| 663 |
+
</Instrument-Model>
|
| 664 |
+
<Contact-Ref ref="contrib1" />
|
| 665 |
+
<Supplementary-Data type="TXT">
|
| 666 |
+
ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4649nnn/GSM4649039/suppl/GSM4649039_Patient3_CpG.txt.gz
|
| 667 |
+
</Supplementary-Data>
|
| 668 |
+
<Relation type="BioSample" target="https://www.ncbi.nlm.nih.gov/biosample/SAMN15420260" />
|
| 669 |
+
<Relation type="SRA" target="https://www.ncbi.nlm.nih.gov/sra?term=SRX8651472" />
|
| 670 |
+
</Sample>
|
| 671 |
+
|
| 672 |
+
<Sample iid="GSM4649040">
|
| 673 |
+
<Status database="GEO">
|
| 674 |
+
<Submission-Date>2020-07-01</Submission-Date>
|
| 675 |
+
<Release-Date>2020-07-02</Release-Date>
|
| 676 |
+
<Last-Update-Date>2020-07-02</Last-Update-Date>
|
| 677 |
+
</Status>
|
| 678 |
+
<Title>Patient4</Title>
|
| 679 |
+
<Accession database="GEO">GSM4649040</Accession>
|
| 680 |
+
<Type>SRA</Type>
|
| 681 |
+
<Channel-Count>1</Channel-Count>
|
| 682 |
+
<Channel position="1">
|
| 683 |
+
<Source>Peripheral Blood Mononuclear Cells</Source>
|
| 684 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 685 |
+
<Characteristics tag="disease state">
|
| 686 |
+
Patient
|
| 687 |
+
</Characteristics>
|
| 688 |
+
<Molecule>genomic DNA</Molecule>
|
| 689 |
+
<Extract-Protocol>
|
| 690 |
+
DNA was extracted from 200ul of PBMCs
|
| 691 |
+
MSPI digestion (purify), end repair (purify), A-tialing and adaptor ligation (purify), PCR amplification (purify), Gel size selection and gel extraction (purify)
|
| 692 |
+
</Extract-Protocol>
|
| 693 |
+
</Channel>
|
| 694 |
+
<Data-Processing>
|
| 695 |
+
reads were adaptor trimmed using bismark that used a file of adaptor sequences and trimmed three bases back from any detected adaptor to delete the C invorporated and rejecting any reads that were trimmed to less than 10bp
|
| 696 |
+
reads were aligned to the hg19 genome using bismark with the following specifications: a tolerance for one non-bisulfite mismatch per read, the default minimum alignment score (L,O, -02), and with ignore - quals in order to calculate the mismatch penalty by considering the quality value at the mismatched position to be the highest possible
|
| 697 |
+
bam files generated by Bismark alignment were then processed using DMAP to compare control vs. patients with the following specifications: ANOVA F test on fragments 40-220bp in length, with the fragment requireing at lest 2 CpGs to have 10 or more sequence reads. The differential methylation file was then annotated with protein coding gene information using the DMAP command identgeneloc. DMAPmatrix.csv file contains this data.
|
| 698 |
+
the bam files were additionally analysed following a MethylKit based pipeline where first the data was filtered for low read coverage (less than 10 times coverage) and normalised basde on mean coverage distribution before comparing pooled patient and control groups using a Fisher's test. Methmatrix.csv file contains this data
|
| 699 |
+
Genome_build: hg19
|
| 700 |
+
Supplementary_files_format_and_content: Individual .txt files for each sample containing C and T frequency per base and coverage. Matrix (csv file) containing methylation percentages for each sample used in the control vs patient analysis for the MethylKit single CpG pipeline.
|
| 701 |
+
Supplementary_files_format_and_content: A matrix containing the DMAP output data (individual sample percentages, significance values, associated genomic features, fragment length, CpG per fragment). .
|
| 702 |
+
</Data-Processing>
|
| 703 |
+
<Platform-Ref ref="GPL16791" />
|
| 704 |
+
<Library-Strategy>Bisulfite-Seq</Library-Strategy>
|
| 705 |
+
<Library-Source>genomic</Library-Source>
|
| 706 |
+
<Library-Selection>Reduced Representation</Library-Selection>
|
| 707 |
+
<Instrument-Model>
|
| 708 |
+
<Predefined>Illumina HiSeq 2500</Predefined>
|
| 709 |
+
</Instrument-Model>
|
| 710 |
+
<Contact-Ref ref="contrib1" />
|
| 711 |
+
<Supplementary-Data type="TXT">
|
| 712 |
+
ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4649nnn/GSM4649040/suppl/GSM4649040_Patient4_CpG.txt.gz
|
| 713 |
+
</Supplementary-Data>
|
| 714 |
+
<Relation type="BioSample" target="https://www.ncbi.nlm.nih.gov/biosample/SAMN15420259" />
|
| 715 |
+
<Relation type="SRA" target="https://www.ncbi.nlm.nih.gov/sra?term=SRX8651473" />
|
| 716 |
+
</Sample>
|
| 717 |
+
|
| 718 |
+
<Sample iid="GSM4649041">
|
| 719 |
+
<Status database="GEO">
|
| 720 |
+
<Submission-Date>2020-07-01</Submission-Date>
|
| 721 |
+
<Release-Date>2020-07-02</Release-Date>
|
| 722 |
+
<Last-Update-Date>2020-07-02</Last-Update-Date>
|
| 723 |
+
</Status>
|
| 724 |
+
<Title>Patient5</Title>
|
| 725 |
+
<Accession database="GEO">GSM4649041</Accession>
|
| 726 |
+
<Type>SRA</Type>
|
| 727 |
+
<Channel-Count>1</Channel-Count>
|
| 728 |
+
<Channel position="1">
|
| 729 |
+
<Source>Peripheral Blood Mononuclear Cells</Source>
|
| 730 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 731 |
+
<Characteristics tag="disease state">
|
| 732 |
+
Patient
|
| 733 |
+
</Characteristics>
|
| 734 |
+
<Molecule>genomic DNA</Molecule>
|
| 735 |
+
<Extract-Protocol>
|
| 736 |
+
DNA was extracted from 200ul of PBMCs
|
| 737 |
+
MSPI digestion (purify), end repair (purify), A-tialing and adaptor ligation (purify), PCR amplification (purify), Gel size selection and gel extraction (purify)
|
| 738 |
+
</Extract-Protocol>
|
| 739 |
+
</Channel>
|
| 740 |
+
<Data-Processing>
|
| 741 |
+
reads were adaptor trimmed using bismark that used a file of adaptor sequences and trimmed three bases back from any detected adaptor to delete the C invorporated and rejecting any reads that were trimmed to less than 10bp
|
| 742 |
+
reads were aligned to the hg19 genome using bismark with the following specifications: a tolerance for one non-bisulfite mismatch per read, the default minimum alignment score (L,O, -02), and with ignore - quals in order to calculate the mismatch penalty by considering the quality value at the mismatched position to be the highest possible
|
| 743 |
+
bam files generated by Bismark alignment were then processed using DMAP to compare control vs. patients with the following specifications: ANOVA F test on fragments 40-220bp in length, with the fragment requireing at lest 2 CpGs to have 10 or more sequence reads. The differential methylation file was then annotated with protein coding gene information using the DMAP command identgeneloc. DMAPmatrix.csv file contains this data.
|
| 744 |
+
the bam files were additionally analysed following a MethylKit based pipeline where first the data was filtered for low read coverage (less than 10 times coverage) and normalised basde on mean coverage distribution before comparing pooled patient and control groups using a Fisher's test. Methmatrix.csv file contains this data
|
| 745 |
+
Genome_build: hg19
|
| 746 |
+
Supplementary_files_format_and_content: Individual .txt files for each sample containing C and T frequency per base and coverage. Matrix (csv file) containing methylation percentages for each sample used in the control vs patient analysis for the MethylKit single CpG pipeline.
|
| 747 |
+
Supplementary_files_format_and_content: A matrix containing the DMAP output data (individual sample percentages, significance values, associated genomic features, fragment length, CpG per fragment). .
|
| 748 |
+
</Data-Processing>
|
| 749 |
+
<Platform-Ref ref="GPL16791" />
|
| 750 |
+
<Library-Strategy>Bisulfite-Seq</Library-Strategy>
|
| 751 |
+
<Library-Source>genomic</Library-Source>
|
| 752 |
+
<Library-Selection>Reduced Representation</Library-Selection>
|
| 753 |
+
<Instrument-Model>
|
| 754 |
+
<Predefined>Illumina HiSeq 2500</Predefined>
|
| 755 |
+
</Instrument-Model>
|
| 756 |
+
<Contact-Ref ref="contrib1" />
|
| 757 |
+
<Supplementary-Data type="TXT">
|
| 758 |
+
ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4649nnn/GSM4649041/suppl/GSM4649041_Patient5_CpG.txt.gz
|
| 759 |
+
</Supplementary-Data>
|
| 760 |
+
<Relation type="BioSample" target="https://www.ncbi.nlm.nih.gov/biosample/SAMN15420258" />
|
| 761 |
+
<Relation type="SRA" target="https://www.ncbi.nlm.nih.gov/sra?term=SRX8651474" />
|
| 762 |
+
</Sample>
|
| 763 |
+
|
| 764 |
+
<Sample iid="GSM4649042">
|
| 765 |
+
<Status database="GEO">
|
| 766 |
+
<Submission-Date>2020-07-01</Submission-Date>
|
| 767 |
+
<Release-Date>2020-07-02</Release-Date>
|
| 768 |
+
<Last-Update-Date>2020-07-02</Last-Update-Date>
|
| 769 |
+
</Status>
|
| 770 |
+
<Title>Patient6</Title>
|
| 771 |
+
<Accession database="GEO">GSM4649042</Accession>
|
| 772 |
+
<Type>SRA</Type>
|
| 773 |
+
<Channel-Count>1</Channel-Count>
|
| 774 |
+
<Channel position="1">
|
| 775 |
+
<Source>Peripheral Blood Mononuclear Cells</Source>
|
| 776 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 777 |
+
<Characteristics tag="disease state">
|
| 778 |
+
Patient
|
| 779 |
+
</Characteristics>
|
| 780 |
+
<Molecule>genomic DNA</Molecule>
|
| 781 |
+
<Extract-Protocol>
|
| 782 |
+
DNA was extracted from 200ul of PBMCs
|
| 783 |
+
MSPI digestion (purify), end repair (purify), A-tialing and adaptor ligation (purify), PCR amplification (purify), Gel size selection and gel extraction (purify)
|
| 784 |
+
</Extract-Protocol>
|
| 785 |
+
</Channel>
|
| 786 |
+
<Data-Processing>
|
| 787 |
+
reads were adaptor trimmed using bismark that used a file of adaptor sequences and trimmed three bases back from any detected adaptor to delete the C invorporated and rejecting any reads that were trimmed to less than 10bp
|
| 788 |
+
reads were aligned to the hg19 genome using bismark with the following specifications: a tolerance for one non-bisulfite mismatch per read, the default minimum alignment score (L,O, -02), and with ignore - quals in order to calculate the mismatch penalty by considering the quality value at the mismatched position to be the highest possible
|
| 789 |
+
bam files generated by Bismark alignment were then processed using DMAP to compare control vs. patients with the following specifications: ANOVA F test on fragments 40-220bp in length, with the fragment requireing at lest 2 CpGs to have 10 or more sequence reads. The differential methylation file was then annotated with protein coding gene information using the DMAP command identgeneloc. DMAPmatrix.csv file contains this data.
|
| 790 |
+
the bam files were additionally analysed following a MethylKit based pipeline where first the data was filtered for low read coverage (less than 10 times coverage) and normalised basde on mean coverage distribution before comparing pooled patient and control groups using a Fisher's test. Methmatrix.csv file contains this data
|
| 791 |
+
Genome_build: hg19
|
| 792 |
+
Supplementary_files_format_and_content: Individual .txt files for each sample containing C and T frequency per base and coverage. Matrix (csv file) containing methylation percentages for each sample used in the control vs patient analysis for the MethylKit single CpG pipeline.
|
| 793 |
+
Supplementary_files_format_and_content: A matrix containing the DMAP output data (individual sample percentages, significance values, associated genomic features, fragment length, CpG per fragment). .
|
| 794 |
+
</Data-Processing>
|
| 795 |
+
<Platform-Ref ref="GPL16791" />
|
| 796 |
+
<Library-Strategy>Bisulfite-Seq</Library-Strategy>
|
| 797 |
+
<Library-Source>genomic</Library-Source>
|
| 798 |
+
<Library-Selection>Reduced Representation</Library-Selection>
|
| 799 |
+
<Instrument-Model>
|
| 800 |
+
<Predefined>Illumina HiSeq 2500</Predefined>
|
| 801 |
+
</Instrument-Model>
|
| 802 |
+
<Contact-Ref ref="contrib1" />
|
| 803 |
+
<Supplementary-Data type="TXT">
|
| 804 |
+
ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4649nnn/GSM4649042/suppl/GSM4649042_Patient6_CpG.txt.gz
|
| 805 |
+
</Supplementary-Data>
|
| 806 |
+
<Relation type="BioSample" target="https://www.ncbi.nlm.nih.gov/biosample/SAMN15420257" />
|
| 807 |
+
<Relation type="SRA" target="https://www.ncbi.nlm.nih.gov/sra?term=SRX8651475" />
|
| 808 |
+
</Sample>
|
| 809 |
+
|
| 810 |
+
<Sample iid="GSM4649043">
|
| 811 |
+
<Status database="GEO">
|
| 812 |
+
<Submission-Date>2020-07-01</Submission-Date>
|
| 813 |
+
<Release-Date>2020-07-02</Release-Date>
|
| 814 |
+
<Last-Update-Date>2020-07-02</Last-Update-Date>
|
| 815 |
+
</Status>
|
| 816 |
+
<Title>Patient7</Title>
|
| 817 |
+
<Accession database="GEO">GSM4649043</Accession>
|
| 818 |
+
<Type>SRA</Type>
|
| 819 |
+
<Channel-Count>1</Channel-Count>
|
| 820 |
+
<Channel position="1">
|
| 821 |
+
<Source>Peripheral Blood Mononuclear Cells</Source>
|
| 822 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 823 |
+
<Characteristics tag="disease state">
|
| 824 |
+
Patient
|
| 825 |
+
</Characteristics>
|
| 826 |
+
<Molecule>genomic DNA</Molecule>
|
| 827 |
+
<Extract-Protocol>
|
| 828 |
+
DNA was extracted from 200ul of PBMCs
|
| 829 |
+
MSPI digestion (purify), end repair (purify), A-tialing and adaptor ligation (purify), PCR amplification (purify), Gel size selection and gel extraction (purify)
|
| 830 |
+
</Extract-Protocol>
|
| 831 |
+
</Channel>
|
| 832 |
+
<Data-Processing>
|
| 833 |
+
reads were adaptor trimmed using bismark that used a file of adaptor sequences and trimmed three bases back from any detected adaptor to delete the C invorporated and rejecting any reads that were trimmed to less than 10bp
|
| 834 |
+
reads were aligned to the hg19 genome using bismark with the following specifications: a tolerance for one non-bisulfite mismatch per read, the default minimum alignment score (L,O, -02), and with ignore - quals in order to calculate the mismatch penalty by considering the quality value at the mismatched position to be the highest possible
|
| 835 |
+
bam files generated by Bismark alignment were then processed using DMAP to compare control vs. patients with the following specifications: ANOVA F test on fragments 40-220bp in length, with the fragment requireing at lest 2 CpGs to have 10 or more sequence reads. The differential methylation file was then annotated with protein coding gene information using the DMAP command identgeneloc. DMAPmatrix.csv file contains this data.
|
| 836 |
+
the bam files were additionally analysed following a MethylKit based pipeline where first the data was filtered for low read coverage (less than 10 times coverage) and normalised basde on mean coverage distribution before comparing pooled patient and control groups using a Fisher's test. Methmatrix.csv file contains this data
|
| 837 |
+
Genome_build: hg19
|
| 838 |
+
Supplementary_files_format_and_content: Individual .txt files for each sample containing C and T frequency per base and coverage. Matrix (csv file) containing methylation percentages for each sample used in the control vs patient analysis for the MethylKit single CpG pipeline.
|
| 839 |
+
Supplementary_files_format_and_content: A matrix containing the DMAP output data (individual sample percentages, significance values, associated genomic features, fragment length, CpG per fragment). .
|
| 840 |
+
</Data-Processing>
|
| 841 |
+
<Platform-Ref ref="GPL16791" />
|
| 842 |
+
<Library-Strategy>Bisulfite-Seq</Library-Strategy>
|
| 843 |
+
<Library-Source>genomic</Library-Source>
|
| 844 |
+
<Library-Selection>Reduced Representation</Library-Selection>
|
| 845 |
+
<Instrument-Model>
|
| 846 |
+
<Predefined>Illumina HiSeq 2500</Predefined>
|
| 847 |
+
</Instrument-Model>
|
| 848 |
+
<Contact-Ref ref="contrib1" />
|
| 849 |
+
<Supplementary-Data type="TXT">
|
| 850 |
+
ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4649nnn/GSM4649043/suppl/GSM4649043_Patient7_CpG.txt.gz
|
| 851 |
+
</Supplementary-Data>
|
| 852 |
+
<Relation type="BioSample" target="https://www.ncbi.nlm.nih.gov/biosample/SAMN15420256" />
|
| 853 |
+
<Relation type="SRA" target="https://www.ncbi.nlm.nih.gov/sra?term=SRX8651476" />
|
| 854 |
+
</Sample>
|
| 855 |
+
|
| 856 |
+
<Sample iid="GSM4649044">
|
| 857 |
+
<Status database="GEO">
|
| 858 |
+
<Submission-Date>2020-07-01</Submission-Date>
|
| 859 |
+
<Release-Date>2020-07-02</Release-Date>
|
| 860 |
+
<Last-Update-Date>2020-07-02</Last-Update-Date>
|
| 861 |
+
</Status>
|
| 862 |
+
<Title>Patient8</Title>
|
| 863 |
+
<Accession database="GEO">GSM4649044</Accession>
|
| 864 |
+
<Type>SRA</Type>
|
| 865 |
+
<Channel-Count>1</Channel-Count>
|
| 866 |
+
<Channel position="1">
|
| 867 |
+
<Source>Peripheral Blood Mononuclear Cells</Source>
|
| 868 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 869 |
+
<Characteristics tag="disease state">
|
| 870 |
+
Patient
|
| 871 |
+
</Characteristics>
|
| 872 |
+
<Molecule>genomic DNA</Molecule>
|
| 873 |
+
<Extract-Protocol>
|
| 874 |
+
DNA was extracted from 200ul of PBMCs
|
| 875 |
+
MSPI digestion (purify), end repair (purify), A-tialing and adaptor ligation (purify), PCR amplification (purify), Gel size selection and gel extraction (purify)
|
| 876 |
+
</Extract-Protocol>
|
| 877 |
+
</Channel>
|
| 878 |
+
<Data-Processing>
|
| 879 |
+
reads were adaptor trimmed using bismark that used a file of adaptor sequences and trimmed three bases back from any detected adaptor to delete the C invorporated and rejecting any reads that were trimmed to less than 10bp
|
| 880 |
+
reads were aligned to the hg19 genome using bismark with the following specifications: a tolerance for one non-bisulfite mismatch per read, the default minimum alignment score (L,O, -02), and with ignore - quals in order to calculate the mismatch penalty by considering the quality value at the mismatched position to be the highest possible
|
| 881 |
+
bam files generated by Bismark alignment were then processed using DMAP to compare control vs. patients with the following specifications: ANOVA F test on fragments 40-220bp in length, with the fragment requireing at lest 2 CpGs to have 10 or more sequence reads. The differential methylation file was then annotated with protein coding gene information using the DMAP command identgeneloc. DMAPmatrix.csv file contains this data.
|
| 882 |
+
the bam files were additionally analysed following a MethylKit based pipeline where first the data was filtered for low read coverage (less than 10 times coverage) and normalised basde on mean coverage distribution before comparing pooled patient and control groups using a Fisher's test. Methmatrix.csv file contains this data
|
| 883 |
+
Genome_build: hg19
|
| 884 |
+
Supplementary_files_format_and_content: Individual .txt files for each sample containing C and T frequency per base and coverage. Matrix (csv file) containing methylation percentages for each sample used in the control vs patient analysis for the MethylKit single CpG pipeline.
|
| 885 |
+
Supplementary_files_format_and_content: A matrix containing the DMAP output data (individual sample percentages, significance values, associated genomic features, fragment length, CpG per fragment). .
|
| 886 |
+
</Data-Processing>
|
| 887 |
+
<Platform-Ref ref="GPL16791" />
|
| 888 |
+
<Library-Strategy>Bisulfite-Seq</Library-Strategy>
|
| 889 |
+
<Library-Source>genomic</Library-Source>
|
| 890 |
+
<Library-Selection>Reduced Representation</Library-Selection>
|
| 891 |
+
<Instrument-Model>
|
| 892 |
+
<Predefined>Illumina HiSeq 2500</Predefined>
|
| 893 |
+
</Instrument-Model>
|
| 894 |
+
<Contact-Ref ref="contrib1" />
|
| 895 |
+
<Supplementary-Data type="TXT">
|
| 896 |
+
ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4649nnn/GSM4649044/suppl/GSM4649044_Patient8_CpG.txt.gz
|
| 897 |
+
</Supplementary-Data>
|
| 898 |
+
<Relation type="BioSample" target="https://www.ncbi.nlm.nih.gov/biosample/SAMN15420255" />
|
| 899 |
+
<Relation type="SRA" target="https://www.ncbi.nlm.nih.gov/sra?term=SRX8651477" />
|
| 900 |
+
</Sample>
|
| 901 |
+
|
| 902 |
+
<Sample iid="GSM4649045">
|
| 903 |
+
<Status database="GEO">
|
| 904 |
+
<Submission-Date>2020-07-01</Submission-Date>
|
| 905 |
+
<Release-Date>2020-07-02</Release-Date>
|
| 906 |
+
<Last-Update-Date>2020-07-02</Last-Update-Date>
|
| 907 |
+
</Status>
|
| 908 |
+
<Title>Patient9</Title>
|
| 909 |
+
<Accession database="GEO">GSM4649045</Accession>
|
| 910 |
+
<Type>SRA</Type>
|
| 911 |
+
<Channel-Count>1</Channel-Count>
|
| 912 |
+
<Channel position="1">
|
| 913 |
+
<Source>Peripheral Blood Mononuclear Cells</Source>
|
| 914 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 915 |
+
<Characteristics tag="disease state">
|
| 916 |
+
Patient
|
| 917 |
+
</Characteristics>
|
| 918 |
+
<Molecule>genomic DNA</Molecule>
|
| 919 |
+
<Extract-Protocol>
|
| 920 |
+
DNA was extracted from 200ul of PBMCs
|
| 921 |
+
MSPI digestion (purify), end repair (purify), A-tialing and adaptor ligation (purify), PCR amplification (purify), Gel size selection and gel extraction (purify)
|
| 922 |
+
</Extract-Protocol>
|
| 923 |
+
</Channel>
|
| 924 |
+
<Data-Processing>
|
| 925 |
+
reads were adaptor trimmed using bismark that used a file of adaptor sequences and trimmed three bases back from any detected adaptor to delete the C invorporated and rejecting any reads that were trimmed to less than 10bp
|
| 926 |
+
reads were aligned to the hg19 genome using bismark with the following specifications: a tolerance for one non-bisulfite mismatch per read, the default minimum alignment score (L,O, -02), and with ignore - quals in order to calculate the mismatch penalty by considering the quality value at the mismatched position to be the highest possible
|
| 927 |
+
bam files generated by Bismark alignment were then processed using DMAP to compare control vs. patients with the following specifications: ANOVA F test on fragments 40-220bp in length, with the fragment requireing at lest 2 CpGs to have 10 or more sequence reads. The differential methylation file was then annotated with protein coding gene information using the DMAP command identgeneloc. DMAPmatrix.csv file contains this data.
|
| 928 |
+
the bam files were additionally analysed following a MethylKit based pipeline where first the data was filtered for low read coverage (less than 10 times coverage) and normalised basde on mean coverage distribution before comparing pooled patient and control groups using a Fisher's test. Methmatrix.csv file contains this data
|
| 929 |
+
Genome_build: hg19
|
| 930 |
+
Supplementary_files_format_and_content: Individual .txt files for each sample containing C and T frequency per base and coverage. Matrix (csv file) containing methylation percentages for each sample used in the control vs patient analysis for the MethylKit single CpG pipeline.
|
| 931 |
+
Supplementary_files_format_and_content: A matrix containing the DMAP output data (individual sample percentages, significance values, associated genomic features, fragment length, CpG per fragment). .
|
| 932 |
+
</Data-Processing>
|
| 933 |
+
<Platform-Ref ref="GPL16791" />
|
| 934 |
+
<Library-Strategy>Bisulfite-Seq</Library-Strategy>
|
| 935 |
+
<Library-Source>genomic</Library-Source>
|
| 936 |
+
<Library-Selection>Reduced Representation</Library-Selection>
|
| 937 |
+
<Instrument-Model>
|
| 938 |
+
<Predefined>Illumina HiSeq 2500</Predefined>
|
| 939 |
+
</Instrument-Model>
|
| 940 |
+
<Contact-Ref ref="contrib1" />
|
| 941 |
+
<Supplementary-Data type="TXT">
|
| 942 |
+
ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4649nnn/GSM4649045/suppl/GSM4649045_Patient9_CpG.txt.gz
|
| 943 |
+
</Supplementary-Data>
|
| 944 |
+
<Relation type="BioSample" target="https://www.ncbi.nlm.nih.gov/biosample/SAMN15420254" />
|
| 945 |
+
<Relation type="SRA" target="https://www.ncbi.nlm.nih.gov/sra?term=SRX8651478" />
|
| 946 |
+
</Sample>
|
| 947 |
+
|
| 948 |
+
<Sample iid="GSM4649046">
|
| 949 |
+
<Status database="GEO">
|
| 950 |
+
<Submission-Date>2020-07-01</Submission-Date>
|
| 951 |
+
<Release-Date>2020-07-02</Release-Date>
|
| 952 |
+
<Last-Update-Date>2020-07-02</Last-Update-Date>
|
| 953 |
+
</Status>
|
| 954 |
+
<Title>Patient10</Title>
|
| 955 |
+
<Accession database="GEO">GSM4649046</Accession>
|
| 956 |
+
<Type>SRA</Type>
|
| 957 |
+
<Channel-Count>1</Channel-Count>
|
| 958 |
+
<Channel position="1">
|
| 959 |
+
<Source>Peripheral Blood Mononuclear Cells</Source>
|
| 960 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 961 |
+
<Characteristics tag="disease state">
|
| 962 |
+
Patient
|
| 963 |
+
</Characteristics>
|
| 964 |
+
<Molecule>genomic DNA</Molecule>
|
| 965 |
+
<Extract-Protocol>
|
| 966 |
+
DNA was extracted from 200ul of PBMCs
|
| 967 |
+
MSPI digestion (purify), end repair (purify), A-tialing and adaptor ligation (purify), PCR amplification (purify), Gel size selection and gel extraction (purify)
|
| 968 |
+
</Extract-Protocol>
|
| 969 |
+
</Channel>
|
| 970 |
+
<Data-Processing>
|
| 971 |
+
reads were adaptor trimmed using bismark that used a file of adaptor sequences and trimmed three bases back from any detected adaptor to delete the C invorporated and rejecting any reads that were trimmed to less than 10bp
|
| 972 |
+
reads were aligned to the hg19 genome using bismark with the following specifications: a tolerance for one non-bisulfite mismatch per read, the default minimum alignment score (L,O, -02), and with ignore - quals in order to calculate the mismatch penalty by considering the quality value at the mismatched position to be the highest possible
|
| 973 |
+
bam files generated by Bismark alignment were then processed using DMAP to compare control vs. patients with the following specifications: ANOVA F test on fragments 40-220bp in length, with the fragment requireing at lest 2 CpGs to have 10 or more sequence reads. The differential methylation file was then annotated with protein coding gene information using the DMAP command identgeneloc. DMAPmatrix.csv file contains this data.
|
| 974 |
+
the bam files were additionally analysed following a MethylKit based pipeline where first the data was filtered for low read coverage (less than 10 times coverage) and normalised basde on mean coverage distribution before comparing pooled patient and control groups using a Fisher's test. Methmatrix.csv file contains this data
|
| 975 |
+
Genome_build: hg19
|
| 976 |
+
Supplementary_files_format_and_content: Individual .txt files for each sample containing C and T frequency per base and coverage. Matrix (csv file) containing methylation percentages for each sample used in the control vs patient analysis for the MethylKit single CpG pipeline.
|
| 977 |
+
Supplementary_files_format_and_content: A matrix containing the DMAP output data (individual sample percentages, significance values, associated genomic features, fragment length, CpG per fragment). .
|
| 978 |
+
</Data-Processing>
|
| 979 |
+
<Platform-Ref ref="GPL16791" />
|
| 980 |
+
<Library-Strategy>Bisulfite-Seq</Library-Strategy>
|
| 981 |
+
<Library-Source>genomic</Library-Source>
|
| 982 |
+
<Library-Selection>Reduced Representation</Library-Selection>
|
| 983 |
+
<Instrument-Model>
|
| 984 |
+
<Predefined>Illumina HiSeq 2500</Predefined>
|
| 985 |
+
</Instrument-Model>
|
| 986 |
+
<Contact-Ref ref="contrib1" />
|
| 987 |
+
<Supplementary-Data type="TXT">
|
| 988 |
+
ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4649nnn/GSM4649046/suppl/GSM4649046_Patient10_CpG.txt.gz
|
| 989 |
+
</Supplementary-Data>
|
| 990 |
+
<Relation type="BioSample" target="https://www.ncbi.nlm.nih.gov/biosample/SAMN15420253" />
|
| 991 |
+
<Relation type="SRA" target="https://www.ncbi.nlm.nih.gov/sra?term=SRX8651479" />
|
| 992 |
+
</Sample>
|
| 993 |
+
|
| 994 |
+
<Series iid="GSE153667">
|
| 995 |
+
<Status database="GEO">
|
| 996 |
+
<Submission-Date>2020-07-01</Submission-Date>
|
| 997 |
+
<Release-Date>2020-07-02</Release-Date>
|
| 998 |
+
<Last-Update-Date>2020-11-09</Last-Update-Date>
|
| 999 |
+
</Status>
|
| 1000 |
+
<Title>Changes in the Epigenetic Landscape of Myalgic Encephalomyelitis/Chronic Fatigue Syndrome Reflect Systemic Dysfunctions</Title>
|
| 1001 |
+
<Accession database="GEO">GSE153667</Accession>
|
| 1002 |
+
<Pubmed-ID>33148325</Pubmed-ID>
|
| 1003 |
+
<Summary>
|
| 1004 |
+
Purpose: ME/CFS is a lifelong debilitating disease that affects approximately 1% of the global population. Previous studies have identified dysfunctional activity in metabolic, immune and neurological pathways. The goal of this study is to identify ME/CFS specific variations in DNA methylation to determine whether the patient specific epigenetic patterns provide insight into the disease pathophysiology.
|
| 1005 |
+
Methods: DNA was extracted from the PBMCs of 10 ME/CFS patients and age/gender matched controls. After performing RRBS the sequence was aligned to hg19 genome using Bismark. The data was analyzed using first an ANOVA F test through DMAP in order to determine variation between the patient and control groups across 40-220bp fragments of the genome. Additional analysis was performed following a MethylKit pipeline, which analyzed the variation on a single CpG basis using a Fishers test.
|
| 1006 |
+
Results: From a total of 146,575 DMAP fragments we identified 76 differentially methylated fragments (P <0.05, Diff meth +/- 15%). A total of 31 were associated with gene regions (intronic/exonic). MethylKit analysis also identified a total of 394 differentially methylated cytosines (FDR corrected P <0.05, Diff meth +/- 15%) from a total of 196,172 individual analyzed cytosines, 91 of the statistically significant cytosines fell within gene regions. Comparison of both methylomes and regions where both the DMAP fragments and multiple MethylKit cytosines fell highlighted areas of the genome containing regulatory elements associated with metabolic and immune activity. Gene body pathway enrichment additionally identified immune metabolic and neurological related functions.
|
| 1007 |
+
Conclusions: Our study represents the first investigation of ME/CFS patients using reduced representation bisulfite sequencing. We identified a number of major differences between patients that distinguished them from healthy controls. Our results identified a number of differentially methylated regulatory elements and gene bodies that highlight the disturbed pathophysiology in ME/CFS. In particular the large number of enriched neurotransmitter and neuropeptide reactome pathways highlighted a disturbed neurological pathophysiology in patients.
|
| 1008 |
+
</Summary>
|
| 1009 |
+
<Overall-Design>
|
| 1010 |
+
RRBS Analysis of 10 ME/CFS patients vs. Controls
|
| 1011 |
+
</Overall-Design>
|
| 1012 |
+
<Type>Methylation profiling by high throughput sequencing</Type>
|
| 1013 |
+
<Contributor-Ref ref="contrib1" position="1" />
|
| 1014 |
+
<Contributor-Ref ref="contrib3" position="2" />
|
| 1015 |
+
<Contributor-Ref ref="contrib4" position="3" />
|
| 1016 |
+
<Contributor-Ref ref="contrib5" position="4" />
|
| 1017 |
+
<Contributor-Ref ref="contrib6" position="5" />
|
| 1018 |
+
<Contributor-Ref ref="contrib7" position="6" />
|
| 1019 |
+
<Contact-Ref ref="contrib1" />
|
| 1020 |
+
<Sample-Ref ref="GSM4649027" />
|
| 1021 |
+
<Sample-Ref ref="GSM4649028" />
|
| 1022 |
+
<Sample-Ref ref="GSM4649029" />
|
| 1023 |
+
<Sample-Ref ref="GSM4649030" />
|
| 1024 |
+
<Sample-Ref ref="GSM4649031" />
|
| 1025 |
+
<Sample-Ref ref="GSM4649032" />
|
| 1026 |
+
<Sample-Ref ref="GSM4649033" />
|
| 1027 |
+
<Sample-Ref ref="GSM4649034" />
|
| 1028 |
+
<Sample-Ref ref="GSM4649035" />
|
| 1029 |
+
<Sample-Ref ref="GSM4649036" />
|
| 1030 |
+
<Sample-Ref ref="GSM4649037" />
|
| 1031 |
+
<Sample-Ref ref="GSM4649038" />
|
| 1032 |
+
<Sample-Ref ref="GSM4649039" />
|
| 1033 |
+
<Sample-Ref ref="GSM4649040" />
|
| 1034 |
+
<Sample-Ref ref="GSM4649041" />
|
| 1035 |
+
<Sample-Ref ref="GSM4649042" />
|
| 1036 |
+
<Sample-Ref ref="GSM4649043" />
|
| 1037 |
+
<Sample-Ref ref="GSM4649044" />
|
| 1038 |
+
<Sample-Ref ref="GSM4649045" />
|
| 1039 |
+
<Sample-Ref ref="GSM4649046" />
|
| 1040 |
+
<Supplementary-Data type="CSV">
|
| 1041 |
+
ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE153nnn/GSE153667/suppl/GSE153667_DMAP_matrix.csv.gz
|
| 1042 |
+
</Supplementary-Data>
|
| 1043 |
+
<Supplementary-Data type="XLSX">
|
| 1044 |
+
ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE153nnn/GSE153667/suppl/GSE153667_GeneMatrix.xlsx
|
| 1045 |
+
</Supplementary-Data>
|
| 1046 |
+
<Supplementary-Data type="CSV">
|
| 1047 |
+
ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE153nnn/GSE153667/suppl/GSE153667_Meth_Matrix.csv.gz
|
| 1048 |
+
</Supplementary-Data>
|
| 1049 |
+
<Supplementary-Data type="TAR">
|
| 1050 |
+
ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE153nnn/GSE153667/suppl/GSE153667_RAW.tar
|
| 1051 |
+
</Supplementary-Data>
|
| 1052 |
+
<Relation type="BioProject" target="https://www.ncbi.nlm.nih.gov/bioproject/PRJNA643579" />
|
| 1053 |
+
<Relation type="SRA" target="https://www.ncbi.nlm.nih.gov/sra?term=SRP269624" />
|
| 1054 |
+
</Series>
|
| 1055 |
+
|
| 1056 |
+
</MINiML>
|
ME/GSE153667/meta/GSE153667_series_matrix.txt
ADDED
|
@@ -0,0 +1,76 @@
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|
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|
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|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
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| 1 |
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!Series_title "Changes in the Epigenetic Landscape of Myalgic Encephalomyelitis/Chronic Fatigue Syndrome Reflect Systemic Dysfunctions"
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| 2 |
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!Series_geo_accession "GSE153667"
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| 3 |
+
!Series_status "Public on Jul 02 2020"
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| 4 |
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!Series_submission_date "Jul 01 2020"
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| 5 |
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!Series_last_update_date "Nov 09 2020"
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| 6 |
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!Series_pubmed_id "33148325"
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| 7 |
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!Series_summary "Purpose: ME/CFS is a lifelong debilitating disease that affects approximately 1% of the global population. Previous studies have identified dysfunctional activity in metabolic, immune and neurological pathways. The goal of this study is to identify ME/CFS specific variations in DNA methylation to determine whether the patient specific epigenetic patterns provide insight into the disease pathophysiology."
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| 8 |
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!Series_summary "Methods: DNA was extracted from the PBMCs of 10 ME/CFS patients and age/gender matched controls. After performing RRBS the sequence was aligned to hg19 genome using Bismark. The data was analyzed using first an ANOVA F test through DMAP in order to determine variation between the patient and control groups across 40-220bp fragments of the genome. Additional analysis was performed following a MethylKit pipeline, which analyzed the variation on a single CpG basis using a Fishers test."
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| 9 |
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!Series_summary "Results: From a total of 146,575 DMAP fragments we identified 76 differentially methylated fragments (P <0.05, Diff meth +/- 15%). A total of 31 were associated with gene regions (intronic/exonic). MethylKit analysis also identified a total of 394 differentially methylated cytosines (FDR corrected P <0.05, Diff meth +/- 15%) from a total of 196,172 individual analyzed cytosines, 91 of the statistically significant cytosines fell within gene regions. Comparison of both methylomes and regions where both the DMAP fragments and multiple MethylKit cytosines fell highlighted areas of the genome containing regulatory elements associated with metabolic and immune activity. Gene body pathway enrichment additionally identified immune metabolic and neurological related functions."
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| 10 |
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!Series_summary "Conclusions: Our study represents the first investigation of ME/CFS patients using reduced representation bisulfite sequencing. We identified a number of major differences between patients that distinguished them from healthy controls. Our results identified a number of differentially methylated regulatory elements and gene bodies that highlight the disturbed pathophysiology in ME/CFS. In particular the large number of enriched neurotransmitter and neuropeptide reactome pathways highlighted a disturbed neurological pathophysiology in patients."
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| 11 |
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!Series_overall_design "RRBS Analysis of 10 ME/CFS patients vs. Controls"
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| 12 |
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!Series_type "Methylation profiling by high throughput sequencing"
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| 13 |
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!Series_contributor "Amber,,Helliwell"
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| 14 |
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!Series_contributor "Warren,,Tate"
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| 15 |
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!Series_contributor "Aniruddha,,Chatterjee"
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| 16 |
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!Series_contributor "Peter,,Stockwell"
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| 17 |
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!Series_contributor "Eiren,,Sweetman"
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| 18 |
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!Series_contributor "Tina,,Edgar"
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| 19 |
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!Series_sample_id "GSM4649027 GSM4649028 GSM4649029 GSM4649030 GSM4649031 GSM4649032 GSM4649033 GSM4649034 GSM4649035 GSM4649036 GSM4649037 GSM4649038 GSM4649039 GSM4649040 GSM4649041 GSM4649042 GSM4649043 GSM4649044 GSM4649045 GSM4649046 "
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| 20 |
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!Series_contact_name "Amber,,Helliwell"
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| 21 |
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!Series_contact_department "Biochemistry Department"
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| 22 |
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!Series_contact_institute "University of Otago"
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| 23 |
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!Series_contact_address "710 Cumberland Road"
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| 24 |
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!Series_contact_city "Dunedin"
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| 25 |
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!Series_contact_zip/postal_code "9016"
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| 26 |
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!Series_contact_country "New Zealand"
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| 27 |
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!Series_supplementary_file "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE153nnn/GSE153667/suppl/GSE153667_DMAP_matrix.csv.gz"
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| 28 |
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!Series_supplementary_file "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE153nnn/GSE153667/suppl/GSE153667_GeneMatrix.xlsx"
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| 29 |
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!Series_supplementary_file "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE153nnn/GSE153667/suppl/GSE153667_Meth_Matrix.csv.gz"
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| 30 |
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!Series_supplementary_file "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE153nnn/GSE153667/suppl/GSE153667_RAW.tar"
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| 31 |
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!Series_platform_id "GPL16791"
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| 32 |
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!Series_platform_taxid "9606"
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| 33 |
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!Series_sample_taxid "9606"
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| 34 |
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!Series_relation "BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA643579"
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| 35 |
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!Series_relation "SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP269624"
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| 36 |
+
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| 37 |
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!Sample_title "Control1" "Control2" "Control3" "Control4" "Control5" "Control6" "Control7" "Control8" "Control9" "Control10" "Patient1" "Patient2" "Patient3" "Patient4" "Patient5" "Patient6" "Patient7" "Patient8" "Patient9" "Patient10"
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| 38 |
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!Sample_geo_accession "GSM4649027" "GSM4649028" "GSM4649029" "GSM4649030" "GSM4649031" "GSM4649032" "GSM4649033" "GSM4649034" "GSM4649035" "GSM4649036" "GSM4649037" "GSM4649038" "GSM4649039" "GSM4649040" "GSM4649041" "GSM4649042" "GSM4649043" "GSM4649044" "GSM4649045" "GSM4649046"
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| 39 |
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!Sample_status "Public on Jul 02 2020" "Public on Jul 02 2020" "Public on Jul 02 2020" "Public on Jul 02 2020" "Public on Jul 02 2020" "Public on Jul 02 2020" "Public on Jul 02 2020" "Public on Jul 02 2020" "Public on Jul 02 2020" "Public on Jul 02 2020" "Public on Jul 02 2020" "Public on Jul 02 2020" "Public on Jul 02 2020" "Public on Jul 02 2020" "Public on Jul 02 2020" "Public on Jul 02 2020" "Public on Jul 02 2020" "Public on Jul 02 2020" "Public on Jul 02 2020" "Public on Jul 02 2020"
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| 40 |
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!Sample_submission_date "Jul 01 2020" "Jul 01 2020" "Jul 01 2020" "Jul 01 2020" "Jul 01 2020" "Jul 01 2020" "Jul 01 2020" "Jul 01 2020" "Jul 01 2020" "Jul 01 2020" "Jul 01 2020" "Jul 01 2020" "Jul 01 2020" "Jul 01 2020" "Jul 01 2020" "Jul 01 2020" "Jul 01 2020" "Jul 01 2020" "Jul 01 2020" "Jul 01 2020"
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| 41 |
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!Sample_last_update_date "Jul 02 2020" "Jul 02 2020" "Jul 02 2020" "Jul 02 2020" "Jul 02 2020" "Jul 02 2020" "Jul 02 2020" "Jul 02 2020" "Jul 02 2020" "Jul 02 2020" "Jul 02 2020" "Jul 02 2020" "Jul 02 2020" "Jul 02 2020" "Jul 02 2020" "Jul 02 2020" "Jul 02 2020" "Jul 02 2020" "Jul 02 2020" "Jul 02 2020"
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| 42 |
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!Sample_type "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "SRA"
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| 43 |
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!Sample_channel_count "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1"
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| 44 |
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!Sample_source_name_ch1 "Peripheral Blood Mononuclear Cells" "Peripheral Blood Mononuclear Cells" "Peripheral Blood Mononuclear Cells" "Peripheral Blood Mononuclear Cells" "Peripheral Blood Mononuclear Cells" "Peripheral Blood Mononuclear Cells" "Peripheral Blood Mononuclear Cells" "Peripheral Blood Mononuclear Cells" "Peripheral Blood Mononuclear Cells" "Peripheral Blood Mononuclear Cells" "Peripheral Blood Mononuclear Cells" "Peripheral Blood Mononuclear Cells" "Peripheral Blood Mononuclear Cells" "Peripheral Blood Mononuclear Cells" "Peripheral Blood Mononuclear Cells" "Peripheral Blood Mononuclear Cells" "Peripheral Blood Mononuclear Cells" "Peripheral Blood Mononuclear Cells" "Peripheral Blood Mononuclear Cells" "Peripheral Blood Mononuclear Cells"
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| 45 |
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!Sample_organism_ch1 "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens"
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| 46 |
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!Sample_characteristics_ch1 "disease state: Control" "disease state: Control" "disease state: Control" "disease state: Control" "disease state: Control" "disease state: Control" "disease state: Control" "disease state: Control" "disease state: Control" "disease state: Control" "disease state: Patient" "disease state: Patient" "disease state: Patient" "disease state: Patient" "disease state: Patient" "disease state: Patient" "disease state: Patient" "disease state: Patient" "disease state: Patient" "disease state: Patient"
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| 47 |
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!Sample_molecule_ch1 "genomic DNA" "genomic DNA" "genomic DNA" "genomic DNA" "genomic DNA" "genomic DNA" "genomic DNA" "genomic DNA" "genomic DNA" "genomic DNA" "genomic DNA" "genomic DNA" "genomic DNA" "genomic DNA" "genomic DNA" "genomic DNA" "genomic DNA" "genomic DNA" "genomic DNA" "genomic DNA"
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| 48 |
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!Sample_extract_protocol_ch1 "DNA was extracted from 200ul of PBMCs" "DNA was extracted from 200ul of PBMCs" "DNA was extracted from 200ul of PBMCs" "DNA was extracted from 200ul of PBMCs" "DNA was extracted from 200ul of PBMCs" "DNA was extracted from 200ul of PBMCs" "DNA was extracted from 200ul of PBMCs" "DNA was extracted from 200ul of PBMCs" "DNA was extracted from 200ul of PBMCs" "DNA was extracted from 200ul of PBMCs" "DNA was extracted from 200ul of PBMCs" "DNA was extracted from 200ul of PBMCs" "DNA was extracted from 200ul of PBMCs" "DNA was extracted from 200ul of PBMCs" "DNA was extracted from 200ul of PBMCs" "DNA was extracted from 200ul of PBMCs" "DNA was extracted from 200ul of PBMCs" "DNA was extracted from 200ul of PBMCs" "DNA was extracted from 200ul of PBMCs" "DNA was extracted from 200ul of PBMCs"
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| 49 |
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!Sample_extract_protocol_ch1 "MSPI digestion (purify), end repair (purify), A-tialing and adaptor ligation (purify), PCR amplification (purify), Gel size selection and gel extraction (purify)" "MSPI digestion (purify), end repair (purify), A-tialing and adaptor ligation (purify), PCR amplification (purify), Gel size selection and gel extraction (purify)" "MSPI digestion (purify), end repair (purify), A-tialing and adaptor ligation (purify), PCR amplification (purify), Gel size selection and gel extraction (purify)" "MSPI digestion (purify), end repair (purify), A-tialing and adaptor ligation (purify), PCR amplification (purify), Gel size selection and gel extraction (purify)" "MSPI digestion (purify), end repair (purify), A-tialing and adaptor ligation (purify), PCR amplification (purify), Gel size selection and gel extraction (purify)" "MSPI digestion (purify), end repair (purify), A-tialing and adaptor ligation (purify), PCR amplification (purify), Gel size selection and gel extraction (purify)" "MSPI digestion (purify), end repair (purify), A-tialing and adaptor ligation (purify), PCR amplification (purify), Gel size selection and gel extraction (purify)" "MSPI digestion (purify), end repair (purify), A-tialing and adaptor ligation (purify), PCR amplification (purify), Gel size selection and gel extraction (purify)" "MSPI digestion (purify), end repair (purify), A-tialing and adaptor ligation (purify), PCR amplification (purify), Gel size selection and gel extraction (purify)" "MSPI digestion (purify), end repair (purify), A-tialing and adaptor ligation (purify), PCR amplification (purify), Gel size selection and gel extraction (purify)" "MSPI digestion (purify), end repair (purify), A-tialing and adaptor ligation (purify), PCR amplification (purify), Gel size selection and gel extraction (purify)" "MSPI digestion (purify), end repair (purify), A-tialing and adaptor ligation (purify), PCR amplification (purify), Gel size selection and gel extraction (purify)" "MSPI digestion (purify), end repair (purify), A-tialing and adaptor ligation (purify), PCR amplification (purify), Gel size selection and gel extraction (purify)" "MSPI digestion (purify), end repair (purify), A-tialing and adaptor ligation (purify), PCR amplification (purify), Gel size selection and gel extraction (purify)" "MSPI digestion (purify), end repair (purify), A-tialing and adaptor ligation (purify), PCR amplification (purify), Gel size selection and gel extraction (purify)" "MSPI digestion (purify), end repair (purify), A-tialing and adaptor ligation (purify), PCR amplification (purify), Gel size selection and gel extraction (purify)" "MSPI digestion (purify), end repair (purify), A-tialing and adaptor ligation (purify), PCR amplification (purify), Gel size selection and gel extraction (purify)" "MSPI digestion (purify), end repair (purify), A-tialing and adaptor ligation (purify), PCR amplification (purify), Gel size selection and gel extraction (purify)" "MSPI digestion (purify), end repair (purify), A-tialing and adaptor ligation (purify), PCR amplification (purify), Gel size selection and gel extraction (purify)" "MSPI digestion (purify), end repair (purify), A-tialing and adaptor ligation (purify), PCR amplification (purify), Gel size selection and gel extraction (purify)"
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| 50 |
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!Sample_taxid_ch1 "9606" "9606" "9606" "9606" "9606" "9606" "9606" "9606" "9606" "9606" "9606" "9606" "9606" "9606" "9606" "9606" "9606" "9606" "9606" "9606"
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| 51 |
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!Sample_data_processing "reads were adaptor trimmed using bismark that used a file of adaptor sequences and trimmed three bases back from any detected adaptor to delete the C invorporated and rejecting any reads that were trimmed to less than 10bp" "reads were adaptor trimmed using bismark that used a file of adaptor sequences and trimmed three bases back from any detected adaptor to delete the C invorporated and rejecting any reads that were trimmed to less than 10bp" "reads were adaptor trimmed using bismark that used a file of adaptor sequences and trimmed three bases back from any detected adaptor to delete the C invorporated and rejecting any reads that were trimmed to less than 10bp" "reads were adaptor trimmed using bismark that used a file of adaptor sequences and trimmed three bases back from any detected adaptor to delete the C invorporated and rejecting any reads that were trimmed to less than 10bp" "reads were adaptor trimmed using bismark that used a file of adaptor sequences and trimmed three bases back from any detected adaptor to delete the C invorporated and rejecting any reads that were trimmed to less than 10bp" "reads were adaptor trimmed using bismark that used a file of adaptor sequences and trimmed three bases back from any detected adaptor to delete the C invorporated and rejecting any reads that were trimmed to less than 10bp" "reads were adaptor trimmed using bismark that used a file of adaptor sequences and trimmed three bases back from any detected adaptor to delete the C invorporated and rejecting any reads that were trimmed to less than 10bp" "reads were adaptor trimmed using bismark that used a file of adaptor sequences and trimmed three bases back from any detected adaptor to delete the C invorporated and rejecting any reads that were trimmed to less than 10bp" "reads were adaptor trimmed using bismark that used a file of adaptor sequences and trimmed three bases back from any detected adaptor to delete the C invorporated and rejecting any reads that were trimmed to less than 10bp" "reads were adaptor trimmed using bismark that used a file of adaptor sequences and trimmed three bases back from any detected adaptor to delete the C invorporated and rejecting any reads that were trimmed to less than 10bp" "reads were adaptor trimmed using bismark that used a file of adaptor sequences and trimmed three bases back from any detected adaptor to delete the C invorporated and rejecting any reads that were trimmed to less than 10bp" "reads were adaptor trimmed using bismark that used a file of adaptor sequences and trimmed three bases back from any detected adaptor to delete the C invorporated and rejecting any reads that were trimmed to less than 10bp" "reads were adaptor trimmed using bismark that used a file of adaptor sequences and trimmed three bases back from any detected adaptor to delete the C invorporated and rejecting any reads that were trimmed to less than 10bp" "reads were adaptor trimmed using bismark that used a file of adaptor sequences and trimmed three bases back from any detected adaptor to delete the C invorporated and rejecting any reads that were trimmed to less than 10bp" "reads were adaptor trimmed using bismark that used a file of adaptor sequences and trimmed three bases back from any detected adaptor to delete the C invorporated and rejecting any reads that were trimmed to less than 10bp" "reads were adaptor trimmed using bismark that used a file of adaptor sequences and trimmed three bases back from any detected adaptor to delete the C invorporated and rejecting any reads that were trimmed to less than 10bp" "reads were adaptor trimmed using bismark that used a file of adaptor sequences and trimmed three bases back from any detected adaptor to delete the C invorporated and rejecting any reads that were trimmed to less than 10bp" "reads were adaptor trimmed using bismark that used a file of adaptor sequences and trimmed three bases back from any detected adaptor to delete the C invorporated and rejecting any reads that were trimmed to less than 10bp" "reads were adaptor trimmed using bismark that used a file of adaptor sequences and trimmed three bases back from any detected adaptor to delete the C invorporated and rejecting any reads that were trimmed to less than 10bp" "reads were adaptor trimmed using bismark that used a file of adaptor sequences and trimmed three bases back from any detected adaptor to delete the C invorporated and rejecting any reads that were trimmed to less than 10bp"
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| 52 |
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!Sample_data_processing "reads were aligned to the hg19 genome using bismark with the following specifications: a tolerance for one non-bisulfite mismatch per read, the default minimum alignment score (L,O, -02), and with ignore - quals in order to calculate the mismatch penalty by considering the quality value at the mismatched position to be the highest possible" "reads were aligned to the hg19 genome using bismark with the following specifications: a tolerance for one non-bisulfite mismatch per read, the default minimum alignment score (L,O, -02), and with ignore - quals in order to calculate the mismatch penalty by considering the quality value at the mismatched position to be the highest possible" "reads were aligned to the hg19 genome using bismark with the following specifications: a tolerance for one non-bisulfite mismatch per read, the default minimum alignment score (L,O, -02), and with ignore - quals in order to calculate the mismatch penalty by considering the quality value at the mismatched position to be the highest possible" "reads were aligned to the hg19 genome using bismark with the following specifications: a tolerance for one non-bisulfite mismatch per read, the default minimum alignment score (L,O, -02), and with ignore - quals in order to calculate the mismatch penalty by considering the quality value at the mismatched position to be the highest possible" "reads were aligned to the hg19 genome using bismark with the following specifications: a tolerance for one non-bisulfite mismatch per read, the default minimum alignment score (L,O, -02), and with ignore - quals in order to calculate the mismatch penalty by considering the quality value at the mismatched position to be the highest possible" "reads were aligned to the hg19 genome using bismark with the following specifications: a tolerance for one non-bisulfite mismatch per read, the default minimum alignment score (L,O, -02), and with ignore - quals in order to calculate the mismatch penalty by considering the quality value at the mismatched position to be the highest possible" "reads were aligned to the hg19 genome using bismark with the following specifications: a tolerance for one non-bisulfite mismatch per read, the default minimum alignment score (L,O, -02), and with ignore - quals in order to calculate the mismatch penalty by considering the quality value at the mismatched position to be the highest possible" "reads were aligned to the hg19 genome using bismark with the following specifications: a tolerance for one non-bisulfite mismatch per read, the default minimum alignment score (L,O, -02), and with ignore - quals in order to calculate the mismatch penalty by considering the quality value at the mismatched position to be the highest possible" "reads were aligned to the hg19 genome using bismark with the following specifications: a tolerance for one non-bisulfite mismatch per read, the default minimum alignment score (L,O, -02), and with ignore - quals in order to calculate the mismatch penalty by considering the quality value at the mismatched position to be the highest possible" "reads were aligned to the hg19 genome using bismark with the following specifications: a tolerance for one non-bisulfite mismatch per read, the default minimum alignment score (L,O, -02), and with ignore - quals in order to calculate the mismatch penalty by considering the quality value at the mismatched position to be the highest possible" "reads were aligned to the hg19 genome using bismark with the following specifications: a tolerance for one non-bisulfite mismatch per read, the default minimum alignment score (L,O, -02), and with ignore - quals in order to calculate the mismatch penalty by considering the quality value at the mismatched position to be the highest possible" "reads were aligned to the hg19 genome using bismark with the following specifications: a tolerance for one non-bisulfite mismatch per read, the default minimum alignment score (L,O, -02), and with ignore - quals in order to calculate the mismatch penalty by considering the quality value at the mismatched position to be the highest possible" "reads were aligned to the hg19 genome using bismark with the following specifications: a tolerance for one non-bisulfite mismatch per read, the default minimum alignment score (L,O, -02), and with ignore - quals in order to calculate the mismatch penalty by considering the quality value at the mismatched position to be the highest possible" "reads were aligned to the hg19 genome using bismark with the following specifications: a tolerance for one non-bisulfite mismatch per read, the default minimum alignment score (L,O, -02), and with ignore - quals in order to calculate the mismatch penalty by considering the quality value at the mismatched position to be the highest possible" "reads were aligned to the hg19 genome using bismark with the following specifications: a tolerance for one non-bisulfite mismatch per read, the default minimum alignment score (L,O, -02), and with ignore - quals in order to calculate the mismatch penalty by considering the quality value at the mismatched position to be the highest possible" "reads were aligned to the hg19 genome using bismark with the following specifications: a tolerance for one non-bisulfite mismatch per read, the default minimum alignment score (L,O, -02), and with ignore - quals in order to calculate the mismatch penalty by considering the quality value at the mismatched position to be the highest possible" "reads were aligned to the hg19 genome using bismark with the following specifications: a tolerance for one non-bisulfite mismatch per read, the default minimum alignment score (L,O, -02), and with ignore - quals in order to calculate the mismatch penalty by considering the quality value at the mismatched position to be the highest possible" "reads were aligned to the hg19 genome using bismark with the following specifications: a tolerance for one non-bisulfite mismatch per read, the default minimum alignment score (L,O, -02), and with ignore - quals in order to calculate the mismatch penalty by considering the quality value at the mismatched position to be the highest possible" "reads were aligned to the hg19 genome using bismark with the following specifications: a tolerance for one non-bisulfite mismatch per read, the default minimum alignment score (L,O, -02), and with ignore - quals in order to calculate the mismatch penalty by considering the quality value at the mismatched position to be the highest possible" "reads were aligned to the hg19 genome using bismark with the following specifications: a tolerance for one non-bisulfite mismatch per read, the default minimum alignment score (L,O, -02), and with ignore - quals in order to calculate the mismatch penalty by considering the quality value at the mismatched position to be the highest possible"
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| 53 |
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!Sample_data_processing "bam files generated by Bismark alignment were then processed using DMAP to compare control vs. patients with the following specifications: ANOVA F test on fragments 40-220bp in length, with the fragment requireing at lest 2 CpGs to have 10 or more sequence reads. The differential methylation file was then annotated with protein coding gene information using the DMAP command identgeneloc. DMAPmatrix.csv file contains this data." "bam files generated by Bismark alignment were then processed using DMAP to compare control vs. patients with the following specifications: ANOVA F test on fragments 40-220bp in length, with the fragment requireing at lest 2 CpGs to have 10 or more sequence reads. The differential methylation file was then annotated with protein coding gene information using the DMAP command identgeneloc. DMAPmatrix.csv file contains this data." "bam files generated by Bismark alignment were then processed using DMAP to compare control vs. patients with the following specifications: ANOVA F test on fragments 40-220bp in length, with the fragment requireing at lest 2 CpGs to have 10 or more sequence reads. The differential methylation file was then annotated with protein coding gene information using the DMAP command identgeneloc. DMAPmatrix.csv file contains this data." "bam files generated by Bismark alignment were then processed using DMAP to compare control vs. patients with the following specifications: ANOVA F test on fragments 40-220bp in length, with the fragment requireing at lest 2 CpGs to have 10 or more sequence reads. The differential methylation file was then annotated with protein coding gene information using the DMAP command identgeneloc. DMAPmatrix.csv file contains this data." "bam files generated by Bismark alignment were then processed using DMAP to compare control vs. patients with the following specifications: ANOVA F test on fragments 40-220bp in length, with the fragment requireing at lest 2 CpGs to have 10 or more sequence reads. The differential methylation file was then annotated with protein coding gene information using the DMAP command identgeneloc. DMAPmatrix.csv file contains this data." "bam files generated by Bismark alignment were then processed using DMAP to compare control vs. patients with the following specifications: ANOVA F test on fragments 40-220bp in length, with the fragment requireing at lest 2 CpGs to have 10 or more sequence reads. The differential methylation file was then annotated with protein coding gene information using the DMAP command identgeneloc. DMAPmatrix.csv file contains this data." "bam files generated by Bismark alignment were then processed using DMAP to compare control vs. patients with the following specifications: ANOVA F test on fragments 40-220bp in length, with the fragment requireing at lest 2 CpGs to have 10 or more sequence reads. The differential methylation file was then annotated with protein coding gene information using the DMAP command identgeneloc. DMAPmatrix.csv file contains this data." "bam files generated by Bismark alignment were then processed using DMAP to compare control vs. patients with the following specifications: ANOVA F test on fragments 40-220bp in length, with the fragment requireing at lest 2 CpGs to have 10 or more sequence reads. The differential methylation file was then annotated with protein coding gene information using the DMAP command identgeneloc. DMAPmatrix.csv file contains this data." "bam files generated by Bismark alignment were then processed using DMAP to compare control vs. patients with the following specifications: ANOVA F test on fragments 40-220bp in length, with the fragment requireing at lest 2 CpGs to have 10 or more sequence reads. The differential methylation file was then annotated with protein coding gene information using the DMAP command identgeneloc. DMAPmatrix.csv file contains this data." "bam files generated by Bismark alignment were then processed using DMAP to compare control vs. patients with the following specifications: ANOVA F test on fragments 40-220bp in length, with the fragment requireing at lest 2 CpGs to have 10 or more sequence reads. The differential methylation file was then annotated with protein coding gene information using the DMAP command identgeneloc. DMAPmatrix.csv file contains this data." "bam files generated by Bismark alignment were then processed using DMAP to compare control vs. patients with the following specifications: ANOVA F test on fragments 40-220bp in length, with the fragment requireing at lest 2 CpGs to have 10 or more sequence reads. The differential methylation file was then annotated with protein coding gene information using the DMAP command identgeneloc. DMAPmatrix.csv file contains this data." "bam files generated by Bismark alignment were then processed using DMAP to compare control vs. patients with the following specifications: ANOVA F test on fragments 40-220bp in length, with the fragment requireing at lest 2 CpGs to have 10 or more sequence reads. The differential methylation file was then annotated with protein coding gene information using the DMAP command identgeneloc. DMAPmatrix.csv file contains this data." "bam files generated by Bismark alignment were then processed using DMAP to compare control vs. patients with the following specifications: ANOVA F test on fragments 40-220bp in length, with the fragment requireing at lest 2 CpGs to have 10 or more sequence reads. The differential methylation file was then annotated with protein coding gene information using the DMAP command identgeneloc. DMAPmatrix.csv file contains this data." "bam files generated by Bismark alignment were then processed using DMAP to compare control vs. patients with the following specifications: ANOVA F test on fragments 40-220bp in length, with the fragment requireing at lest 2 CpGs to have 10 or more sequence reads. The differential methylation file was then annotated with protein coding gene information using the DMAP command identgeneloc. DMAPmatrix.csv file contains this data." "bam files generated by Bismark alignment were then processed using DMAP to compare control vs. patients with the following specifications: ANOVA F test on fragments 40-220bp in length, with the fragment requireing at lest 2 CpGs to have 10 or more sequence reads. The differential methylation file was then annotated with protein coding gene information using the DMAP command identgeneloc. DMAPmatrix.csv file contains this data." "bam files generated by Bismark alignment were then processed using DMAP to compare control vs. patients with the following specifications: ANOVA F test on fragments 40-220bp in length, with the fragment requireing at lest 2 CpGs to have 10 or more sequence reads. The differential methylation file was then annotated with protein coding gene information using the DMAP command identgeneloc. DMAPmatrix.csv file contains this data." "bam files generated by Bismark alignment were then processed using DMAP to compare control vs. patients with the following specifications: ANOVA F test on fragments 40-220bp in length, with the fragment requireing at lest 2 CpGs to have 10 or more sequence reads. The differential methylation file was then annotated with protein coding gene information using the DMAP command identgeneloc. DMAPmatrix.csv file contains this data." "bam files generated by Bismark alignment were then processed using DMAP to compare control vs. patients with the following specifications: ANOVA F test on fragments 40-220bp in length, with the fragment requireing at lest 2 CpGs to have 10 or more sequence reads. The differential methylation file was then annotated with protein coding gene information using the DMAP command identgeneloc. DMAPmatrix.csv file contains this data." "bam files generated by Bismark alignment were then processed using DMAP to compare control vs. patients with the following specifications: ANOVA F test on fragments 40-220bp in length, with the fragment requireing at lest 2 CpGs to have 10 or more sequence reads. The differential methylation file was then annotated with protein coding gene information using the DMAP command identgeneloc. DMAPmatrix.csv file contains this data." "bam files generated by Bismark alignment were then processed using DMAP to compare control vs. patients with the following specifications: ANOVA F test on fragments 40-220bp in length, with the fragment requireing at lest 2 CpGs to have 10 or more sequence reads. The differential methylation file was then annotated with protein coding gene information using the DMAP command identgeneloc. DMAPmatrix.csv file contains this data."
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+
!Sample_data_processing "the bam files were additionally analysed following a MethylKit based pipeline where first the data was filtered for low read coverage (less than 10 times coverage) and normalised basde on mean coverage distribution before comparing pooled patient and control groups using a Fisher's test. Methmatrix.csv file contains this data" "the bam files were additionally analysed following a MethylKit based pipeline where first the data was filtered for low read coverage (less than 10 times coverage) and normalised basde on mean coverage distribution before comparing pooled patient and control groups using a Fisher's test. Methmatrix.csv file contains this data" "the bam files were additionally analysed following a MethylKit based pipeline where first the data was filtered for low read coverage (less than 10 times coverage) and normalised basde on mean coverage distribution before comparing pooled patient and control groups using a Fisher's test. Methmatrix.csv file contains this data" "the bam files were additionally analysed following a MethylKit based pipeline where first the data was filtered for low read coverage (less than 10 times coverage) and normalised basde on mean coverage distribution before comparing pooled patient and control groups using a Fisher's test. Methmatrix.csv file contains this data" "the bam files were additionally analysed following a MethylKit based pipeline where first the data was filtered for low read coverage (less than 10 times coverage) and normalised basde on mean coverage distribution before comparing pooled patient and control groups using a Fisher's test. Methmatrix.csv file contains this data" "the bam files were additionally analysed following a MethylKit based pipeline where first the data was filtered for low read coverage (less than 10 times coverage) and normalised basde on mean coverage distribution before comparing pooled patient and control groups using a Fisher's test. Methmatrix.csv file contains this data" "the bam files were additionally analysed following a MethylKit based pipeline where first the data was filtered for low read coverage (less than 10 times coverage) and normalised basde on mean coverage distribution before comparing pooled patient and control groups using a Fisher's test. Methmatrix.csv file contains this data" "the bam files were additionally analysed following a MethylKit based pipeline where first the data was filtered for low read coverage (less than 10 times coverage) and normalised basde on mean coverage distribution before comparing pooled patient and control groups using a Fisher's test. Methmatrix.csv file contains this data" "the bam files were additionally analysed following a MethylKit based pipeline where first the data was filtered for low read coverage (less than 10 times coverage) and normalised basde on mean coverage distribution before comparing pooled patient and control groups using a Fisher's test. Methmatrix.csv file contains this data" "the bam files were additionally analysed following a MethylKit based pipeline where first the data was filtered for low read coverage (less than 10 times coverage) and normalised basde on mean coverage distribution before comparing pooled patient and control groups using a Fisher's test. Methmatrix.csv file contains this data" "the bam files were additionally analysed following a MethylKit based pipeline where first the data was filtered for low read coverage (less than 10 times coverage) and normalised basde on mean coverage distribution before comparing pooled patient and control groups using a Fisher's test. Methmatrix.csv file contains this data" "the bam files were additionally analysed following a MethylKit based pipeline where first the data was filtered for low read coverage (less than 10 times coverage) and normalised basde on mean coverage distribution before comparing pooled patient and control groups using a Fisher's test. Methmatrix.csv file contains this data" "the bam files were additionally analysed following a MethylKit based pipeline where first the data was filtered for low read coverage (less than 10 times coverage) and normalised basde on mean coverage distribution before comparing pooled patient and control groups using a Fisher's test. Methmatrix.csv file contains this data" "the bam files were additionally analysed following a MethylKit based pipeline where first the data was filtered for low read coverage (less than 10 times coverage) and normalised basde on mean coverage distribution before comparing pooled patient and control groups using a Fisher's test. Methmatrix.csv file contains this data" "the bam files were additionally analysed following a MethylKit based pipeline where first the data was filtered for low read coverage (less than 10 times coverage) and normalised basde on mean coverage distribution before comparing pooled patient and control groups using a Fisher's test. Methmatrix.csv file contains this data" "the bam files were additionally analysed following a MethylKit based pipeline where first the data was filtered for low read coverage (less than 10 times coverage) and normalised basde on mean coverage distribution before comparing pooled patient and control groups using a Fisher's test. Methmatrix.csv file contains this data" "the bam files were additionally analysed following a MethylKit based pipeline where first the data was filtered for low read coverage (less than 10 times coverage) and normalised basde on mean coverage distribution before comparing pooled patient and control groups using a Fisher's test. Methmatrix.csv file contains this data" "the bam files were additionally analysed following a MethylKit based pipeline where first the data was filtered for low read coverage (less than 10 times coverage) and normalised basde on mean coverage distribution before comparing pooled patient and control groups using a Fisher's test. Methmatrix.csv file contains this data" "the bam files were additionally analysed following a MethylKit based pipeline where first the data was filtered for low read coverage (less than 10 times coverage) and normalised basde on mean coverage distribution before comparing pooled patient and control groups using a Fisher's test. Methmatrix.csv file contains this data" "the bam files were additionally analysed following a MethylKit based pipeline where first the data was filtered for low read coverage (less than 10 times coverage) and normalised basde on mean coverage distribution before comparing pooled patient and control groups using a Fisher's test. Methmatrix.csv file contains this data"
|
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+
!Sample_data_processing "Genome_build: hg19" "Genome_build: hg19" "Genome_build: hg19" "Genome_build: hg19" "Genome_build: hg19" "Genome_build: hg19" "Genome_build: hg19" "Genome_build: hg19" "Genome_build: hg19" "Genome_build: hg19" "Genome_build: hg19" "Genome_build: hg19" "Genome_build: hg19" "Genome_build: hg19" "Genome_build: hg19" "Genome_build: hg19" "Genome_build: hg19" "Genome_build: hg19" "Genome_build: hg19" "Genome_build: hg19"
|
| 56 |
+
!Sample_data_processing "Supplementary_files_format_and_content: Individual .txt files for each sample containing C and T frequency per base and coverage. Matrix (csv file) containing methylation percentages for each sample used in the control vs patient analysis for the MethylKit single CpG pipeline." "Supplementary_files_format_and_content: Individual .txt files for each sample containing C and T frequency per base and coverage. Matrix (csv file) containing methylation percentages for each sample used in the control vs patient analysis for the MethylKit single CpG pipeline." "Supplementary_files_format_and_content: Individual .txt files for each sample containing C and T frequency per base and coverage. Matrix (csv file) containing methylation percentages for each sample used in the control vs patient analysis for the MethylKit single CpG pipeline." "Supplementary_files_format_and_content: Individual .txt files for each sample containing C and T frequency per base and coverage. Matrix (csv file) containing methylation percentages for each sample used in the control vs patient analysis for the MethylKit single CpG pipeline." "Supplementary_files_format_and_content: Individual .txt files for each sample containing C and T frequency per base and coverage. Matrix (csv file) containing methylation percentages for each sample used in the control vs patient analysis for the MethylKit single CpG pipeline." "Supplementary_files_format_and_content: Individual .txt files for each sample containing C and T frequency per base and coverage. Matrix (csv file) containing methylation percentages for each sample used in the control vs patient analysis for the MethylKit single CpG pipeline." "Supplementary_files_format_and_content: Individual .txt files for each sample containing C and T frequency per base and coverage. Matrix (csv file) containing methylation percentages for each sample used in the control vs patient analysis for the MethylKit single CpG pipeline." "Supplementary_files_format_and_content: Individual .txt files for each sample containing C and T frequency per base and coverage. Matrix (csv file) containing methylation percentages for each sample used in the control vs patient analysis for the MethylKit single CpG pipeline." "Supplementary_files_format_and_content: Individual .txt files for each sample containing C and T frequency per base and coverage. Matrix (csv file) containing methylation percentages for each sample used in the control vs patient analysis for the MethylKit single CpG pipeline." "Supplementary_files_format_and_content: Individual .txt files for each sample containing C and T frequency per base and coverage. Matrix (csv file) containing methylation percentages for each sample used in the control vs patient analysis for the MethylKit single CpG pipeline." "Supplementary_files_format_and_content: Individual .txt files for each sample containing C and T frequency per base and coverage. Matrix (csv file) containing methylation percentages for each sample used in the control vs patient analysis for the MethylKit single CpG pipeline." "Supplementary_files_format_and_content: Individual .txt files for each sample containing C and T frequency per base and coverage. Matrix (csv file) containing methylation percentages for each sample used in the control vs patient analysis for the MethylKit single CpG pipeline." "Supplementary_files_format_and_content: Individual .txt files for each sample containing C and T frequency per base and coverage. Matrix (csv file) containing methylation percentages for each sample used in the control vs patient analysis for the MethylKit single CpG pipeline." "Supplementary_files_format_and_content: Individual .txt files for each sample containing C and T frequency per base and coverage. Matrix (csv file) containing methylation percentages for each sample used in the control vs patient analysis for the MethylKit single CpG pipeline." "Supplementary_files_format_and_content: Individual .txt files for each sample containing C and T frequency per base and coverage. Matrix (csv file) containing methylation percentages for each sample used in the control vs patient analysis for the MethylKit single CpG pipeline." "Supplementary_files_format_and_content: Individual .txt files for each sample containing C and T frequency per base and coverage. Matrix (csv file) containing methylation percentages for each sample used in the control vs patient analysis for the MethylKit single CpG pipeline." "Supplementary_files_format_and_content: Individual .txt files for each sample containing C and T frequency per base and coverage. Matrix (csv file) containing methylation percentages for each sample used in the control vs patient analysis for the MethylKit single CpG pipeline." "Supplementary_files_format_and_content: Individual .txt files for each sample containing C and T frequency per base and coverage. Matrix (csv file) containing methylation percentages for each sample used in the control vs patient analysis for the MethylKit single CpG pipeline." "Supplementary_files_format_and_content: Individual .txt files for each sample containing C and T frequency per base and coverage. Matrix (csv file) containing methylation percentages for each sample used in the control vs patient analysis for the MethylKit single CpG pipeline." "Supplementary_files_format_and_content: Individual .txt files for each sample containing C and T frequency per base and coverage. Matrix (csv file) containing methylation percentages for each sample used in the control vs patient analysis for the MethylKit single CpG pipeline."
|
| 57 |
+
!Sample_data_processing "Supplementary_files_format_and_content: A matrix containing the DMAP output data (individual sample percentages, significance values, associated genomic features, fragment length, CpG per fragment). ." "Supplementary_files_format_and_content: A matrix containing the DMAP output data (individual sample percentages, significance values, associated genomic features, fragment length, CpG per fragment). ." "Supplementary_files_format_and_content: A matrix containing the DMAP output data (individual sample percentages, significance values, associated genomic features, fragment length, CpG per fragment). ." "Supplementary_files_format_and_content: A matrix containing the DMAP output data (individual sample percentages, significance values, associated genomic features, fragment length, CpG per fragment). ." "Supplementary_files_format_and_content: A matrix containing the DMAP output data (individual sample percentages, significance values, associated genomic features, fragment length, CpG per fragment). ." "Supplementary_files_format_and_content: A matrix containing the DMAP output data (individual sample percentages, significance values, associated genomic features, fragment length, CpG per fragment). ." "Supplementary_files_format_and_content: A matrix containing the DMAP output data (individual sample percentages, significance values, associated genomic features, fragment length, CpG per fragment). ." "Supplementary_files_format_and_content: A matrix containing the DMAP output data (individual sample percentages, significance values, associated genomic features, fragment length, CpG per fragment). ." "Supplementary_files_format_and_content: A matrix containing the DMAP output data (individual sample percentages, significance values, associated genomic features, fragment length, CpG per fragment). ." "Supplementary_files_format_and_content: A matrix containing the DMAP output data (individual sample percentages, significance values, associated genomic features, fragment length, CpG per fragment). ." "Supplementary_files_format_and_content: A matrix containing the DMAP output data (individual sample percentages, significance values, associated genomic features, fragment length, CpG per fragment). ." "Supplementary_files_format_and_content: A matrix containing the DMAP output data (individual sample percentages, significance values, associated genomic features, fragment length, CpG per fragment). ." "Supplementary_files_format_and_content: A matrix containing the DMAP output data (individual sample percentages, significance values, associated genomic features, fragment length, CpG per fragment). ." "Supplementary_files_format_and_content: A matrix containing the DMAP output data (individual sample percentages, significance values, associated genomic features, fragment length, CpG per fragment). ." "Supplementary_files_format_and_content: A matrix containing the DMAP output data (individual sample percentages, significance values, associated genomic features, fragment length, CpG per fragment). ." "Supplementary_files_format_and_content: A matrix containing the DMAP output data (individual sample percentages, significance values, associated genomic features, fragment length, CpG per fragment). ." "Supplementary_files_format_and_content: A matrix containing the DMAP output data (individual sample percentages, significance values, associated genomic features, fragment length, CpG per fragment). ." "Supplementary_files_format_and_content: A matrix containing the DMAP output data (individual sample percentages, significance values, associated genomic features, fragment length, CpG per fragment). ." "Supplementary_files_format_and_content: A matrix containing the DMAP output data (individual sample percentages, significance values, associated genomic features, fragment length, CpG per fragment). ." "Supplementary_files_format_and_content: A matrix containing the DMAP output data (individual sample percentages, significance values, associated genomic features, fragment length, CpG per fragment). ."
|
| 58 |
+
!Sample_platform_id "GPL16791" "GPL16791" "GPL16791" "GPL16791" "GPL16791" "GPL16791" "GPL16791" "GPL16791" "GPL16791" "GPL16791" "GPL16791" "GPL16791" "GPL16791" "GPL16791" "GPL16791" "GPL16791" "GPL16791" "GPL16791" "GPL16791" "GPL16791"
|
| 59 |
+
!Sample_contact_name "Amber,,Helliwell" "Amber,,Helliwell" "Amber,,Helliwell" "Amber,,Helliwell" "Amber,,Helliwell" "Amber,,Helliwell" "Amber,,Helliwell" "Amber,,Helliwell" "Amber,,Helliwell" "Amber,,Helliwell" "Amber,,Helliwell" "Amber,,Helliwell" "Amber,,Helliwell" "Amber,,Helliwell" "Amber,,Helliwell" "Amber,,Helliwell" "Amber,,Helliwell" "Amber,,Helliwell" "Amber,,Helliwell" "Amber,,Helliwell"
|
| 60 |
+
!Sample_contact_department "Biochemistry Department" "Biochemistry Department" "Biochemistry Department" "Biochemistry Department" "Biochemistry Department" "Biochemistry Department" "Biochemistry Department" "Biochemistry Department" "Biochemistry Department" "Biochemistry Department" "Biochemistry Department" "Biochemistry Department" "Biochemistry Department" "Biochemistry Department" "Biochemistry Department" "Biochemistry Department" "Biochemistry Department" "Biochemistry Department" "Biochemistry Department" "Biochemistry Department"
|
| 61 |
+
!Sample_contact_institute "University of Otago" "University of Otago" "University of Otago" "University of Otago" "University of Otago" "University of Otago" "University of Otago" "University of Otago" "University of Otago" "University of Otago" "University of Otago" "University of Otago" "University of Otago" "University of Otago" "University of Otago" "University of Otago" "University of Otago" "University of Otago" "University of Otago" "University of Otago"
|
| 62 |
+
!Sample_contact_address "710 Cumberland Road" "710 Cumberland Road" "710 Cumberland Road" "710 Cumberland Road" "710 Cumberland Road" "710 Cumberland Road" "710 Cumberland Road" "710 Cumberland Road" "710 Cumberland Road" "710 Cumberland Road" "710 Cumberland Road" "710 Cumberland Road" "710 Cumberland Road" "710 Cumberland Road" "710 Cumberland Road" "710 Cumberland Road" "710 Cumberland Road" "710 Cumberland Road" "710 Cumberland Road" "710 Cumberland Road"
|
| 63 |
+
!Sample_contact_city "Dunedin" "Dunedin" "Dunedin" "Dunedin" "Dunedin" "Dunedin" "Dunedin" "Dunedin" "Dunedin" "Dunedin" "Dunedin" "Dunedin" "Dunedin" "Dunedin" "Dunedin" "Dunedin" "Dunedin" "Dunedin" "Dunedin" "Dunedin"
|
| 64 |
+
!Sample_contact_zip/postal_code "9016" "9016" "9016" "9016" "9016" "9016" "9016" "9016" "9016" "9016" "9016" "9016" "9016" "9016" "9016" "9016" "9016" "9016" "9016" "9016"
|
| 65 |
+
!Sample_contact_country "New Zealand" "New Zealand" "New Zealand" "New Zealand" "New Zealand" "New Zealand" "New Zealand" "New Zealand" "New Zealand" "New Zealand" "New Zealand" "New Zealand" "New Zealand" "New Zealand" "New Zealand" "New Zealand" "New Zealand" "New Zealand" "New Zealand" "New Zealand"
|
| 66 |
+
!Sample_data_row_count "0" "0" "0" "0" "0" "0" "0" "0" "0" "0" "0" "0" "0" "0" "0" "0" "0" "0" "0" "0"
|
| 67 |
+
!Sample_instrument_model "Illumina HiSeq 2500" "Illumina HiSeq 2500" "Illumina HiSeq 2500" "Illumina HiSeq 2500" "Illumina HiSeq 2500" "Illumina HiSeq 2500" "Illumina HiSeq 2500" "Illumina HiSeq 2500" "Illumina HiSeq 2500" "Illumina HiSeq 2500" "Illumina HiSeq 2500" "Illumina HiSeq 2500" "Illumina HiSeq 2500" "Illumina HiSeq 2500" "Illumina HiSeq 2500" "Illumina HiSeq 2500" "Illumina HiSeq 2500" "Illumina HiSeq 2500" "Illumina HiSeq 2500" "Illumina HiSeq 2500"
|
| 68 |
+
!Sample_library_selection "Reduced Representation" "Reduced Representation" "Reduced Representation" "Reduced Representation" "Reduced Representation" "Reduced Representation" "Reduced Representation" "Reduced Representation" "Reduced Representation" "Reduced Representation" "Reduced Representation" "Reduced Representation" "Reduced Representation" "Reduced Representation" "Reduced Representation" "Reduced Representation" "Reduced Representation" "Reduced Representation" "Reduced Representation" "Reduced Representation"
|
| 69 |
+
!Sample_library_source "genomic" "genomic" "genomic" "genomic" "genomic" "genomic" "genomic" "genomic" "genomic" "genomic" "genomic" "genomic" "genomic" "genomic" "genomic" "genomic" "genomic" "genomic" "genomic" "genomic"
|
| 70 |
+
!Sample_library_strategy "Bisulfite-Seq" "Bisulfite-Seq" "Bisulfite-Seq" "Bisulfite-Seq" "Bisulfite-Seq" "Bisulfite-Seq" "Bisulfite-Seq" "Bisulfite-Seq" "Bisulfite-Seq" "Bisulfite-Seq" "Bisulfite-Seq" "Bisulfite-Seq" "Bisulfite-Seq" "Bisulfite-Seq" "Bisulfite-Seq" "Bisulfite-Seq" "Bisulfite-Seq" "Bisulfite-Seq" "Bisulfite-Seq" "Bisulfite-Seq"
|
| 71 |
+
!Sample_relation "BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN15420272" "BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN15420271" "BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN15420270" "BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN15420269" "BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN15420268" "BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN15420267" "BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN15420266" "BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN15420265" "BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN15420264" "BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN15420263" "BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN15420262" "BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN15420261" "BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN15420260" "BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN15420259" "BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN15420258" "BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN15420257" "BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN15420256" "BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN15420255" "BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN15420254" "BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN15420253"
|
| 72 |
+
!Sample_relation "SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8651460" "SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8651461" "SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8651462" "SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8651463" "SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8651464" "SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8651465" "SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8651466" "SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8651467" "SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8651468" "SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8651469" "SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8651470" "SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8651471" "SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8651472" "SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8651473" "SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8651474" "SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8651475" "SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8651476" "SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8651477" "SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8651478" "SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8651479"
|
| 73 |
+
!Sample_supplementary_file_1 "ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4649nnn/GSM4649027/suppl/GSM4649027_Control1_CpG.txt.gz" "ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4649nnn/GSM4649028/suppl/GSM4649028_Control2_CpG.txt.gz" "ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4649nnn/GSM4649029/suppl/GSM4649029_Control3_CpG.txt.gz" "ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4649nnn/GSM4649030/suppl/GSM4649030_Control4_CpG.txt.gz" "ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4649nnn/GSM4649031/suppl/GSM4649031_Control5_CpG.txt.gz" "ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4649nnn/GSM4649032/suppl/GSM4649032_Control6_CpG.txt.gz" "ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4649nnn/GSM4649033/suppl/GSM4649033_Control7_CpG.txt.gz" "ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4649nnn/GSM4649034/suppl/GSM4649034_Control8_CpG.txt.gz" "ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4649nnn/GSM4649035/suppl/GSM4649035_Control9_CpG.txt.gz" "ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4649nnn/GSM4649036/suppl/GSM4649036_Control10_CpG.txt.gz" "ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4649nnn/GSM4649037/suppl/GSM4649037_Patient1_CpG.txt.gz" "ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4649nnn/GSM4649038/suppl/GSM4649038_Patient2_CpG.txt.gz" "ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4649nnn/GSM4649039/suppl/GSM4649039_Patient3_CpG.txt.gz" "ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4649nnn/GSM4649040/suppl/GSM4649040_Patient4_CpG.txt.gz" "ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4649nnn/GSM4649041/suppl/GSM4649041_Patient5_CpG.txt.gz" "ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4649nnn/GSM4649042/suppl/GSM4649042_Patient6_CpG.txt.gz" "ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4649nnn/GSM4649043/suppl/GSM4649043_Patient7_CpG.txt.gz" "ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4649nnn/GSM4649044/suppl/GSM4649044_Patient8_CpG.txt.gz" "ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4649nnn/GSM4649045/suppl/GSM4649045_Patient9_CpG.txt.gz" "ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4649nnn/GSM4649046/suppl/GSM4649046_Patient10_CpG.txt.gz"
|
| 74 |
+
!series_matrix_table_begin
|
| 75 |
+
"ID_REF" "GSM4649027" "GSM4649028" "GSM4649029" "GSM4649030" "GSM4649031" "GSM4649032" "GSM4649033" "GSM4649034" "GSM4649035" "GSM4649036" "GSM4649037" "GSM4649038" "GSM4649039" "GSM4649040" "GSM4649041" "GSM4649042" "GSM4649043" "GSM4649044" "GSM4649045" "GSM4649046"
|
| 76 |
+
!series_matrix_table_end
|
ME/GSE156792/._GSE156792_detection_pval.txt
ADDED
|
Binary file (4.1 kB). View file
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|
ME/GSE156792/._GSE156792_meth_intensities.txt
ADDED
|
Binary file (4.1 kB). View file
|
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|
ME/GSE166592/GSE166592_RAW/GSM5076049_ME007E_CpG.txt
ADDED
|
The diff for this file is too large to render.
See raw diff
|
|
|
ME/GSE166592/meta/._GSE166592_family.soft
ADDED
|
Binary file (4.1 kB). View file
|
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|
ME/GSE166592/meta/._GSE166592_family.xml
ADDED
|
Binary file (4.1 kB). View file
|
|
|
ME/GSE166592/meta/._GSE166592_series_matrix.txt
ADDED
|
Binary file (4.1 kB). View file
|
|
|
ME/GSE166592/meta/GSE166592_family.soft
ADDED
|
@@ -0,0 +1,681 @@
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|
| 1 |
+
^DATABASE = GeoMiame
|
| 2 |
+
!Database_name = Gene Expression Omnibus (GEO)
|
| 3 |
+
!Database_institute = NCBI NLM NIH
|
| 4 |
+
!Database_web_link = http://www.ncbi.nlm.nih.gov/geo
|
| 5 |
+
!Database_email = geo@ncbi.nlm.nih.gov
|
| 6 |
+
^SERIES = GSE166592
|
| 7 |
+
!Series_title = Dynamic Epigenetic Changes during a Relapse and Recovery Cycle in Myalgic Encephalomyelitis/Chronic Fatigue Syndrome
|
| 8 |
+
!Series_geo_accession = GSE166592
|
| 9 |
+
!Series_status = Public on Feb 11 2021
|
| 10 |
+
!Series_submission_date = Feb 10 2021
|
| 11 |
+
!Series_last_update_date = Mar 17 2021
|
| 12 |
+
!Series_summary = Purpose: ME/CFS is a debilitating and complex disease. The majority of patients exist in a chronic state of health where they are affected by relapse events. Precision medicine following patients can capture changes in the DNA methylation indicative of biological dysfunction
|
| 13 |
+
!Series_summary = Methods: DNA was extracted from the PBMCs of 2 ME/CFS patients and a age/gender matched control at five different time points. After performing RRBS the sequence was aligned to hg19 genome using Bismark. The data was analyzed using a Chi squared test through DMAP in order to determine variation between the patient and control groups across 40-220bp fragments of the genome.
|
| 14 |
+
!Series_summary = Results: A total of 17 and 14 statistically significant variably methylated fragements were indentified in each patient that strongly associated with a relapse event. These fragements were found on regions of regulatory importance of the genome that associated with immune (primarily inflammatory) and metabolic function.
|
| 15 |
+
!Series_summary = Conclusions: Our study represents the first investigation of ME/CFS patients using reduced representation bisulfite sequencing along a longitudinal timeframe. We captured a number of major variably methylated fragments in each patient that associated with their relapse events. Our results identified a number of differentially methylated regulatory elements and gene bodies that highlight the disturbed pathophysiology in ME/CFS. DNA methylation that differentiates disease variability in ongoing ME/CFS may have practical applications for strategies to deacrease the frequency and severity of relapse events.
|
| 16 |
+
!Series_overall_design = RRBS Analysis of 2 ME/CFS patients and matched control over eleven months
|
| 17 |
+
!Series_type = Methylation profiling by high throughput sequencing
|
| 18 |
+
!Series_contributor = Amber,,Helliwell
|
| 19 |
+
!Series_contributor = Warren,,Tate
|
| 20 |
+
!Series_contributor = Aniruddha,,Chatterjee
|
| 21 |
+
!Series_contributor = Peter,,Stockwell
|
| 22 |
+
!Series_contributor = Tina,,Edgar
|
| 23 |
+
!Series_sample_id = GSM5076040
|
| 24 |
+
!Series_sample_id = GSM5076041
|
| 25 |
+
!Series_sample_id = GSM5076042
|
| 26 |
+
!Series_sample_id = GSM5076043
|
| 27 |
+
!Series_sample_id = GSM5076044
|
| 28 |
+
!Series_sample_id = GSM5076045
|
| 29 |
+
!Series_sample_id = GSM5076046
|
| 30 |
+
!Series_sample_id = GSM5076047
|
| 31 |
+
!Series_sample_id = GSM5076048
|
| 32 |
+
!Series_sample_id = GSM5076049
|
| 33 |
+
!Series_sample_id = GSM5076050
|
| 34 |
+
!Series_sample_id = GSM5076051
|
| 35 |
+
!Series_sample_id = GSM5076052
|
| 36 |
+
!Series_sample_id = GSM5076053
|
| 37 |
+
!Series_sample_id = GSM5076054
|
| 38 |
+
!Series_contact_name = Amber,,Helliwell
|
| 39 |
+
!Series_contact_department = Biochemistry Department
|
| 40 |
+
!Series_contact_institute = University of Otago
|
| 41 |
+
!Series_contact_address = 710 Cumberland Road
|
| 42 |
+
!Series_contact_city = Dunedin
|
| 43 |
+
!Series_contact_zip/postal_code = 9016
|
| 44 |
+
!Series_contact_country = New Zealand
|
| 45 |
+
!Series_supplementary_file = ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE166nnn/GSE166592/suppl/GSE166592_C012_Full.xlsx
|
| 46 |
+
!Series_supplementary_file = ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE166nnn/GSE166592/suppl/GSE166592_ME007_Full.xlsx
|
| 47 |
+
!Series_supplementary_file = ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE166nnn/GSE166592/suppl/GSE166592_ME016_Full.xlsx
|
| 48 |
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!Series_supplementary_file = ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE166nnn/GSE166592/suppl/GSE166592_RAW.tar
|
| 49 |
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!Series_platform_id = GPL16791
|
| 50 |
+
!Series_platform_taxid = 9606
|
| 51 |
+
!Series_sample_taxid = 9606
|
| 52 |
+
!Series_relation = BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA701322
|
| 53 |
+
!Series_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP305748
|
| 54 |
+
^PLATFORM = GPL16791
|
| 55 |
+
!Platform_title = Illumina HiSeq 2500 (Homo sapiens)
|
| 56 |
+
!Platform_geo_accession = GPL16791
|
| 57 |
+
!Platform_status = Public on Mar 14 2013
|
| 58 |
+
!Platform_submission_date = Mar 14 2013
|
| 59 |
+
!Platform_last_update_date = Mar 27 2019
|
| 60 |
+
!Platform_technology = high-throughput sequencing
|
| 61 |
+
!Platform_distribution = virtual
|
| 62 |
+
!Platform_organism = Homo sapiens
|
| 63 |
+
!Platform_taxid = 9606
|
| 64 |
+
!Platform_contact_name = ,,GEO
|
| 65 |
+
!Platform_contact_country = USA
|
| 66 |
+
!Platform_data_row_count = 0
|
| 67 |
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^SAMPLE = GSM5076040
|
| 68 |
+
!Sample_title = C012A
|
| 69 |
+
!Sample_geo_accession = GSM5076040
|
| 70 |
+
!Sample_status = Public on Feb 11 2021
|
| 71 |
+
!Sample_submission_date = Feb 10 2021
|
| 72 |
+
!Sample_last_update_date = Feb 12 2021
|
| 73 |
+
!Sample_type = SRA
|
| 74 |
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!Sample_channel_count = 1
|
| 75 |
+
!Sample_source_name_ch1 = Peripheral Blood Mononuclear Cells
|
| 76 |
+
!Sample_organism_ch1 = Homo sapiens
|
| 77 |
+
!Sample_taxid_ch1 = 9606
|
| 78 |
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!Sample_characteristics_ch1 = disease state: Control
|
| 79 |
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!Sample_characteristics_ch1 = individual: C012
|
| 80 |
+
!Sample_characteristics_ch1 = time point: A
|
| 81 |
+
!Sample_characteristics_ch1 = cell type: Peripheral Blood Mononuclear Cells
|
| 82 |
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!Sample_molecule_ch1 = genomic DNA
|
| 83 |
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!Sample_extract_protocol_ch1 = DNA was extracted from 200ul of PBMCs
|
| 84 |
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!Sample_extract_protocol_ch1 = MSPI digestion (purify), end repair (purify), A-tialing and adaptor ligation (purify), PCR amplification (purify), Gel size selection and gel extraction (purify)
|
| 85 |
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!Sample_description = C012A
|
| 86 |
+
!Sample_data_processing = reads were adaptor trimmed using bismark that used a file of adaptor sequences and trimmed three bases back from any detected adaptor to delete the C invorporated and rejecting any reads that were trimmed to less than 10bp
|
| 87 |
+
!Sample_data_processing = reads were aligned to the hg19 genome using bismark with the following specifications: a tolerance for one non-bisulfite mismatch per read, the default minimum alignment score (L,O, -02), and with ignore - quals in order to calculate the mismatch penalty by considering the quality value at the mismatched position to be the highest possible
|
| 88 |
+
!Sample_data_processing = bam files generated by Bismark alignment were then processed using DMAP to compare control vs. patients with the following specifications: Chi squared test on fragments 40-220bp in length, with the fragment requireing at lest 2 CpGs to have 10 or more sequence reads. The differential methylation file was then annotated with protein coding gene information using the DMAP command identgeneloc. DMAPmatrix.csv file contains this data.
|
| 89 |
+
!Sample_data_processing = Genome_build: hg19
|
| 90 |
+
!Sample_data_processing = Supplementary_files_format_and_content: Individual .txt files for each sample containing C and T frequency per base and coverage. C012_Full, ME007_Full and ME016_Full are excel files that contain, for the control, patient one, and patient two respectively, information about the per fragment methylation data including, genomic location, gene feature information, CpG relative location and fragment size.
|
| 91 |
+
!Sample_platform_id = GPL16791
|
| 92 |
+
!Sample_contact_name = Amber,,Helliwell
|
| 93 |
+
!Sample_contact_department = Biochemistry Department
|
| 94 |
+
!Sample_contact_institute = University of Otago
|
| 95 |
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!Sample_contact_address = 710 Cumberland Road
|
| 96 |
+
!Sample_contact_city = Dunedin
|
| 97 |
+
!Sample_contact_zip/postal_code = 9016
|
| 98 |
+
!Sample_contact_country = New Zealand
|
| 99 |
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!Sample_instrument_model = Illumina HiSeq 2500
|
| 100 |
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!Sample_library_selection = Reduced Representation
|
| 101 |
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!Sample_library_source = genomic
|
| 102 |
+
!Sample_library_strategy = Bisulfite-Seq
|
| 103 |
+
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN17862810
|
| 104 |
+
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10073447
|
| 105 |
+
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5076nnn/GSM5076040/suppl/GSM5076040_C012A_CpG.txt.gz
|
| 106 |
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!Sample_series_id = GSE166592
|
| 107 |
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|
| 108 |
+
^SAMPLE = GSM5076041
|
| 109 |
+
!Sample_title = C012B
|
| 110 |
+
!Sample_geo_accession = GSM5076041
|
| 111 |
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!Sample_status = Public on Feb 11 2021
|
| 112 |
+
!Sample_submission_date = Feb 10 2021
|
| 113 |
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!Sample_last_update_date = Feb 12 2021
|
| 114 |
+
!Sample_type = SRA
|
| 115 |
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!Sample_channel_count = 1
|
| 116 |
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!Sample_source_name_ch1 = Peripheral Blood Mononuclear Cells
|
| 117 |
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!Sample_organism_ch1 = Homo sapiens
|
| 118 |
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!Sample_taxid_ch1 = 9606
|
| 119 |
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!Sample_characteristics_ch1 = disease state: Control
|
| 120 |
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!Sample_characteristics_ch1 = individual: C012
|
| 121 |
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!Sample_characteristics_ch1 = time point: B
|
| 122 |
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!Sample_characteristics_ch1 = cell type: Peripheral Blood Mononuclear Cells
|
| 123 |
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!Sample_molecule_ch1 = genomic DNA
|
| 124 |
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!Sample_extract_protocol_ch1 = DNA was extracted from 200ul of PBMCs
|
| 125 |
+
!Sample_extract_protocol_ch1 = MSPI digestion (purify), end repair (purify), A-tialing and adaptor ligation (purify), PCR amplification (purify), Gel size selection and gel extraction (purify)
|
| 126 |
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!Sample_description = C012B
|
| 127 |
+
!Sample_data_processing = reads were adaptor trimmed using bismark that used a file of adaptor sequences and trimmed three bases back from any detected adaptor to delete the C invorporated and rejecting any reads that were trimmed to less than 10bp
|
| 128 |
+
!Sample_data_processing = reads were aligned to the hg19 genome using bismark with the following specifications: a tolerance for one non-bisulfite mismatch per read, the default minimum alignment score (L,O, -02), and with ignore - quals in order to calculate the mismatch penalty by considering the quality value at the mismatched position to be the highest possible
|
| 129 |
+
!Sample_data_processing = bam files generated by Bismark alignment were then processed using DMAP to compare control vs. patients with the following specifications: Chi squared test on fragments 40-220bp in length, with the fragment requireing at lest 2 CpGs to have 10 or more sequence reads. The differential methylation file was then annotated with protein coding gene information using the DMAP command identgeneloc. DMAPmatrix.csv file contains this data.
|
| 130 |
+
!Sample_data_processing = Genome_build: hg19
|
| 131 |
+
!Sample_data_processing = Supplementary_files_format_and_content: Individual .txt files for each sample containing C and T frequency per base and coverage. C012_Full, ME007_Full and ME016_Full are excel files that contain, for the control, patient one, and patient two respectively, information about the per fragment methylation data including, genomic location, gene feature information, CpG relative location and fragment size.
|
| 132 |
+
!Sample_platform_id = GPL16791
|
| 133 |
+
!Sample_contact_name = Amber,,Helliwell
|
| 134 |
+
!Sample_contact_department = Biochemistry Department
|
| 135 |
+
!Sample_contact_institute = University of Otago
|
| 136 |
+
!Sample_contact_address = 710 Cumberland Road
|
| 137 |
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!Sample_contact_city = Dunedin
|
| 138 |
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!Sample_contact_zip/postal_code = 9016
|
| 139 |
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!Sample_contact_country = New Zealand
|
| 140 |
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!Sample_instrument_model = Illumina HiSeq 2500
|
| 141 |
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!Sample_library_selection = Reduced Representation
|
| 142 |
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!Sample_library_source = genomic
|
| 143 |
+
!Sample_library_strategy = Bisulfite-Seq
|
| 144 |
+
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN17862809
|
| 145 |
+
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10073448
|
| 146 |
+
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5076nnn/GSM5076041/suppl/GSM5076041_C012B_CpG.txt.gz
|
| 147 |
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!Sample_series_id = GSE166592
|
| 148 |
+
!Sample_data_row_count = 0
|
| 149 |
+
^SAMPLE = GSM5076042
|
| 150 |
+
!Sample_title = C012C
|
| 151 |
+
!Sample_geo_accession = GSM5076042
|
| 152 |
+
!Sample_status = Public on Feb 11 2021
|
| 153 |
+
!Sample_submission_date = Feb 10 2021
|
| 154 |
+
!Sample_last_update_date = Feb 12 2021
|
| 155 |
+
!Sample_type = SRA
|
| 156 |
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!Sample_channel_count = 1
|
| 157 |
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!Sample_source_name_ch1 = Peripheral Blood Mononuclear Cells
|
| 158 |
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!Sample_organism_ch1 = Homo sapiens
|
| 159 |
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!Sample_taxid_ch1 = 9606
|
| 160 |
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!Sample_characteristics_ch1 = disease state: Control
|
| 161 |
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!Sample_characteristics_ch1 = individual: C012
|
| 162 |
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!Sample_characteristics_ch1 = time point: C
|
| 163 |
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!Sample_characteristics_ch1 = cell type: Peripheral Blood Mononuclear Cells
|
| 164 |
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!Sample_molecule_ch1 = genomic DNA
|
| 165 |
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!Sample_extract_protocol_ch1 = DNA was extracted from 200ul of PBMCs
|
| 166 |
+
!Sample_extract_protocol_ch1 = MSPI digestion (purify), end repair (purify), A-tialing and adaptor ligation (purify), PCR amplification (purify), Gel size selection and gel extraction (purify)
|
| 167 |
+
!Sample_description = C012C
|
| 168 |
+
!Sample_data_processing = reads were adaptor trimmed using bismark that used a file of adaptor sequences and trimmed three bases back from any detected adaptor to delete the C invorporated and rejecting any reads that were trimmed to less than 10bp
|
| 169 |
+
!Sample_data_processing = reads were aligned to the hg19 genome using bismark with the following specifications: a tolerance for one non-bisulfite mismatch per read, the default minimum alignment score (L,O, -02), and with ignore - quals in order to calculate the mismatch penalty by considering the quality value at the mismatched position to be the highest possible
|
| 170 |
+
!Sample_data_processing = bam files generated by Bismark alignment were then processed using DMAP to compare control vs. patients with the following specifications: Chi squared test on fragments 40-220bp in length, with the fragment requireing at lest 2 CpGs to have 10 or more sequence reads. The differential methylation file was then annotated with protein coding gene information using the DMAP command identgeneloc. DMAPmatrix.csv file contains this data.
|
| 171 |
+
!Sample_data_processing = Genome_build: hg19
|
| 172 |
+
!Sample_data_processing = Supplementary_files_format_and_content: Individual .txt files for each sample containing C and T frequency per base and coverage. C012_Full, ME007_Full and ME016_Full are excel files that contain, for the control, patient one, and patient two respectively, information about the per fragment methylation data including, genomic location, gene feature information, CpG relative location and fragment size.
|
| 173 |
+
!Sample_platform_id = GPL16791
|
| 174 |
+
!Sample_contact_name = Amber,,Helliwell
|
| 175 |
+
!Sample_contact_department = Biochemistry Department
|
| 176 |
+
!Sample_contact_institute = University of Otago
|
| 177 |
+
!Sample_contact_address = 710 Cumberland Road
|
| 178 |
+
!Sample_contact_city = Dunedin
|
| 179 |
+
!Sample_contact_zip/postal_code = 9016
|
| 180 |
+
!Sample_contact_country = New Zealand
|
| 181 |
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!Sample_instrument_model = Illumina HiSeq 2500
|
| 182 |
+
!Sample_library_selection = Reduced Representation
|
| 183 |
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!Sample_library_source = genomic
|
| 184 |
+
!Sample_library_strategy = Bisulfite-Seq
|
| 185 |
+
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN17862808
|
| 186 |
+
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10073449
|
| 187 |
+
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5076nnn/GSM5076042/suppl/GSM5076042_C012C_CpG.txt.gz
|
| 188 |
+
!Sample_series_id = GSE166592
|
| 189 |
+
!Sample_data_row_count = 0
|
| 190 |
+
^SAMPLE = GSM5076043
|
| 191 |
+
!Sample_title = C012D
|
| 192 |
+
!Sample_geo_accession = GSM5076043
|
| 193 |
+
!Sample_status = Public on Feb 11 2021
|
| 194 |
+
!Sample_submission_date = Feb 10 2021
|
| 195 |
+
!Sample_last_update_date = Feb 12 2021
|
| 196 |
+
!Sample_type = SRA
|
| 197 |
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!Sample_channel_count = 1
|
| 198 |
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!Sample_source_name_ch1 = Peripheral Blood Mononuclear Cells
|
| 199 |
+
!Sample_organism_ch1 = Homo sapiens
|
| 200 |
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!Sample_taxid_ch1 = 9606
|
| 201 |
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!Sample_characteristics_ch1 = disease state: Control
|
| 202 |
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!Sample_characteristics_ch1 = individual: C012
|
| 203 |
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!Sample_characteristics_ch1 = time point: D
|
| 204 |
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!Sample_characteristics_ch1 = cell type: Peripheral Blood Mononuclear Cells
|
| 205 |
+
!Sample_molecule_ch1 = genomic DNA
|
| 206 |
+
!Sample_extract_protocol_ch1 = DNA was extracted from 200ul of PBMCs
|
| 207 |
+
!Sample_extract_protocol_ch1 = MSPI digestion (purify), end repair (purify), A-tialing and adaptor ligation (purify), PCR amplification (purify), Gel size selection and gel extraction (purify)
|
| 208 |
+
!Sample_description = C012D
|
| 209 |
+
!Sample_data_processing = reads were adaptor trimmed using bismark that used a file of adaptor sequences and trimmed three bases back from any detected adaptor to delete the C invorporated and rejecting any reads that were trimmed to less than 10bp
|
| 210 |
+
!Sample_data_processing = reads were aligned to the hg19 genome using bismark with the following specifications: a tolerance for one non-bisulfite mismatch per read, the default minimum alignment score (L,O, -02), and with ignore - quals in order to calculate the mismatch penalty by considering the quality value at the mismatched position to be the highest possible
|
| 211 |
+
!Sample_data_processing = bam files generated by Bismark alignment were then processed using DMAP to compare control vs. patients with the following specifications: Chi squared test on fragments 40-220bp in length, with the fragment requireing at lest 2 CpGs to have 10 or more sequence reads. The differential methylation file was then annotated with protein coding gene information using the DMAP command identgeneloc. DMAPmatrix.csv file contains this data.
|
| 212 |
+
!Sample_data_processing = Genome_build: hg19
|
| 213 |
+
!Sample_data_processing = Supplementary_files_format_and_content: Individual .txt files for each sample containing C and T frequency per base and coverage. C012_Full, ME007_Full and ME016_Full are excel files that contain, for the control, patient one, and patient two respectively, information about the per fragment methylation data including, genomic location, gene feature information, CpG relative location and fragment size.
|
| 214 |
+
!Sample_platform_id = GPL16791
|
| 215 |
+
!Sample_contact_name = Amber,,Helliwell
|
| 216 |
+
!Sample_contact_department = Biochemistry Department
|
| 217 |
+
!Sample_contact_institute = University of Otago
|
| 218 |
+
!Sample_contact_address = 710 Cumberland Road
|
| 219 |
+
!Sample_contact_city = Dunedin
|
| 220 |
+
!Sample_contact_zip/postal_code = 9016
|
| 221 |
+
!Sample_contact_country = New Zealand
|
| 222 |
+
!Sample_instrument_model = Illumina HiSeq 2500
|
| 223 |
+
!Sample_library_selection = Reduced Representation
|
| 224 |
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!Sample_library_source = genomic
|
| 225 |
+
!Sample_library_strategy = Bisulfite-Seq
|
| 226 |
+
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN17862807
|
| 227 |
+
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10073450
|
| 228 |
+
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5076nnn/GSM5076043/suppl/GSM5076043_C012D_CpG.txt.gz
|
| 229 |
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!Sample_series_id = GSE166592
|
| 230 |
+
!Sample_data_row_count = 0
|
| 231 |
+
^SAMPLE = GSM5076044
|
| 232 |
+
!Sample_title = C012E
|
| 233 |
+
!Sample_geo_accession = GSM5076044
|
| 234 |
+
!Sample_status = Public on Feb 11 2021
|
| 235 |
+
!Sample_submission_date = Feb 10 2021
|
| 236 |
+
!Sample_last_update_date = Feb 12 2021
|
| 237 |
+
!Sample_type = SRA
|
| 238 |
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!Sample_channel_count = 1
|
| 239 |
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!Sample_source_name_ch1 = Peripheral Blood Mononuclear Cells
|
| 240 |
+
!Sample_organism_ch1 = Homo sapiens
|
| 241 |
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!Sample_taxid_ch1 = 9606
|
| 242 |
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!Sample_characteristics_ch1 = disease state: Control
|
| 243 |
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!Sample_characteristics_ch1 = individual: C012
|
| 244 |
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!Sample_characteristics_ch1 = time point: E
|
| 245 |
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!Sample_characteristics_ch1 = cell type: Peripheral Blood Mononuclear Cells
|
| 246 |
+
!Sample_molecule_ch1 = genomic DNA
|
| 247 |
+
!Sample_extract_protocol_ch1 = DNA was extracted from 200ul of PBMCs
|
| 248 |
+
!Sample_extract_protocol_ch1 = MSPI digestion (purify), end repair (purify), A-tialing and adaptor ligation (purify), PCR amplification (purify), Gel size selection and gel extraction (purify)
|
| 249 |
+
!Sample_description = C012E
|
| 250 |
+
!Sample_data_processing = reads were adaptor trimmed using bismark that used a file of adaptor sequences and trimmed three bases back from any detected adaptor to delete the C invorporated and rejecting any reads that were trimmed to less than 10bp
|
| 251 |
+
!Sample_data_processing = reads were aligned to the hg19 genome using bismark with the following specifications: a tolerance for one non-bisulfite mismatch per read, the default minimum alignment score (L,O, -02), and with ignore - quals in order to calculate the mismatch penalty by considering the quality value at the mismatched position to be the highest possible
|
| 252 |
+
!Sample_data_processing = bam files generated by Bismark alignment were then processed using DMAP to compare control vs. patients with the following specifications: Chi squared test on fragments 40-220bp in length, with the fragment requireing at lest 2 CpGs to have 10 or more sequence reads. The differential methylation file was then annotated with protein coding gene information using the DMAP command identgeneloc. DMAPmatrix.csv file contains this data.
|
| 253 |
+
!Sample_data_processing = Genome_build: hg19
|
| 254 |
+
!Sample_data_processing = Supplementary_files_format_and_content: Individual .txt files for each sample containing C and T frequency per base and coverage. C012_Full, ME007_Full and ME016_Full are excel files that contain, for the control, patient one, and patient two respectively, information about the per fragment methylation data including, genomic location, gene feature information, CpG relative location and fragment size.
|
| 255 |
+
!Sample_platform_id = GPL16791
|
| 256 |
+
!Sample_contact_name = Amber,,Helliwell
|
| 257 |
+
!Sample_contact_department = Biochemistry Department
|
| 258 |
+
!Sample_contact_institute = University of Otago
|
| 259 |
+
!Sample_contact_address = 710 Cumberland Road
|
| 260 |
+
!Sample_contact_city = Dunedin
|
| 261 |
+
!Sample_contact_zip/postal_code = 9016
|
| 262 |
+
!Sample_contact_country = New Zealand
|
| 263 |
+
!Sample_instrument_model = Illumina HiSeq 2500
|
| 264 |
+
!Sample_library_selection = Reduced Representation
|
| 265 |
+
!Sample_library_source = genomic
|
| 266 |
+
!Sample_library_strategy = Bisulfite-Seq
|
| 267 |
+
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN17862806
|
| 268 |
+
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10073451
|
| 269 |
+
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5076nnn/GSM5076044/suppl/GSM5076044_C012E_CpG.txt.gz
|
| 270 |
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!Sample_series_id = GSE166592
|
| 271 |
+
!Sample_data_row_count = 0
|
| 272 |
+
^SAMPLE = GSM5076045
|
| 273 |
+
!Sample_title = Patient_One_A
|
| 274 |
+
!Sample_geo_accession = GSM5076045
|
| 275 |
+
!Sample_status = Public on Feb 11 2021
|
| 276 |
+
!Sample_submission_date = Feb 10 2021
|
| 277 |
+
!Sample_last_update_date = Mar 17 2021
|
| 278 |
+
!Sample_type = SRA
|
| 279 |
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!Sample_channel_count = 1
|
| 280 |
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!Sample_source_name_ch1 = Peripheral Blood Mononuclear Cells
|
| 281 |
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!Sample_organism_ch1 = Homo sapiens
|
| 282 |
+
!Sample_taxid_ch1 = 9606
|
| 283 |
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!Sample_characteristics_ch1 = disease state: myalgic encephalomyelitis/chronic fatigue syndrome
|
| 284 |
+
!Sample_characteristics_ch1 = individual: Patient_One
|
| 285 |
+
!Sample_characteristics_ch1 = time point: A
|
| 286 |
+
!Sample_characteristics_ch1 = cell type: Peripheral Blood Mononuclear Cells
|
| 287 |
+
!Sample_molecule_ch1 = genomic DNA
|
| 288 |
+
!Sample_extract_protocol_ch1 = DNA was extracted from 200ul of PBMCs
|
| 289 |
+
!Sample_extract_protocol_ch1 = MSPI digestion (purify), end repair (purify), A-tialing and adaptor ligation (purify), PCR amplification (purify), Gel size selection and gel extraction (purify)
|
| 290 |
+
!Sample_description = ME007A
|
| 291 |
+
!Sample_data_processing = reads were adaptor trimmed using bismark that used a file of adaptor sequences and trimmed three bases back from any detected adaptor to delete the C invorporated and rejecting any reads that were trimmed to less than 10bp
|
| 292 |
+
!Sample_data_processing = reads were aligned to the hg19 genome using bismark with the following specifications: a tolerance for one non-bisulfite mismatch per read, the default minimum alignment score (L,O, -02), and with ignore - quals in order to calculate the mismatch penalty by considering the quality value at the mismatched position to be the highest possible
|
| 293 |
+
!Sample_data_processing = bam files generated by Bismark alignment were then processed using DMAP to compare control vs. patients with the following specifications: Chi squared test on fragments 40-220bp in length, with the fragment requireing at lest 2 CpGs to have 10 or more sequence reads. The differential methylation file was then annotated with protein coding gene information using the DMAP command identgeneloc. DMAPmatrix.csv file contains this data.
|
| 294 |
+
!Sample_data_processing = Genome_build: hg19
|
| 295 |
+
!Sample_data_processing = Supplementary_files_format_and_content: Individual .txt files for each sample containing C and T frequency per base and coverage. C012_Full, ME007_Full and ME016_Full are excel files that contain, for the control, patient one, and patient two respectively, information about the per fragment methylation data including, genomic location, gene feature information, CpG relative location and fragment size.
|
| 296 |
+
!Sample_platform_id = GPL16791
|
| 297 |
+
!Sample_contact_name = Amber,,Helliwell
|
| 298 |
+
!Sample_contact_department = Biochemistry Department
|
| 299 |
+
!Sample_contact_institute = University of Otago
|
| 300 |
+
!Sample_contact_address = 710 Cumberland Road
|
| 301 |
+
!Sample_contact_city = Dunedin
|
| 302 |
+
!Sample_contact_zip/postal_code = 9016
|
| 303 |
+
!Sample_contact_country = New Zealand
|
| 304 |
+
!Sample_instrument_model = Illumina HiSeq 2500
|
| 305 |
+
!Sample_library_selection = Reduced Representation
|
| 306 |
+
!Sample_library_source = genomic
|
| 307 |
+
!Sample_library_strategy = Bisulfite-Seq
|
| 308 |
+
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN17862805
|
| 309 |
+
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10073452
|
| 310 |
+
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5076nnn/GSM5076045/suppl/GSM5076045_ME007A_CpG.txt.gz
|
| 311 |
+
!Sample_series_id = GSE166592
|
| 312 |
+
!Sample_data_row_count = 0
|
| 313 |
+
^SAMPLE = GSM5076046
|
| 314 |
+
!Sample_title = Patient_One_B
|
| 315 |
+
!Sample_geo_accession = GSM5076046
|
| 316 |
+
!Sample_status = Public on Feb 11 2021
|
| 317 |
+
!Sample_submission_date = Feb 10 2021
|
| 318 |
+
!Sample_last_update_date = Feb 12 2021
|
| 319 |
+
!Sample_type = SRA
|
| 320 |
+
!Sample_channel_count = 1
|
| 321 |
+
!Sample_source_name_ch1 = Peripheral Blood Mononuclear Cells
|
| 322 |
+
!Sample_organism_ch1 = Homo sapiens
|
| 323 |
+
!Sample_taxid_ch1 = 9606
|
| 324 |
+
!Sample_characteristics_ch1 = disease state: myalgic encephalomyelitis/chronic fatigue syndrome
|
| 325 |
+
!Sample_characteristics_ch1 = individual: Patient_One
|
| 326 |
+
!Sample_characteristics_ch1 = time point: B
|
| 327 |
+
!Sample_characteristics_ch1 = cell type: Peripheral Blood Mononuclear Cells
|
| 328 |
+
!Sample_molecule_ch1 = genomic DNA
|
| 329 |
+
!Sample_extract_protocol_ch1 = DNA was extracted from 200ul of PBMCs
|
| 330 |
+
!Sample_extract_protocol_ch1 = MSPI digestion (purify), end repair (purify), A-tialing and adaptor ligation (purify), PCR amplification (purify), Gel size selection and gel extraction (purify)
|
| 331 |
+
!Sample_description = ME007B
|
| 332 |
+
!Sample_data_processing = reads were adaptor trimmed using bismark that used a file of adaptor sequences and trimmed three bases back from any detected adaptor to delete the C invorporated and rejecting any reads that were trimmed to less than 10bp
|
| 333 |
+
!Sample_data_processing = reads were aligned to the hg19 genome using bismark with the following specifications: a tolerance for one non-bisulfite mismatch per read, the default minimum alignment score (L,O, -02), and with ignore - quals in order to calculate the mismatch penalty by considering the quality value at the mismatched position to be the highest possible
|
| 334 |
+
!Sample_data_processing = bam files generated by Bismark alignment were then processed using DMAP to compare control vs. patients with the following specifications: Chi squared test on fragments 40-220bp in length, with the fragment requireing at lest 2 CpGs to have 10 or more sequence reads. The differential methylation file was then annotated with protein coding gene information using the DMAP command identgeneloc. DMAPmatrix.csv file contains this data.
|
| 335 |
+
!Sample_data_processing = Genome_build: hg19
|
| 336 |
+
!Sample_data_processing = Supplementary_files_format_and_content: Individual .txt files for each sample containing C and T frequency per base and coverage. C012_Full, ME007_Full and ME016_Full are excel files that contain, for the control, patient one, and patient two respectively, information about the per fragment methylation data including, genomic location, gene feature information, CpG relative location and fragment size.
|
| 337 |
+
!Sample_platform_id = GPL16791
|
| 338 |
+
!Sample_contact_name = Amber,,Helliwell
|
| 339 |
+
!Sample_contact_department = Biochemistry Department
|
| 340 |
+
!Sample_contact_institute = University of Otago
|
| 341 |
+
!Sample_contact_address = 710 Cumberland Road
|
| 342 |
+
!Sample_contact_city = Dunedin
|
| 343 |
+
!Sample_contact_zip/postal_code = 9016
|
| 344 |
+
!Sample_contact_country = New Zealand
|
| 345 |
+
!Sample_instrument_model = Illumina HiSeq 2500
|
| 346 |
+
!Sample_library_selection = Reduced Representation
|
| 347 |
+
!Sample_library_source = genomic
|
| 348 |
+
!Sample_library_strategy = Bisulfite-Seq
|
| 349 |
+
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN17862804
|
| 350 |
+
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10073453
|
| 351 |
+
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5076nnn/GSM5076046/suppl/GSM5076046_ME007B_CpG.txt.gz
|
| 352 |
+
!Sample_series_id = GSE166592
|
| 353 |
+
!Sample_data_row_count = 0
|
| 354 |
+
^SAMPLE = GSM5076047
|
| 355 |
+
!Sample_title = Patient_One_C
|
| 356 |
+
!Sample_geo_accession = GSM5076047
|
| 357 |
+
!Sample_status = Public on Feb 11 2021
|
| 358 |
+
!Sample_submission_date = Feb 10 2021
|
| 359 |
+
!Sample_last_update_date = Feb 12 2021
|
| 360 |
+
!Sample_type = SRA
|
| 361 |
+
!Sample_channel_count = 1
|
| 362 |
+
!Sample_source_name_ch1 = Peripheral Blood Mononuclear Cells
|
| 363 |
+
!Sample_organism_ch1 = Homo sapiens
|
| 364 |
+
!Sample_taxid_ch1 = 9606
|
| 365 |
+
!Sample_characteristics_ch1 = disease state: myalgic encephalomyelitis/chronic fatigue syndrome
|
| 366 |
+
!Sample_characteristics_ch1 = individual: Patient_One
|
| 367 |
+
!Sample_characteristics_ch1 = time point: C
|
| 368 |
+
!Sample_characteristics_ch1 = cell type: Peripheral Blood Mononuclear Cells
|
| 369 |
+
!Sample_molecule_ch1 = genomic DNA
|
| 370 |
+
!Sample_extract_protocol_ch1 = DNA was extracted from 200ul of PBMCs
|
| 371 |
+
!Sample_extract_protocol_ch1 = MSPI digestion (purify), end repair (purify), A-tialing and adaptor ligation (purify), PCR amplification (purify), Gel size selection and gel extraction (purify)
|
| 372 |
+
!Sample_description = ME007C
|
| 373 |
+
!Sample_data_processing = reads were adaptor trimmed using bismark that used a file of adaptor sequences and trimmed three bases back from any detected adaptor to delete the C invorporated and rejecting any reads that were trimmed to less than 10bp
|
| 374 |
+
!Sample_data_processing = reads were aligned to the hg19 genome using bismark with the following specifications: a tolerance for one non-bisulfite mismatch per read, the default minimum alignment score (L,O, -02), and with ignore - quals in order to calculate the mismatch penalty by considering the quality value at the mismatched position to be the highest possible
|
| 375 |
+
!Sample_data_processing = bam files generated by Bismark alignment were then processed using DMAP to compare control vs. patients with the following specifications: Chi squared test on fragments 40-220bp in length, with the fragment requireing at lest 2 CpGs to have 10 or more sequence reads. The differential methylation file was then annotated with protein coding gene information using the DMAP command identgeneloc. DMAPmatrix.csv file contains this data.
|
| 376 |
+
!Sample_data_processing = Genome_build: hg19
|
| 377 |
+
!Sample_data_processing = Supplementary_files_format_and_content: Individual .txt files for each sample containing C and T frequency per base and coverage. C012_Full, ME007_Full and ME016_Full are excel files that contain, for the control, patient one, and patient two respectively, information about the per fragment methylation data including, genomic location, gene feature information, CpG relative location and fragment size.
|
| 378 |
+
!Sample_platform_id = GPL16791
|
| 379 |
+
!Sample_contact_name = Amber,,Helliwell
|
| 380 |
+
!Sample_contact_department = Biochemistry Department
|
| 381 |
+
!Sample_contact_institute = University of Otago
|
| 382 |
+
!Sample_contact_address = 710 Cumberland Road
|
| 383 |
+
!Sample_contact_city = Dunedin
|
| 384 |
+
!Sample_contact_zip/postal_code = 9016
|
| 385 |
+
!Sample_contact_country = New Zealand
|
| 386 |
+
!Sample_instrument_model = Illumina HiSeq 2500
|
| 387 |
+
!Sample_library_selection = Reduced Representation
|
| 388 |
+
!Sample_library_source = genomic
|
| 389 |
+
!Sample_library_strategy = Bisulfite-Seq
|
| 390 |
+
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN17862803
|
| 391 |
+
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10073454
|
| 392 |
+
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5076nnn/GSM5076047/suppl/GSM5076047_ME007C_CpG.txt.gz
|
| 393 |
+
!Sample_series_id = GSE166592
|
| 394 |
+
!Sample_data_row_count = 0
|
| 395 |
+
^SAMPLE = GSM5076048
|
| 396 |
+
!Sample_title = Patient_One_D
|
| 397 |
+
!Sample_geo_accession = GSM5076048
|
| 398 |
+
!Sample_status = Public on Feb 11 2021
|
| 399 |
+
!Sample_submission_date = Feb 10 2021
|
| 400 |
+
!Sample_last_update_date = Feb 12 2021
|
| 401 |
+
!Sample_type = SRA
|
| 402 |
+
!Sample_channel_count = 1
|
| 403 |
+
!Sample_source_name_ch1 = Peripheral Blood Mononuclear Cells
|
| 404 |
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!Sample_organism_ch1 = Homo sapiens
|
| 405 |
+
!Sample_taxid_ch1 = 9606
|
| 406 |
+
!Sample_characteristics_ch1 = disease state: myalgic encephalomyelitis/chronic fatigue syndrome
|
| 407 |
+
!Sample_characteristics_ch1 = individual: Patient_One
|
| 408 |
+
!Sample_characteristics_ch1 = time point: D
|
| 409 |
+
!Sample_characteristics_ch1 = cell type: Peripheral Blood Mononuclear Cells
|
| 410 |
+
!Sample_molecule_ch1 = genomic DNA
|
| 411 |
+
!Sample_extract_protocol_ch1 = DNA was extracted from 200ul of PBMCs
|
| 412 |
+
!Sample_extract_protocol_ch1 = MSPI digestion (purify), end repair (purify), A-tialing and adaptor ligation (purify), PCR amplification (purify), Gel size selection and gel extraction (purify)
|
| 413 |
+
!Sample_description = ME007D
|
| 414 |
+
!Sample_data_processing = reads were adaptor trimmed using bismark that used a file of adaptor sequences and trimmed three bases back from any detected adaptor to delete the C invorporated and rejecting any reads that were trimmed to less than 10bp
|
| 415 |
+
!Sample_data_processing = reads were aligned to the hg19 genome using bismark with the following specifications: a tolerance for one non-bisulfite mismatch per read, the default minimum alignment score (L,O, -02), and with ignore - quals in order to calculate the mismatch penalty by considering the quality value at the mismatched position to be the highest possible
|
| 416 |
+
!Sample_data_processing = bam files generated by Bismark alignment were then processed using DMAP to compare control vs. patients with the following specifications: Chi squared test on fragments 40-220bp in length, with the fragment requireing at lest 2 CpGs to have 10 or more sequence reads. The differential methylation file was then annotated with protein coding gene information using the DMAP command identgeneloc. DMAPmatrix.csv file contains this data.
|
| 417 |
+
!Sample_data_processing = Genome_build: hg19
|
| 418 |
+
!Sample_data_processing = Supplementary_files_format_and_content: Individual .txt files for each sample containing C and T frequency per base and coverage. C012_Full, ME007_Full and ME016_Full are excel files that contain, for the control, patient one, and patient two respectively, information about the per fragment methylation data including, genomic location, gene feature information, CpG relative location and fragment size.
|
| 419 |
+
!Sample_platform_id = GPL16791
|
| 420 |
+
!Sample_contact_name = Amber,,Helliwell
|
| 421 |
+
!Sample_contact_department = Biochemistry Department
|
| 422 |
+
!Sample_contact_institute = University of Otago
|
| 423 |
+
!Sample_contact_address = 710 Cumberland Road
|
| 424 |
+
!Sample_contact_city = Dunedin
|
| 425 |
+
!Sample_contact_zip/postal_code = 9016
|
| 426 |
+
!Sample_contact_country = New Zealand
|
| 427 |
+
!Sample_instrument_model = Illumina HiSeq 2500
|
| 428 |
+
!Sample_library_selection = Reduced Representation
|
| 429 |
+
!Sample_library_source = genomic
|
| 430 |
+
!Sample_library_strategy = Bisulfite-Seq
|
| 431 |
+
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN17862802
|
| 432 |
+
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10073455
|
| 433 |
+
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5076nnn/GSM5076048/suppl/GSM5076048_ME007D_CpG.txt.gz
|
| 434 |
+
!Sample_series_id = GSE166592
|
| 435 |
+
!Sample_data_row_count = 0
|
| 436 |
+
^SAMPLE = GSM5076049
|
| 437 |
+
!Sample_title = Patient_One_E
|
| 438 |
+
!Sample_geo_accession = GSM5076049
|
| 439 |
+
!Sample_status = Public on Feb 11 2021
|
| 440 |
+
!Sample_submission_date = Feb 10 2021
|
| 441 |
+
!Sample_last_update_date = Feb 12 2021
|
| 442 |
+
!Sample_type = SRA
|
| 443 |
+
!Sample_channel_count = 1
|
| 444 |
+
!Sample_source_name_ch1 = Peripheral Blood Mononuclear Cells
|
| 445 |
+
!Sample_organism_ch1 = Homo sapiens
|
| 446 |
+
!Sample_taxid_ch1 = 9606
|
| 447 |
+
!Sample_characteristics_ch1 = disease state: myalgic encephalomyelitis/chronic fatigue syndrome
|
| 448 |
+
!Sample_characteristics_ch1 = individual: Patient_One
|
| 449 |
+
!Sample_characteristics_ch1 = time point: E
|
| 450 |
+
!Sample_characteristics_ch1 = cell type: Peripheral Blood Mononuclear Cells
|
| 451 |
+
!Sample_molecule_ch1 = genomic DNA
|
| 452 |
+
!Sample_extract_protocol_ch1 = DNA was extracted from 200ul of PBMCs
|
| 453 |
+
!Sample_extract_protocol_ch1 = MSPI digestion (purify), end repair (purify), A-tialing and adaptor ligation (purify), PCR amplification (purify), Gel size selection and gel extraction (purify)
|
| 454 |
+
!Sample_description = ME007E
|
| 455 |
+
!Sample_data_processing = reads were adaptor trimmed using bismark that used a file of adaptor sequences and trimmed three bases back from any detected adaptor to delete the C invorporated and rejecting any reads that were trimmed to less than 10bp
|
| 456 |
+
!Sample_data_processing = reads were aligned to the hg19 genome using bismark with the following specifications: a tolerance for one non-bisulfite mismatch per read, the default minimum alignment score (L,O, -02), and with ignore - quals in order to calculate the mismatch penalty by considering the quality value at the mismatched position to be the highest possible
|
| 457 |
+
!Sample_data_processing = bam files generated by Bismark alignment were then processed using DMAP to compare control vs. patients with the following specifications: Chi squared test on fragments 40-220bp in length, with the fragment requireing at lest 2 CpGs to have 10 or more sequence reads. The differential methylation file was then annotated with protein coding gene information using the DMAP command identgeneloc. DMAPmatrix.csv file contains this data.
|
| 458 |
+
!Sample_data_processing = Genome_build: hg19
|
| 459 |
+
!Sample_data_processing = Supplementary_files_format_and_content: Individual .txt files for each sample containing C and T frequency per base and coverage. C012_Full, ME007_Full and ME016_Full are excel files that contain, for the control, patient one, and patient two respectively, information about the per fragment methylation data including, genomic location, gene feature information, CpG relative location and fragment size.
|
| 460 |
+
!Sample_platform_id = GPL16791
|
| 461 |
+
!Sample_contact_name = Amber,,Helliwell
|
| 462 |
+
!Sample_contact_department = Biochemistry Department
|
| 463 |
+
!Sample_contact_institute = University of Otago
|
| 464 |
+
!Sample_contact_address = 710 Cumberland Road
|
| 465 |
+
!Sample_contact_city = Dunedin
|
| 466 |
+
!Sample_contact_zip/postal_code = 9016
|
| 467 |
+
!Sample_contact_country = New Zealand
|
| 468 |
+
!Sample_instrument_model = Illumina HiSeq 2500
|
| 469 |
+
!Sample_library_selection = Reduced Representation
|
| 470 |
+
!Sample_library_source = genomic
|
| 471 |
+
!Sample_library_strategy = Bisulfite-Seq
|
| 472 |
+
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN17862801
|
| 473 |
+
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10073456
|
| 474 |
+
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5076nnn/GSM5076049/suppl/GSM5076049_ME007E_CpG.txt.gz
|
| 475 |
+
!Sample_series_id = GSE166592
|
| 476 |
+
!Sample_data_row_count = 0
|
| 477 |
+
^SAMPLE = GSM5076050
|
| 478 |
+
!Sample_title = Patient_Two_A
|
| 479 |
+
!Sample_geo_accession = GSM5076050
|
| 480 |
+
!Sample_status = Public on Feb 11 2021
|
| 481 |
+
!Sample_submission_date = Feb 10 2021
|
| 482 |
+
!Sample_last_update_date = Feb 12 2021
|
| 483 |
+
!Sample_type = SRA
|
| 484 |
+
!Sample_channel_count = 1
|
| 485 |
+
!Sample_source_name_ch1 = Peripheral Blood Mononuclear Cells
|
| 486 |
+
!Sample_organism_ch1 = Homo sapiens
|
| 487 |
+
!Sample_taxid_ch1 = 9606
|
| 488 |
+
!Sample_characteristics_ch1 = disease state: myalgic encephalomyelitis/chronic fatigue syndrome
|
| 489 |
+
!Sample_characteristics_ch1 = individual: Patient_Two
|
| 490 |
+
!Sample_characteristics_ch1 = time point: A
|
| 491 |
+
!Sample_characteristics_ch1 = cell type: Peripheral Blood Mononuclear Cells
|
| 492 |
+
!Sample_molecule_ch1 = genomic DNA
|
| 493 |
+
!Sample_extract_protocol_ch1 = DNA was extracted from 200ul of PBMCs
|
| 494 |
+
!Sample_extract_protocol_ch1 = MSPI digestion (purify), end repair (purify), A-tialing and adaptor ligation (purify), PCR amplification (purify), Gel size selection and gel extraction (purify)
|
| 495 |
+
!Sample_description = ME016A
|
| 496 |
+
!Sample_data_processing = reads were adaptor trimmed using bismark that used a file of adaptor sequences and trimmed three bases back from any detected adaptor to delete the C invorporated and rejecting any reads that were trimmed to less than 10bp
|
| 497 |
+
!Sample_data_processing = reads were aligned to the hg19 genome using bismark with the following specifications: a tolerance for one non-bisulfite mismatch per read, the default minimum alignment score (L,O, -02), and with ignore - quals in order to calculate the mismatch penalty by considering the quality value at the mismatched position to be the highest possible
|
| 498 |
+
!Sample_data_processing = bam files generated by Bismark alignment were then processed using DMAP to compare control vs. patients with the following specifications: Chi squared test on fragments 40-220bp in length, with the fragment requireing at lest 2 CpGs to have 10 or more sequence reads. The differential methylation file was then annotated with protein coding gene information using the DMAP command identgeneloc. DMAPmatrix.csv file contains this data.
|
| 499 |
+
!Sample_data_processing = Genome_build: hg19
|
| 500 |
+
!Sample_data_processing = Supplementary_files_format_and_content: Individual .txt files for each sample containing C and T frequency per base and coverage. C012_Full, ME007_Full and ME016_Full are excel files that contain, for the control, patient one, and patient two respectively, information about the per fragment methylation data including, genomic location, gene feature information, CpG relative location and fragment size.
|
| 501 |
+
!Sample_platform_id = GPL16791
|
| 502 |
+
!Sample_contact_name = Amber,,Helliwell
|
| 503 |
+
!Sample_contact_department = Biochemistry Department
|
| 504 |
+
!Sample_contact_institute = University of Otago
|
| 505 |
+
!Sample_contact_address = 710 Cumberland Road
|
| 506 |
+
!Sample_contact_city = Dunedin
|
| 507 |
+
!Sample_contact_zip/postal_code = 9016
|
| 508 |
+
!Sample_contact_country = New Zealand
|
| 509 |
+
!Sample_instrument_model = Illumina HiSeq 2500
|
| 510 |
+
!Sample_library_selection = Reduced Representation
|
| 511 |
+
!Sample_library_source = genomic
|
| 512 |
+
!Sample_library_strategy = Bisulfite-Seq
|
| 513 |
+
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN17862800
|
| 514 |
+
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10073457
|
| 515 |
+
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5076nnn/GSM5076050/suppl/GSM5076050_ME016A_CpG.txt.gz
|
| 516 |
+
!Sample_series_id = GSE166592
|
| 517 |
+
!Sample_data_row_count = 0
|
| 518 |
+
^SAMPLE = GSM5076051
|
| 519 |
+
!Sample_title = Patient_Two_B
|
| 520 |
+
!Sample_geo_accession = GSM5076051
|
| 521 |
+
!Sample_status = Public on Feb 11 2021
|
| 522 |
+
!Sample_submission_date = Feb 10 2021
|
| 523 |
+
!Sample_last_update_date = Feb 12 2021
|
| 524 |
+
!Sample_type = SRA
|
| 525 |
+
!Sample_channel_count = 1
|
| 526 |
+
!Sample_source_name_ch1 = Peripheral Blood Mononuclear Cells
|
| 527 |
+
!Sample_organism_ch1 = Homo sapiens
|
| 528 |
+
!Sample_taxid_ch1 = 9606
|
| 529 |
+
!Sample_characteristics_ch1 = disease state: myalgic encephalomyelitis/chronic fatigue syndrome
|
| 530 |
+
!Sample_characteristics_ch1 = individual: Patient_Two
|
| 531 |
+
!Sample_characteristics_ch1 = time point: B
|
| 532 |
+
!Sample_characteristics_ch1 = cell type: Peripheral Blood Mononuclear Cells
|
| 533 |
+
!Sample_molecule_ch1 = genomic DNA
|
| 534 |
+
!Sample_extract_protocol_ch1 = DNA was extracted from 200ul of PBMCs
|
| 535 |
+
!Sample_extract_protocol_ch1 = MSPI digestion (purify), end repair (purify), A-tialing and adaptor ligation (purify), PCR amplification (purify), Gel size selection and gel extraction (purify)
|
| 536 |
+
!Sample_description = ME016B
|
| 537 |
+
!Sample_data_processing = reads were adaptor trimmed using bismark that used a file of adaptor sequences and trimmed three bases back from any detected adaptor to delete the C invorporated and rejecting any reads that were trimmed to less than 10bp
|
| 538 |
+
!Sample_data_processing = reads were aligned to the hg19 genome using bismark with the following specifications: a tolerance for one non-bisulfite mismatch per read, the default minimum alignment score (L,O, -02), and with ignore - quals in order to calculate the mismatch penalty by considering the quality value at the mismatched position to be the highest possible
|
| 539 |
+
!Sample_data_processing = bam files generated by Bismark alignment were then processed using DMAP to compare control vs. patients with the following specifications: Chi squared test on fragments 40-220bp in length, with the fragment requireing at lest 2 CpGs to have 10 or more sequence reads. The differential methylation file was then annotated with protein coding gene information using the DMAP command identgeneloc. DMAPmatrix.csv file contains this data.
|
| 540 |
+
!Sample_data_processing = Genome_build: hg19
|
| 541 |
+
!Sample_data_processing = Supplementary_files_format_and_content: Individual .txt files for each sample containing C and T frequency per base and coverage. C012_Full, ME007_Full and ME016_Full are excel files that contain, for the control, patient one, and patient two respectively, information about the per fragment methylation data including, genomic location, gene feature information, CpG relative location and fragment size.
|
| 542 |
+
!Sample_platform_id = GPL16791
|
| 543 |
+
!Sample_contact_name = Amber,,Helliwell
|
| 544 |
+
!Sample_contact_department = Biochemistry Department
|
| 545 |
+
!Sample_contact_institute = University of Otago
|
| 546 |
+
!Sample_contact_address = 710 Cumberland Road
|
| 547 |
+
!Sample_contact_city = Dunedin
|
| 548 |
+
!Sample_contact_zip/postal_code = 9016
|
| 549 |
+
!Sample_contact_country = New Zealand
|
| 550 |
+
!Sample_instrument_model = Illumina HiSeq 2500
|
| 551 |
+
!Sample_library_selection = Reduced Representation
|
| 552 |
+
!Sample_library_source = genomic
|
| 553 |
+
!Sample_library_strategy = Bisulfite-Seq
|
| 554 |
+
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN17862799
|
| 555 |
+
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10073458
|
| 556 |
+
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5076nnn/GSM5076051/suppl/GSM5076051_ME016B_CpG.txt.gz
|
| 557 |
+
!Sample_series_id = GSE166592
|
| 558 |
+
!Sample_data_row_count = 0
|
| 559 |
+
^SAMPLE = GSM5076052
|
| 560 |
+
!Sample_title = Patient_Two_C
|
| 561 |
+
!Sample_geo_accession = GSM5076052
|
| 562 |
+
!Sample_status = Public on Feb 11 2021
|
| 563 |
+
!Sample_submission_date = Feb 10 2021
|
| 564 |
+
!Sample_last_update_date = Mar 17 2021
|
| 565 |
+
!Sample_type = SRA
|
| 566 |
+
!Sample_channel_count = 1
|
| 567 |
+
!Sample_source_name_ch1 = Peripheral Blood Mononuclear Cells
|
| 568 |
+
!Sample_organism_ch1 = Homo sapiens
|
| 569 |
+
!Sample_taxid_ch1 = 9606
|
| 570 |
+
!Sample_characteristics_ch1 = disease state: myalgic encephalomyelitis/chronic fatigue syndrome
|
| 571 |
+
!Sample_characteristics_ch1 = individual: Patient_Two
|
| 572 |
+
!Sample_characteristics_ch1 = time point: C
|
| 573 |
+
!Sample_characteristics_ch1 = cell type: Peripheral Blood Mononuclear Cells
|
| 574 |
+
!Sample_molecule_ch1 = genomic DNA
|
| 575 |
+
!Sample_extract_protocol_ch1 = DNA was extracted from 200ul of PBMCs
|
| 576 |
+
!Sample_extract_protocol_ch1 = MSPI digestion (purify), end repair (purify), A-tialing and adaptor ligation (purify), PCR amplification (purify), Gel size selection and gel extraction (purify)
|
| 577 |
+
!Sample_description = ME016C
|
| 578 |
+
!Sample_data_processing = reads were adaptor trimmed using bismark that used a file of adaptor sequences and trimmed three bases back from any detected adaptor to delete the C invorporated and rejecting any reads that were trimmed to less than 10bp
|
| 579 |
+
!Sample_data_processing = reads were aligned to the hg19 genome using bismark with the following specifications: a tolerance for one non-bisulfite mismatch per read, the default minimum alignment score (L,O, -02), and with ignore - quals in order to calculate the mismatch penalty by considering the quality value at the mismatched position to be the highest possible
|
| 580 |
+
!Sample_data_processing = bam files generated by Bismark alignment were then processed using DMAP to compare control vs. patients with the following specifications: Chi squared test on fragments 40-220bp in length, with the fragment requireing at lest 2 CpGs to have 10 or more sequence reads. The differential methylation file was then annotated with protein coding gene information using the DMAP command identgeneloc. DMAPmatrix.csv file contains this data.
|
| 581 |
+
!Sample_data_processing = Genome_build: hg19
|
| 582 |
+
!Sample_data_processing = Supplementary_files_format_and_content: Individual .txt files for each sample containing C and T frequency per base and coverage. C012_Full, ME007_Full and ME016_Full are excel files that contain, for the control, patient one, and patient two respectively, information about the per fragment methylation data including, genomic location, gene feature information, CpG relative location and fragment size.
|
| 583 |
+
!Sample_platform_id = GPL16791
|
| 584 |
+
!Sample_contact_name = Amber,,Helliwell
|
| 585 |
+
!Sample_contact_department = Biochemistry Department
|
| 586 |
+
!Sample_contact_institute = University of Otago
|
| 587 |
+
!Sample_contact_address = 710 Cumberland Road
|
| 588 |
+
!Sample_contact_city = Dunedin
|
| 589 |
+
!Sample_contact_zip/postal_code = 9016
|
| 590 |
+
!Sample_contact_country = New Zealand
|
| 591 |
+
!Sample_instrument_model = Illumina HiSeq 2500
|
| 592 |
+
!Sample_library_selection = Reduced Representation
|
| 593 |
+
!Sample_library_source = genomic
|
| 594 |
+
!Sample_library_strategy = Bisulfite-Seq
|
| 595 |
+
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN17862798
|
| 596 |
+
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10073459
|
| 597 |
+
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5076nnn/GSM5076052/suppl/GSM5076052_ME016C_CpG.txt.gz
|
| 598 |
+
!Sample_series_id = GSE166592
|
| 599 |
+
!Sample_data_row_count = 0
|
| 600 |
+
^SAMPLE = GSM5076053
|
| 601 |
+
!Sample_title = Patient_Two_D
|
| 602 |
+
!Sample_geo_accession = GSM5076053
|
| 603 |
+
!Sample_status = Public on Feb 11 2021
|
| 604 |
+
!Sample_submission_date = Feb 10 2021
|
| 605 |
+
!Sample_last_update_date = Feb 12 2021
|
| 606 |
+
!Sample_type = SRA
|
| 607 |
+
!Sample_channel_count = 1
|
| 608 |
+
!Sample_source_name_ch1 = Peripheral Blood Mononuclear Cells
|
| 609 |
+
!Sample_organism_ch1 = Homo sapiens
|
| 610 |
+
!Sample_taxid_ch1 = 9606
|
| 611 |
+
!Sample_characteristics_ch1 = disease state: myalgic encephalomyelitis/chronic fatigue syndrome
|
| 612 |
+
!Sample_characteristics_ch1 = individual: Patient_Two
|
| 613 |
+
!Sample_characteristics_ch1 = time point: D
|
| 614 |
+
!Sample_characteristics_ch1 = cell type: Peripheral Blood Mononuclear Cells
|
| 615 |
+
!Sample_molecule_ch1 = genomic DNA
|
| 616 |
+
!Sample_extract_protocol_ch1 = DNA was extracted from 200ul of PBMCs
|
| 617 |
+
!Sample_extract_protocol_ch1 = MSPI digestion (purify), end repair (purify), A-tialing and adaptor ligation (purify), PCR amplification (purify), Gel size selection and gel extraction (purify)
|
| 618 |
+
!Sample_description = ME016D
|
| 619 |
+
!Sample_data_processing = reads were adaptor trimmed using bismark that used a file of adaptor sequences and trimmed three bases back from any detected adaptor to delete the C invorporated and rejecting any reads that were trimmed to less than 10bp
|
| 620 |
+
!Sample_data_processing = reads were aligned to the hg19 genome using bismark with the following specifications: a tolerance for one non-bisulfite mismatch per read, the default minimum alignment score (L,O, -02), and with ignore - quals in order to calculate the mismatch penalty by considering the quality value at the mismatched position to be the highest possible
|
| 621 |
+
!Sample_data_processing = bam files generated by Bismark alignment were then processed using DMAP to compare control vs. patients with the following specifications: Chi squared test on fragments 40-220bp in length, with the fragment requireing at lest 2 CpGs to have 10 or more sequence reads. The differential methylation file was then annotated with protein coding gene information using the DMAP command identgeneloc. DMAPmatrix.csv file contains this data.
|
| 622 |
+
!Sample_data_processing = Genome_build: hg19
|
| 623 |
+
!Sample_data_processing = Supplementary_files_format_and_content: Individual .txt files for each sample containing C and T frequency per base and coverage. C012_Full, ME007_Full and ME016_Full are excel files that contain, for the control, patient one, and patient two respectively, information about the per fragment methylation data including, genomic location, gene feature information, CpG relative location and fragment size.
|
| 624 |
+
!Sample_platform_id = GPL16791
|
| 625 |
+
!Sample_contact_name = Amber,,Helliwell
|
| 626 |
+
!Sample_contact_department = Biochemistry Department
|
| 627 |
+
!Sample_contact_institute = University of Otago
|
| 628 |
+
!Sample_contact_address = 710 Cumberland Road
|
| 629 |
+
!Sample_contact_city = Dunedin
|
| 630 |
+
!Sample_contact_zip/postal_code = 9016
|
| 631 |
+
!Sample_contact_country = New Zealand
|
| 632 |
+
!Sample_instrument_model = Illumina HiSeq 2500
|
| 633 |
+
!Sample_library_selection = Reduced Representation
|
| 634 |
+
!Sample_library_source = genomic
|
| 635 |
+
!Sample_library_strategy = Bisulfite-Seq
|
| 636 |
+
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN17862797
|
| 637 |
+
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10073460
|
| 638 |
+
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5076nnn/GSM5076053/suppl/GSM5076053_ME016D_CpG.txt.gz
|
| 639 |
+
!Sample_series_id = GSE166592
|
| 640 |
+
!Sample_data_row_count = 0
|
| 641 |
+
^SAMPLE = GSM5076054
|
| 642 |
+
!Sample_title = Patient_Two_E
|
| 643 |
+
!Sample_geo_accession = GSM5076054
|
| 644 |
+
!Sample_status = Public on Feb 11 2021
|
| 645 |
+
!Sample_submission_date = Feb 10 2021
|
| 646 |
+
!Sample_last_update_date = Feb 12 2021
|
| 647 |
+
!Sample_type = SRA
|
| 648 |
+
!Sample_channel_count = 1
|
| 649 |
+
!Sample_source_name_ch1 = Peripheral Blood Mononuclear Cells
|
| 650 |
+
!Sample_organism_ch1 = Homo sapiens
|
| 651 |
+
!Sample_taxid_ch1 = 9606
|
| 652 |
+
!Sample_characteristics_ch1 = disease state: myalgic encephalomyelitis/chronic fatigue syndrome
|
| 653 |
+
!Sample_characteristics_ch1 = individual: Patient_Two
|
| 654 |
+
!Sample_characteristics_ch1 = time point: E
|
| 655 |
+
!Sample_characteristics_ch1 = cell type: Peripheral Blood Mononuclear Cells
|
| 656 |
+
!Sample_molecule_ch1 = genomic DNA
|
| 657 |
+
!Sample_extract_protocol_ch1 = DNA was extracted from 200ul of PBMCs
|
| 658 |
+
!Sample_extract_protocol_ch1 = MSPI digestion (purify), end repair (purify), A-tialing and adaptor ligation (purify), PCR amplification (purify), Gel size selection and gel extraction (purify)
|
| 659 |
+
!Sample_description = ME016E
|
| 660 |
+
!Sample_data_processing = reads were adaptor trimmed using bismark that used a file of adaptor sequences and trimmed three bases back from any detected adaptor to delete the C invorporated and rejecting any reads that were trimmed to less than 10bp
|
| 661 |
+
!Sample_data_processing = reads were aligned to the hg19 genome using bismark with the following specifications: a tolerance for one non-bisulfite mismatch per read, the default minimum alignment score (L,O, -02), and with ignore - quals in order to calculate the mismatch penalty by considering the quality value at the mismatched position to be the highest possible
|
| 662 |
+
!Sample_data_processing = bam files generated by Bismark alignment were then processed using DMAP to compare control vs. patients with the following specifications: Chi squared test on fragments 40-220bp in length, with the fragment requireing at lest 2 CpGs to have 10 or more sequence reads. The differential methylation file was then annotated with protein coding gene information using the DMAP command identgeneloc. DMAPmatrix.csv file contains this data.
|
| 663 |
+
!Sample_data_processing = Genome_build: hg19
|
| 664 |
+
!Sample_data_processing = Supplementary_files_format_and_content: Individual .txt files for each sample containing C and T frequency per base and coverage. C012_Full, ME007_Full and ME016_Full are excel files that contain, for the control, patient one, and patient two respectively, information about the per fragment methylation data including, genomic location, gene feature information, CpG relative location and fragment size.
|
| 665 |
+
!Sample_platform_id = GPL16791
|
| 666 |
+
!Sample_contact_name = Amber,,Helliwell
|
| 667 |
+
!Sample_contact_department = Biochemistry Department
|
| 668 |
+
!Sample_contact_institute = University of Otago
|
| 669 |
+
!Sample_contact_address = 710 Cumberland Road
|
| 670 |
+
!Sample_contact_city = Dunedin
|
| 671 |
+
!Sample_contact_zip/postal_code = 9016
|
| 672 |
+
!Sample_contact_country = New Zealand
|
| 673 |
+
!Sample_instrument_model = Illumina HiSeq 2500
|
| 674 |
+
!Sample_library_selection = Reduced Representation
|
| 675 |
+
!Sample_library_source = genomic
|
| 676 |
+
!Sample_library_strategy = Bisulfite-Seq
|
| 677 |
+
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN17862796
|
| 678 |
+
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10073461
|
| 679 |
+
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5076nnn/GSM5076054/suppl/GSM5076054_ME016E_CpG.txt.gz
|
| 680 |
+
!Sample_series_id = GSE166592
|
| 681 |
+
!Sample_data_row_count = 0
|
ME/GSE166592/meta/GSE166592_family.xml
ADDED
|
@@ -0,0 +1,965 @@
|
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|
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|
| 1 |
+
<?xml version="1.0" encoding="UTF-8" standalone="no"?>
|
| 2 |
+
|
| 3 |
+
<MINiML
|
| 4 |
+
xmlns="http://www.ncbi.nlm.nih.gov/geo/info/MINiML"
|
| 5 |
+
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
|
| 6 |
+
xsi:schemaLocation="http://www.ncbi.nlm.nih.gov/geo/info/MINiML http://www.ncbi.nlm.nih.gov/geo/info/MINiML.xsd"
|
| 7 |
+
version="0.5.0" >
|
| 8 |
+
|
| 9 |
+
<Contributor iid="contrib1">
|
| 10 |
+
<Person><First>Amber</First><Last>Helliwell</Last></Person>
|
| 11 |
+
<Department>Biochemistry Department</Department>
|
| 12 |
+
<Organization>University of Otago</Organization>
|
| 13 |
+
<Address>
|
| 14 |
+
<Line>710 Cumberland Road</Line>
|
| 15 |
+
<City>Dunedin</City>
|
| 16 |
+
<Postal-Code>9016</Postal-Code>
|
| 17 |
+
<Country>New Zealand</Country>
|
| 18 |
+
</Address>
|
| 19 |
+
</Contributor>
|
| 20 |
+
|
| 21 |
+
<Contributor iid="contrib2">
|
| 22 |
+
<Organization>GEO</Organization>
|
| 23 |
+
<Address>
|
| 24 |
+
<City></City>
|
| 25 |
+
<Country>USA</Country>
|
| 26 |
+
</Address>
|
| 27 |
+
</Contributor>
|
| 28 |
+
|
| 29 |
+
<Contributor iid="contrib3">
|
| 30 |
+
<Person><First>Warren</First><Last>Tate</Last></Person>
|
| 31 |
+
</Contributor>
|
| 32 |
+
|
| 33 |
+
<Contributor iid="contrib4">
|
| 34 |
+
<Person><First>Aniruddha</First><Last>Chatterjee</Last></Person>
|
| 35 |
+
</Contributor>
|
| 36 |
+
|
| 37 |
+
<Contributor iid="contrib5">
|
| 38 |
+
<Person><First>Peter</First><Last>Stockwell</Last></Person>
|
| 39 |
+
</Contributor>
|
| 40 |
+
|
| 41 |
+
<Contributor iid="contrib6">
|
| 42 |
+
<Person><First>Tina</First><Last>Edgar</Last></Person>
|
| 43 |
+
</Contributor>
|
| 44 |
+
|
| 45 |
+
<Database iid="GEO">
|
| 46 |
+
<Name>Gene Expression Omnibus (GEO)</Name>
|
| 47 |
+
<Public-ID>GEO</Public-ID>
|
| 48 |
+
<Organization>NCBI NLM NIH</Organization>
|
| 49 |
+
<Web-Link>http://www.ncbi.nlm.nih.gov/geo</Web-Link>
|
| 50 |
+
<Email>geo@ncbi.nlm.nih.gov</Email>
|
| 51 |
+
</Database>
|
| 52 |
+
|
| 53 |
+
<Platform iid="GPL16791">
|
| 54 |
+
<Status database="GEO">
|
| 55 |
+
<Submission-Date>2013-03-14</Submission-Date>
|
| 56 |
+
<Release-Date>2013-03-14</Release-Date>
|
| 57 |
+
<Last-Update-Date>2019-03-27</Last-Update-Date>
|
| 58 |
+
</Status>
|
| 59 |
+
<Title>Illumina HiSeq 2500 (Homo sapiens)</Title>
|
| 60 |
+
<Accession database="GEO">GPL16791</Accession>
|
| 61 |
+
<Technology>high-throughput sequencing</Technology>
|
| 62 |
+
<Distribution>virtual</Distribution>
|
| 63 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 64 |
+
<Manufacturer></Manufacturer>
|
| 65 |
+
<Manufacture-Protocol>
|
| 66 |
+
</Manufacture-Protocol>
|
| 67 |
+
<Contact-Ref ref="contrib2" />
|
| 68 |
+
</Platform>
|
| 69 |
+
|
| 70 |
+
<Sample iid="GSM5076040">
|
| 71 |
+
<Status database="GEO">
|
| 72 |
+
<Submission-Date>2021-02-10</Submission-Date>
|
| 73 |
+
<Release-Date>2021-02-11</Release-Date>
|
| 74 |
+
<Last-Update-Date>2021-02-12</Last-Update-Date>
|
| 75 |
+
</Status>
|
| 76 |
+
<Title>C012A</Title>
|
| 77 |
+
<Accession database="GEO">GSM5076040</Accession>
|
| 78 |
+
<Type>SRA</Type>
|
| 79 |
+
<Channel-Count>1</Channel-Count>
|
| 80 |
+
<Channel position="1">
|
| 81 |
+
<Source>Peripheral Blood Mononuclear Cells</Source>
|
| 82 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 83 |
+
<Characteristics tag="disease state">
|
| 84 |
+
Control
|
| 85 |
+
</Characteristics>
|
| 86 |
+
<Characteristics tag="individual">
|
| 87 |
+
C012
|
| 88 |
+
</Characteristics>
|
| 89 |
+
<Characteristics tag="time point">
|
| 90 |
+
A
|
| 91 |
+
</Characteristics>
|
| 92 |
+
<Characteristics tag="cell type">
|
| 93 |
+
Peripheral Blood Mononuclear Cells
|
| 94 |
+
</Characteristics>
|
| 95 |
+
<Molecule>genomic DNA</Molecule>
|
| 96 |
+
<Extract-Protocol>
|
| 97 |
+
DNA was extracted from 200ul of PBMCs
|
| 98 |
+
MSPI digestion (purify), end repair (purify), A-tialing and adaptor ligation (purify), PCR amplification (purify), Gel size selection and gel extraction (purify)
|
| 99 |
+
</Extract-Protocol>
|
| 100 |
+
</Channel>
|
| 101 |
+
<Description>
|
| 102 |
+
C012A
|
| 103 |
+
</Description>
|
| 104 |
+
<Data-Processing>
|
| 105 |
+
reads were adaptor trimmed using bismark that used a file of adaptor sequences and trimmed three bases back from any detected adaptor to delete the C invorporated and rejecting any reads that were trimmed to less than 10bp
|
| 106 |
+
reads were aligned to the hg19 genome using bismark with the following specifications: a tolerance for one non-bisulfite mismatch per read, the default minimum alignment score (L,O, -02), and with ignore - quals in order to calculate the mismatch penalty by considering the quality value at the mismatched position to be the highest possible
|
| 107 |
+
bam files generated by Bismark alignment were then processed using DMAP to compare control vs. patients with the following specifications: Chi squared test on fragments 40-220bp in length, with the fragment requireing at lest 2 CpGs to have 10 or more sequence reads. The differential methylation file was then annotated with protein coding gene information using the DMAP command identgeneloc. DMAPmatrix.csv file contains this data.
|
| 108 |
+
Genome_build: hg19
|
| 109 |
+
Supplementary_files_format_and_content: Individual .txt files for each sample containing C and T frequency per base and coverage. C012_Full, ME007_Full and ME016_Full are excel files that contain, for the control, patient one, and patient two respectively, information about the per fragment methylation data including, genomic location, gene feature information, CpG relative location and fragment size.
|
| 110 |
+
</Data-Processing>
|
| 111 |
+
<Platform-Ref ref="GPL16791" />
|
| 112 |
+
<Library-Strategy>Bisulfite-Seq</Library-Strategy>
|
| 113 |
+
<Library-Source>genomic</Library-Source>
|
| 114 |
+
<Library-Selection>Reduced Representation</Library-Selection>
|
| 115 |
+
<Instrument-Model>
|
| 116 |
+
<Predefined>Illumina HiSeq 2500</Predefined>
|
| 117 |
+
</Instrument-Model>
|
| 118 |
+
<Contact-Ref ref="contrib1" />
|
| 119 |
+
<Supplementary-Data type="TXT">
|
| 120 |
+
ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5076nnn/GSM5076040/suppl/GSM5076040_C012A_CpG.txt.gz
|
| 121 |
+
</Supplementary-Data>
|
| 122 |
+
<Relation type="BioSample" target="https://www.ncbi.nlm.nih.gov/biosample/SAMN17862810" />
|
| 123 |
+
<Relation type="SRA" target="https://www.ncbi.nlm.nih.gov/sra?term=SRX10073447" />
|
| 124 |
+
</Sample>
|
| 125 |
+
|
| 126 |
+
<Sample iid="GSM5076041">
|
| 127 |
+
<Status database="GEO">
|
| 128 |
+
<Submission-Date>2021-02-10</Submission-Date>
|
| 129 |
+
<Release-Date>2021-02-11</Release-Date>
|
| 130 |
+
<Last-Update-Date>2021-02-12</Last-Update-Date>
|
| 131 |
+
</Status>
|
| 132 |
+
<Title>C012B</Title>
|
| 133 |
+
<Accession database="GEO">GSM5076041</Accession>
|
| 134 |
+
<Type>SRA</Type>
|
| 135 |
+
<Channel-Count>1</Channel-Count>
|
| 136 |
+
<Channel position="1">
|
| 137 |
+
<Source>Peripheral Blood Mononuclear Cells</Source>
|
| 138 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 139 |
+
<Characteristics tag="disease state">
|
| 140 |
+
Control
|
| 141 |
+
</Characteristics>
|
| 142 |
+
<Characteristics tag="individual">
|
| 143 |
+
C012
|
| 144 |
+
</Characteristics>
|
| 145 |
+
<Characteristics tag="time point">
|
| 146 |
+
B
|
| 147 |
+
</Characteristics>
|
| 148 |
+
<Characteristics tag="cell type">
|
| 149 |
+
Peripheral Blood Mononuclear Cells
|
| 150 |
+
</Characteristics>
|
| 151 |
+
<Molecule>genomic DNA</Molecule>
|
| 152 |
+
<Extract-Protocol>
|
| 153 |
+
DNA was extracted from 200ul of PBMCs
|
| 154 |
+
MSPI digestion (purify), end repair (purify), A-tialing and adaptor ligation (purify), PCR amplification (purify), Gel size selection and gel extraction (purify)
|
| 155 |
+
</Extract-Protocol>
|
| 156 |
+
</Channel>
|
| 157 |
+
<Description>
|
| 158 |
+
C012B
|
| 159 |
+
</Description>
|
| 160 |
+
<Data-Processing>
|
| 161 |
+
reads were adaptor trimmed using bismark that used a file of adaptor sequences and trimmed three bases back from any detected adaptor to delete the C invorporated and rejecting any reads that were trimmed to less than 10bp
|
| 162 |
+
reads were aligned to the hg19 genome using bismark with the following specifications: a tolerance for one non-bisulfite mismatch per read, the default minimum alignment score (L,O, -02), and with ignore - quals in order to calculate the mismatch penalty by considering the quality value at the mismatched position to be the highest possible
|
| 163 |
+
bam files generated by Bismark alignment were then processed using DMAP to compare control vs. patients with the following specifications: Chi squared test on fragments 40-220bp in length, with the fragment requireing at lest 2 CpGs to have 10 or more sequence reads. The differential methylation file was then annotated with protein coding gene information using the DMAP command identgeneloc. DMAPmatrix.csv file contains this data.
|
| 164 |
+
Genome_build: hg19
|
| 165 |
+
Supplementary_files_format_and_content: Individual .txt files for each sample containing C and T frequency per base and coverage. C012_Full, ME007_Full and ME016_Full are excel files that contain, for the control, patient one, and patient two respectively, information about the per fragment methylation data including, genomic location, gene feature information, CpG relative location and fragment size.
|
| 166 |
+
</Data-Processing>
|
| 167 |
+
<Platform-Ref ref="GPL16791" />
|
| 168 |
+
<Library-Strategy>Bisulfite-Seq</Library-Strategy>
|
| 169 |
+
<Library-Source>genomic</Library-Source>
|
| 170 |
+
<Library-Selection>Reduced Representation</Library-Selection>
|
| 171 |
+
<Instrument-Model>
|
| 172 |
+
<Predefined>Illumina HiSeq 2500</Predefined>
|
| 173 |
+
</Instrument-Model>
|
| 174 |
+
<Contact-Ref ref="contrib1" />
|
| 175 |
+
<Supplementary-Data type="TXT">
|
| 176 |
+
ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5076nnn/GSM5076041/suppl/GSM5076041_C012B_CpG.txt.gz
|
| 177 |
+
</Supplementary-Data>
|
| 178 |
+
<Relation type="BioSample" target="https://www.ncbi.nlm.nih.gov/biosample/SAMN17862809" />
|
| 179 |
+
<Relation type="SRA" target="https://www.ncbi.nlm.nih.gov/sra?term=SRX10073448" />
|
| 180 |
+
</Sample>
|
| 181 |
+
|
| 182 |
+
<Sample iid="GSM5076042">
|
| 183 |
+
<Status database="GEO">
|
| 184 |
+
<Submission-Date>2021-02-10</Submission-Date>
|
| 185 |
+
<Release-Date>2021-02-11</Release-Date>
|
| 186 |
+
<Last-Update-Date>2021-02-12</Last-Update-Date>
|
| 187 |
+
</Status>
|
| 188 |
+
<Title>C012C</Title>
|
| 189 |
+
<Accession database="GEO">GSM5076042</Accession>
|
| 190 |
+
<Type>SRA</Type>
|
| 191 |
+
<Channel-Count>1</Channel-Count>
|
| 192 |
+
<Channel position="1">
|
| 193 |
+
<Source>Peripheral Blood Mononuclear Cells</Source>
|
| 194 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 195 |
+
<Characteristics tag="disease state">
|
| 196 |
+
Control
|
| 197 |
+
</Characteristics>
|
| 198 |
+
<Characteristics tag="individual">
|
| 199 |
+
C012
|
| 200 |
+
</Characteristics>
|
| 201 |
+
<Characteristics tag="time point">
|
| 202 |
+
C
|
| 203 |
+
</Characteristics>
|
| 204 |
+
<Characteristics tag="cell type">
|
| 205 |
+
Peripheral Blood Mononuclear Cells
|
| 206 |
+
</Characteristics>
|
| 207 |
+
<Molecule>genomic DNA</Molecule>
|
| 208 |
+
<Extract-Protocol>
|
| 209 |
+
DNA was extracted from 200ul of PBMCs
|
| 210 |
+
MSPI digestion (purify), end repair (purify), A-tialing and adaptor ligation (purify), PCR amplification (purify), Gel size selection and gel extraction (purify)
|
| 211 |
+
</Extract-Protocol>
|
| 212 |
+
</Channel>
|
| 213 |
+
<Description>
|
| 214 |
+
C012C
|
| 215 |
+
</Description>
|
| 216 |
+
<Data-Processing>
|
| 217 |
+
reads were adaptor trimmed using bismark that used a file of adaptor sequences and trimmed three bases back from any detected adaptor to delete the C invorporated and rejecting any reads that were trimmed to less than 10bp
|
| 218 |
+
reads were aligned to the hg19 genome using bismark with the following specifications: a tolerance for one non-bisulfite mismatch per read, the default minimum alignment score (L,O, -02), and with ignore - quals in order to calculate the mismatch penalty by considering the quality value at the mismatched position to be the highest possible
|
| 219 |
+
bam files generated by Bismark alignment were then processed using DMAP to compare control vs. patients with the following specifications: Chi squared test on fragments 40-220bp in length, with the fragment requireing at lest 2 CpGs to have 10 or more sequence reads. The differential methylation file was then annotated with protein coding gene information using the DMAP command identgeneloc. DMAPmatrix.csv file contains this data.
|
| 220 |
+
Genome_build: hg19
|
| 221 |
+
Supplementary_files_format_and_content: Individual .txt files for each sample containing C and T frequency per base and coverage. C012_Full, ME007_Full and ME016_Full are excel files that contain, for the control, patient one, and patient two respectively, information about the per fragment methylation data including, genomic location, gene feature information, CpG relative location and fragment size.
|
| 222 |
+
</Data-Processing>
|
| 223 |
+
<Platform-Ref ref="GPL16791" />
|
| 224 |
+
<Library-Strategy>Bisulfite-Seq</Library-Strategy>
|
| 225 |
+
<Library-Source>genomic</Library-Source>
|
| 226 |
+
<Library-Selection>Reduced Representation</Library-Selection>
|
| 227 |
+
<Instrument-Model>
|
| 228 |
+
<Predefined>Illumina HiSeq 2500</Predefined>
|
| 229 |
+
</Instrument-Model>
|
| 230 |
+
<Contact-Ref ref="contrib1" />
|
| 231 |
+
<Supplementary-Data type="TXT">
|
| 232 |
+
ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5076nnn/GSM5076042/suppl/GSM5076042_C012C_CpG.txt.gz
|
| 233 |
+
</Supplementary-Data>
|
| 234 |
+
<Relation type="BioSample" target="https://www.ncbi.nlm.nih.gov/biosample/SAMN17862808" />
|
| 235 |
+
<Relation type="SRA" target="https://www.ncbi.nlm.nih.gov/sra?term=SRX10073449" />
|
| 236 |
+
</Sample>
|
| 237 |
+
|
| 238 |
+
<Sample iid="GSM5076043">
|
| 239 |
+
<Status database="GEO">
|
| 240 |
+
<Submission-Date>2021-02-10</Submission-Date>
|
| 241 |
+
<Release-Date>2021-02-11</Release-Date>
|
| 242 |
+
<Last-Update-Date>2021-02-12</Last-Update-Date>
|
| 243 |
+
</Status>
|
| 244 |
+
<Title>C012D</Title>
|
| 245 |
+
<Accession database="GEO">GSM5076043</Accession>
|
| 246 |
+
<Type>SRA</Type>
|
| 247 |
+
<Channel-Count>1</Channel-Count>
|
| 248 |
+
<Channel position="1">
|
| 249 |
+
<Source>Peripheral Blood Mononuclear Cells</Source>
|
| 250 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 251 |
+
<Characteristics tag="disease state">
|
| 252 |
+
Control
|
| 253 |
+
</Characteristics>
|
| 254 |
+
<Characteristics tag="individual">
|
| 255 |
+
C012
|
| 256 |
+
</Characteristics>
|
| 257 |
+
<Characteristics tag="time point">
|
| 258 |
+
D
|
| 259 |
+
</Characteristics>
|
| 260 |
+
<Characteristics tag="cell type">
|
| 261 |
+
Peripheral Blood Mononuclear Cells
|
| 262 |
+
</Characteristics>
|
| 263 |
+
<Molecule>genomic DNA</Molecule>
|
| 264 |
+
<Extract-Protocol>
|
| 265 |
+
DNA was extracted from 200ul of PBMCs
|
| 266 |
+
MSPI digestion (purify), end repair (purify), A-tialing and adaptor ligation (purify), PCR amplification (purify), Gel size selection and gel extraction (purify)
|
| 267 |
+
</Extract-Protocol>
|
| 268 |
+
</Channel>
|
| 269 |
+
<Description>
|
| 270 |
+
C012D
|
| 271 |
+
</Description>
|
| 272 |
+
<Data-Processing>
|
| 273 |
+
reads were adaptor trimmed using bismark that used a file of adaptor sequences and trimmed three bases back from any detected adaptor to delete the C invorporated and rejecting any reads that were trimmed to less than 10bp
|
| 274 |
+
reads were aligned to the hg19 genome using bismark with the following specifications: a tolerance for one non-bisulfite mismatch per read, the default minimum alignment score (L,O, -02), and with ignore - quals in order to calculate the mismatch penalty by considering the quality value at the mismatched position to be the highest possible
|
| 275 |
+
bam files generated by Bismark alignment were then processed using DMAP to compare control vs. patients with the following specifications: Chi squared test on fragments 40-220bp in length, with the fragment requireing at lest 2 CpGs to have 10 or more sequence reads. The differential methylation file was then annotated with protein coding gene information using the DMAP command identgeneloc. DMAPmatrix.csv file contains this data.
|
| 276 |
+
Genome_build: hg19
|
| 277 |
+
Supplementary_files_format_and_content: Individual .txt files for each sample containing C and T frequency per base and coverage. C012_Full, ME007_Full and ME016_Full are excel files that contain, for the control, patient one, and patient two respectively, information about the per fragment methylation data including, genomic location, gene feature information, CpG relative location and fragment size.
|
| 278 |
+
</Data-Processing>
|
| 279 |
+
<Platform-Ref ref="GPL16791" />
|
| 280 |
+
<Library-Strategy>Bisulfite-Seq</Library-Strategy>
|
| 281 |
+
<Library-Source>genomic</Library-Source>
|
| 282 |
+
<Library-Selection>Reduced Representation</Library-Selection>
|
| 283 |
+
<Instrument-Model>
|
| 284 |
+
<Predefined>Illumina HiSeq 2500</Predefined>
|
| 285 |
+
</Instrument-Model>
|
| 286 |
+
<Contact-Ref ref="contrib1" />
|
| 287 |
+
<Supplementary-Data type="TXT">
|
| 288 |
+
ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5076nnn/GSM5076043/suppl/GSM5076043_C012D_CpG.txt.gz
|
| 289 |
+
</Supplementary-Data>
|
| 290 |
+
<Relation type="BioSample" target="https://www.ncbi.nlm.nih.gov/biosample/SAMN17862807" />
|
| 291 |
+
<Relation type="SRA" target="https://www.ncbi.nlm.nih.gov/sra?term=SRX10073450" />
|
| 292 |
+
</Sample>
|
| 293 |
+
|
| 294 |
+
<Sample iid="GSM5076044">
|
| 295 |
+
<Status database="GEO">
|
| 296 |
+
<Submission-Date>2021-02-10</Submission-Date>
|
| 297 |
+
<Release-Date>2021-02-11</Release-Date>
|
| 298 |
+
<Last-Update-Date>2021-02-12</Last-Update-Date>
|
| 299 |
+
</Status>
|
| 300 |
+
<Title>C012E</Title>
|
| 301 |
+
<Accession database="GEO">GSM5076044</Accession>
|
| 302 |
+
<Type>SRA</Type>
|
| 303 |
+
<Channel-Count>1</Channel-Count>
|
| 304 |
+
<Channel position="1">
|
| 305 |
+
<Source>Peripheral Blood Mononuclear Cells</Source>
|
| 306 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 307 |
+
<Characteristics tag="disease state">
|
| 308 |
+
Control
|
| 309 |
+
</Characteristics>
|
| 310 |
+
<Characteristics tag="individual">
|
| 311 |
+
C012
|
| 312 |
+
</Characteristics>
|
| 313 |
+
<Characteristics tag="time point">
|
| 314 |
+
E
|
| 315 |
+
</Characteristics>
|
| 316 |
+
<Characteristics tag="cell type">
|
| 317 |
+
Peripheral Blood Mononuclear Cells
|
| 318 |
+
</Characteristics>
|
| 319 |
+
<Molecule>genomic DNA</Molecule>
|
| 320 |
+
<Extract-Protocol>
|
| 321 |
+
DNA was extracted from 200ul of PBMCs
|
| 322 |
+
MSPI digestion (purify), end repair (purify), A-tialing and adaptor ligation (purify), PCR amplification (purify), Gel size selection and gel extraction (purify)
|
| 323 |
+
</Extract-Protocol>
|
| 324 |
+
</Channel>
|
| 325 |
+
<Description>
|
| 326 |
+
C012E
|
| 327 |
+
</Description>
|
| 328 |
+
<Data-Processing>
|
| 329 |
+
reads were adaptor trimmed using bismark that used a file of adaptor sequences and trimmed three bases back from any detected adaptor to delete the C invorporated and rejecting any reads that were trimmed to less than 10bp
|
| 330 |
+
reads were aligned to the hg19 genome using bismark with the following specifications: a tolerance for one non-bisulfite mismatch per read, the default minimum alignment score (L,O, -02), and with ignore - quals in order to calculate the mismatch penalty by considering the quality value at the mismatched position to be the highest possible
|
| 331 |
+
bam files generated by Bismark alignment were then processed using DMAP to compare control vs. patients with the following specifications: Chi squared test on fragments 40-220bp in length, with the fragment requireing at lest 2 CpGs to have 10 or more sequence reads. The differential methylation file was then annotated with protein coding gene information using the DMAP command identgeneloc. DMAPmatrix.csv file contains this data.
|
| 332 |
+
Genome_build: hg19
|
| 333 |
+
Supplementary_files_format_and_content: Individual .txt files for each sample containing C and T frequency per base and coverage. C012_Full, ME007_Full and ME016_Full are excel files that contain, for the control, patient one, and patient two respectively, information about the per fragment methylation data including, genomic location, gene feature information, CpG relative location and fragment size.
|
| 334 |
+
</Data-Processing>
|
| 335 |
+
<Platform-Ref ref="GPL16791" />
|
| 336 |
+
<Library-Strategy>Bisulfite-Seq</Library-Strategy>
|
| 337 |
+
<Library-Source>genomic</Library-Source>
|
| 338 |
+
<Library-Selection>Reduced Representation</Library-Selection>
|
| 339 |
+
<Instrument-Model>
|
| 340 |
+
<Predefined>Illumina HiSeq 2500</Predefined>
|
| 341 |
+
</Instrument-Model>
|
| 342 |
+
<Contact-Ref ref="contrib1" />
|
| 343 |
+
<Supplementary-Data type="TXT">
|
| 344 |
+
ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5076nnn/GSM5076044/suppl/GSM5076044_C012E_CpG.txt.gz
|
| 345 |
+
</Supplementary-Data>
|
| 346 |
+
<Relation type="BioSample" target="https://www.ncbi.nlm.nih.gov/biosample/SAMN17862806" />
|
| 347 |
+
<Relation type="SRA" target="https://www.ncbi.nlm.nih.gov/sra?term=SRX10073451" />
|
| 348 |
+
</Sample>
|
| 349 |
+
|
| 350 |
+
<Sample iid="GSM5076045">
|
| 351 |
+
<Status database="GEO">
|
| 352 |
+
<Submission-Date>2021-02-10</Submission-Date>
|
| 353 |
+
<Release-Date>2021-02-11</Release-Date>
|
| 354 |
+
<Last-Update-Date>2021-03-17</Last-Update-Date>
|
| 355 |
+
</Status>
|
| 356 |
+
<Title>Patient_One_A</Title>
|
| 357 |
+
<Accession database="GEO">GSM5076045</Accession>
|
| 358 |
+
<Type>SRA</Type>
|
| 359 |
+
<Channel-Count>1</Channel-Count>
|
| 360 |
+
<Channel position="1">
|
| 361 |
+
<Source>Peripheral Blood Mononuclear Cells</Source>
|
| 362 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 363 |
+
<Characteristics tag="disease state">
|
| 364 |
+
myalgic encephalomyelitis/chronic fatigue syndrome
|
| 365 |
+
</Characteristics>
|
| 366 |
+
<Characteristics tag="individual">
|
| 367 |
+
Patient_One
|
| 368 |
+
</Characteristics>
|
| 369 |
+
<Characteristics tag="time point">
|
| 370 |
+
A
|
| 371 |
+
</Characteristics>
|
| 372 |
+
<Characteristics tag="cell type">
|
| 373 |
+
Peripheral Blood Mononuclear Cells
|
| 374 |
+
</Characteristics>
|
| 375 |
+
<Molecule>genomic DNA</Molecule>
|
| 376 |
+
<Extract-Protocol>
|
| 377 |
+
DNA was extracted from 200ul of PBMCs
|
| 378 |
+
MSPI digestion (purify), end repair (purify), A-tialing and adaptor ligation (purify), PCR amplification (purify), Gel size selection and gel extraction (purify)
|
| 379 |
+
</Extract-Protocol>
|
| 380 |
+
</Channel>
|
| 381 |
+
<Description>
|
| 382 |
+
ME007A
|
| 383 |
+
</Description>
|
| 384 |
+
<Data-Processing>
|
| 385 |
+
reads were adaptor trimmed using bismark that used a file of adaptor sequences and trimmed three bases back from any detected adaptor to delete the C invorporated and rejecting any reads that were trimmed to less than 10bp
|
| 386 |
+
reads were aligned to the hg19 genome using bismark with the following specifications: a tolerance for one non-bisulfite mismatch per read, the default minimum alignment score (L,O, -02), and with ignore - quals in order to calculate the mismatch penalty by considering the quality value at the mismatched position to be the highest possible
|
| 387 |
+
bam files generated by Bismark alignment were then processed using DMAP to compare control vs. patients with the following specifications: Chi squared test on fragments 40-220bp in length, with the fragment requireing at lest 2 CpGs to have 10 or more sequence reads. The differential methylation file was then annotated with protein coding gene information using the DMAP command identgeneloc. DMAPmatrix.csv file contains this data.
|
| 388 |
+
Genome_build: hg19
|
| 389 |
+
Supplementary_files_format_and_content: Individual .txt files for each sample containing C and T frequency per base and coverage. C012_Full, ME007_Full and ME016_Full are excel files that contain, for the control, patient one, and patient two respectively, information about the per fragment methylation data including, genomic location, gene feature information, CpG relative location and fragment size.
|
| 390 |
+
</Data-Processing>
|
| 391 |
+
<Platform-Ref ref="GPL16791" />
|
| 392 |
+
<Library-Strategy>Bisulfite-Seq</Library-Strategy>
|
| 393 |
+
<Library-Source>genomic</Library-Source>
|
| 394 |
+
<Library-Selection>Reduced Representation</Library-Selection>
|
| 395 |
+
<Instrument-Model>
|
| 396 |
+
<Predefined>Illumina HiSeq 2500</Predefined>
|
| 397 |
+
</Instrument-Model>
|
| 398 |
+
<Contact-Ref ref="contrib1" />
|
| 399 |
+
<Supplementary-Data type="TXT">
|
| 400 |
+
ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5076nnn/GSM5076045/suppl/GSM5076045_ME007A_CpG.txt.gz
|
| 401 |
+
</Supplementary-Data>
|
| 402 |
+
<Relation type="BioSample" target="https://www.ncbi.nlm.nih.gov/biosample/SAMN17862805" />
|
| 403 |
+
<Relation type="SRA" target="https://www.ncbi.nlm.nih.gov/sra?term=SRX10073452" />
|
| 404 |
+
</Sample>
|
| 405 |
+
|
| 406 |
+
<Sample iid="GSM5076046">
|
| 407 |
+
<Status database="GEO">
|
| 408 |
+
<Submission-Date>2021-02-10</Submission-Date>
|
| 409 |
+
<Release-Date>2021-02-11</Release-Date>
|
| 410 |
+
<Last-Update-Date>2021-02-12</Last-Update-Date>
|
| 411 |
+
</Status>
|
| 412 |
+
<Title>Patient_One_B</Title>
|
| 413 |
+
<Accession database="GEO">GSM5076046</Accession>
|
| 414 |
+
<Type>SRA</Type>
|
| 415 |
+
<Channel-Count>1</Channel-Count>
|
| 416 |
+
<Channel position="1">
|
| 417 |
+
<Source>Peripheral Blood Mononuclear Cells</Source>
|
| 418 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 419 |
+
<Characteristics tag="disease state">
|
| 420 |
+
myalgic encephalomyelitis/chronic fatigue syndrome
|
| 421 |
+
</Characteristics>
|
| 422 |
+
<Characteristics tag="individual">
|
| 423 |
+
Patient_One
|
| 424 |
+
</Characteristics>
|
| 425 |
+
<Characteristics tag="time point">
|
| 426 |
+
B
|
| 427 |
+
</Characteristics>
|
| 428 |
+
<Characteristics tag="cell type">
|
| 429 |
+
Peripheral Blood Mononuclear Cells
|
| 430 |
+
</Characteristics>
|
| 431 |
+
<Molecule>genomic DNA</Molecule>
|
| 432 |
+
<Extract-Protocol>
|
| 433 |
+
DNA was extracted from 200ul of PBMCs
|
| 434 |
+
MSPI digestion (purify), end repair (purify), A-tialing and adaptor ligation (purify), PCR amplification (purify), Gel size selection and gel extraction (purify)
|
| 435 |
+
</Extract-Protocol>
|
| 436 |
+
</Channel>
|
| 437 |
+
<Description>
|
| 438 |
+
ME007B
|
| 439 |
+
</Description>
|
| 440 |
+
<Data-Processing>
|
| 441 |
+
reads were adaptor trimmed using bismark that used a file of adaptor sequences and trimmed three bases back from any detected adaptor to delete the C invorporated and rejecting any reads that were trimmed to less than 10bp
|
| 442 |
+
reads were aligned to the hg19 genome using bismark with the following specifications: a tolerance for one non-bisulfite mismatch per read, the default minimum alignment score (L,O, -02), and with ignore - quals in order to calculate the mismatch penalty by considering the quality value at the mismatched position to be the highest possible
|
| 443 |
+
bam files generated by Bismark alignment were then processed using DMAP to compare control vs. patients with the following specifications: Chi squared test on fragments 40-220bp in length, with the fragment requireing at lest 2 CpGs to have 10 or more sequence reads. The differential methylation file was then annotated with protein coding gene information using the DMAP command identgeneloc. DMAPmatrix.csv file contains this data.
|
| 444 |
+
Genome_build: hg19
|
| 445 |
+
Supplementary_files_format_and_content: Individual .txt files for each sample containing C and T frequency per base and coverage. C012_Full, ME007_Full and ME016_Full are excel files that contain, for the control, patient one, and patient two respectively, information about the per fragment methylation data including, genomic location, gene feature information, CpG relative location and fragment size.
|
| 446 |
+
</Data-Processing>
|
| 447 |
+
<Platform-Ref ref="GPL16791" />
|
| 448 |
+
<Library-Strategy>Bisulfite-Seq</Library-Strategy>
|
| 449 |
+
<Library-Source>genomic</Library-Source>
|
| 450 |
+
<Library-Selection>Reduced Representation</Library-Selection>
|
| 451 |
+
<Instrument-Model>
|
| 452 |
+
<Predefined>Illumina HiSeq 2500</Predefined>
|
| 453 |
+
</Instrument-Model>
|
| 454 |
+
<Contact-Ref ref="contrib1" />
|
| 455 |
+
<Supplementary-Data type="TXT">
|
| 456 |
+
ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5076nnn/GSM5076046/suppl/GSM5076046_ME007B_CpG.txt.gz
|
| 457 |
+
</Supplementary-Data>
|
| 458 |
+
<Relation type="BioSample" target="https://www.ncbi.nlm.nih.gov/biosample/SAMN17862804" />
|
| 459 |
+
<Relation type="SRA" target="https://www.ncbi.nlm.nih.gov/sra?term=SRX10073453" />
|
| 460 |
+
</Sample>
|
| 461 |
+
|
| 462 |
+
<Sample iid="GSM5076047">
|
| 463 |
+
<Status database="GEO">
|
| 464 |
+
<Submission-Date>2021-02-10</Submission-Date>
|
| 465 |
+
<Release-Date>2021-02-11</Release-Date>
|
| 466 |
+
<Last-Update-Date>2021-02-12</Last-Update-Date>
|
| 467 |
+
</Status>
|
| 468 |
+
<Title>Patient_One_C</Title>
|
| 469 |
+
<Accession database="GEO">GSM5076047</Accession>
|
| 470 |
+
<Type>SRA</Type>
|
| 471 |
+
<Channel-Count>1</Channel-Count>
|
| 472 |
+
<Channel position="1">
|
| 473 |
+
<Source>Peripheral Blood Mononuclear Cells</Source>
|
| 474 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 475 |
+
<Characteristics tag="disease state">
|
| 476 |
+
myalgic encephalomyelitis/chronic fatigue syndrome
|
| 477 |
+
</Characteristics>
|
| 478 |
+
<Characteristics tag="individual">
|
| 479 |
+
Patient_One
|
| 480 |
+
</Characteristics>
|
| 481 |
+
<Characteristics tag="time point">
|
| 482 |
+
C
|
| 483 |
+
</Characteristics>
|
| 484 |
+
<Characteristics tag="cell type">
|
| 485 |
+
Peripheral Blood Mononuclear Cells
|
| 486 |
+
</Characteristics>
|
| 487 |
+
<Molecule>genomic DNA</Molecule>
|
| 488 |
+
<Extract-Protocol>
|
| 489 |
+
DNA was extracted from 200ul of PBMCs
|
| 490 |
+
MSPI digestion (purify), end repair (purify), A-tialing and adaptor ligation (purify), PCR amplification (purify), Gel size selection and gel extraction (purify)
|
| 491 |
+
</Extract-Protocol>
|
| 492 |
+
</Channel>
|
| 493 |
+
<Description>
|
| 494 |
+
ME007C
|
| 495 |
+
</Description>
|
| 496 |
+
<Data-Processing>
|
| 497 |
+
reads were adaptor trimmed using bismark that used a file of adaptor sequences and trimmed three bases back from any detected adaptor to delete the C invorporated and rejecting any reads that were trimmed to less than 10bp
|
| 498 |
+
reads were aligned to the hg19 genome using bismark with the following specifications: a tolerance for one non-bisulfite mismatch per read, the default minimum alignment score (L,O, -02), and with ignore - quals in order to calculate the mismatch penalty by considering the quality value at the mismatched position to be the highest possible
|
| 499 |
+
bam files generated by Bismark alignment were then processed using DMAP to compare control vs. patients with the following specifications: Chi squared test on fragments 40-220bp in length, with the fragment requireing at lest 2 CpGs to have 10 or more sequence reads. The differential methylation file was then annotated with protein coding gene information using the DMAP command identgeneloc. DMAPmatrix.csv file contains this data.
|
| 500 |
+
Genome_build: hg19
|
| 501 |
+
Supplementary_files_format_and_content: Individual .txt files for each sample containing C and T frequency per base and coverage. C012_Full, ME007_Full and ME016_Full are excel files that contain, for the control, patient one, and patient two respectively, information about the per fragment methylation data including, genomic location, gene feature information, CpG relative location and fragment size.
|
| 502 |
+
</Data-Processing>
|
| 503 |
+
<Platform-Ref ref="GPL16791" />
|
| 504 |
+
<Library-Strategy>Bisulfite-Seq</Library-Strategy>
|
| 505 |
+
<Library-Source>genomic</Library-Source>
|
| 506 |
+
<Library-Selection>Reduced Representation</Library-Selection>
|
| 507 |
+
<Instrument-Model>
|
| 508 |
+
<Predefined>Illumina HiSeq 2500</Predefined>
|
| 509 |
+
</Instrument-Model>
|
| 510 |
+
<Contact-Ref ref="contrib1" />
|
| 511 |
+
<Supplementary-Data type="TXT">
|
| 512 |
+
ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5076nnn/GSM5076047/suppl/GSM5076047_ME007C_CpG.txt.gz
|
| 513 |
+
</Supplementary-Data>
|
| 514 |
+
<Relation type="BioSample" target="https://www.ncbi.nlm.nih.gov/biosample/SAMN17862803" />
|
| 515 |
+
<Relation type="SRA" target="https://www.ncbi.nlm.nih.gov/sra?term=SRX10073454" />
|
| 516 |
+
</Sample>
|
| 517 |
+
|
| 518 |
+
<Sample iid="GSM5076048">
|
| 519 |
+
<Status database="GEO">
|
| 520 |
+
<Submission-Date>2021-02-10</Submission-Date>
|
| 521 |
+
<Release-Date>2021-02-11</Release-Date>
|
| 522 |
+
<Last-Update-Date>2021-02-12</Last-Update-Date>
|
| 523 |
+
</Status>
|
| 524 |
+
<Title>Patient_One_D</Title>
|
| 525 |
+
<Accession database="GEO">GSM5076048</Accession>
|
| 526 |
+
<Type>SRA</Type>
|
| 527 |
+
<Channel-Count>1</Channel-Count>
|
| 528 |
+
<Channel position="1">
|
| 529 |
+
<Source>Peripheral Blood Mononuclear Cells</Source>
|
| 530 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 531 |
+
<Characteristics tag="disease state">
|
| 532 |
+
myalgic encephalomyelitis/chronic fatigue syndrome
|
| 533 |
+
</Characteristics>
|
| 534 |
+
<Characteristics tag="individual">
|
| 535 |
+
Patient_One
|
| 536 |
+
</Characteristics>
|
| 537 |
+
<Characteristics tag="time point">
|
| 538 |
+
D
|
| 539 |
+
</Characteristics>
|
| 540 |
+
<Characteristics tag="cell type">
|
| 541 |
+
Peripheral Blood Mononuclear Cells
|
| 542 |
+
</Characteristics>
|
| 543 |
+
<Molecule>genomic DNA</Molecule>
|
| 544 |
+
<Extract-Protocol>
|
| 545 |
+
DNA was extracted from 200ul of PBMCs
|
| 546 |
+
MSPI digestion (purify), end repair (purify), A-tialing and adaptor ligation (purify), PCR amplification (purify), Gel size selection and gel extraction (purify)
|
| 547 |
+
</Extract-Protocol>
|
| 548 |
+
</Channel>
|
| 549 |
+
<Description>
|
| 550 |
+
ME007D
|
| 551 |
+
</Description>
|
| 552 |
+
<Data-Processing>
|
| 553 |
+
reads were adaptor trimmed using bismark that used a file of adaptor sequences and trimmed three bases back from any detected adaptor to delete the C invorporated and rejecting any reads that were trimmed to less than 10bp
|
| 554 |
+
reads were aligned to the hg19 genome using bismark with the following specifications: a tolerance for one non-bisulfite mismatch per read, the default minimum alignment score (L,O, -02), and with ignore - quals in order to calculate the mismatch penalty by considering the quality value at the mismatched position to be the highest possible
|
| 555 |
+
bam files generated by Bismark alignment were then processed using DMAP to compare control vs. patients with the following specifications: Chi squared test on fragments 40-220bp in length, with the fragment requireing at lest 2 CpGs to have 10 or more sequence reads. The differential methylation file was then annotated with protein coding gene information using the DMAP command identgeneloc. DMAPmatrix.csv file contains this data.
|
| 556 |
+
Genome_build: hg19
|
| 557 |
+
Supplementary_files_format_and_content: Individual .txt files for each sample containing C and T frequency per base and coverage. C012_Full, ME007_Full and ME016_Full are excel files that contain, for the control, patient one, and patient two respectively, information about the per fragment methylation data including, genomic location, gene feature information, CpG relative location and fragment size.
|
| 558 |
+
</Data-Processing>
|
| 559 |
+
<Platform-Ref ref="GPL16791" />
|
| 560 |
+
<Library-Strategy>Bisulfite-Seq</Library-Strategy>
|
| 561 |
+
<Library-Source>genomic</Library-Source>
|
| 562 |
+
<Library-Selection>Reduced Representation</Library-Selection>
|
| 563 |
+
<Instrument-Model>
|
| 564 |
+
<Predefined>Illumina HiSeq 2500</Predefined>
|
| 565 |
+
</Instrument-Model>
|
| 566 |
+
<Contact-Ref ref="contrib1" />
|
| 567 |
+
<Supplementary-Data type="TXT">
|
| 568 |
+
ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5076nnn/GSM5076048/suppl/GSM5076048_ME007D_CpG.txt.gz
|
| 569 |
+
</Supplementary-Data>
|
| 570 |
+
<Relation type="BioSample" target="https://www.ncbi.nlm.nih.gov/biosample/SAMN17862802" />
|
| 571 |
+
<Relation type="SRA" target="https://www.ncbi.nlm.nih.gov/sra?term=SRX10073455" />
|
| 572 |
+
</Sample>
|
| 573 |
+
|
| 574 |
+
<Sample iid="GSM5076049">
|
| 575 |
+
<Status database="GEO">
|
| 576 |
+
<Submission-Date>2021-02-10</Submission-Date>
|
| 577 |
+
<Release-Date>2021-02-11</Release-Date>
|
| 578 |
+
<Last-Update-Date>2021-02-12</Last-Update-Date>
|
| 579 |
+
</Status>
|
| 580 |
+
<Title>Patient_One_E</Title>
|
| 581 |
+
<Accession database="GEO">GSM5076049</Accession>
|
| 582 |
+
<Type>SRA</Type>
|
| 583 |
+
<Channel-Count>1</Channel-Count>
|
| 584 |
+
<Channel position="1">
|
| 585 |
+
<Source>Peripheral Blood Mononuclear Cells</Source>
|
| 586 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 587 |
+
<Characteristics tag="disease state">
|
| 588 |
+
myalgic encephalomyelitis/chronic fatigue syndrome
|
| 589 |
+
</Characteristics>
|
| 590 |
+
<Characteristics tag="individual">
|
| 591 |
+
Patient_One
|
| 592 |
+
</Characteristics>
|
| 593 |
+
<Characteristics tag="time point">
|
| 594 |
+
E
|
| 595 |
+
</Characteristics>
|
| 596 |
+
<Characteristics tag="cell type">
|
| 597 |
+
Peripheral Blood Mononuclear Cells
|
| 598 |
+
</Characteristics>
|
| 599 |
+
<Molecule>genomic DNA</Molecule>
|
| 600 |
+
<Extract-Protocol>
|
| 601 |
+
DNA was extracted from 200ul of PBMCs
|
| 602 |
+
MSPI digestion (purify), end repair (purify), A-tialing and adaptor ligation (purify), PCR amplification (purify), Gel size selection and gel extraction (purify)
|
| 603 |
+
</Extract-Protocol>
|
| 604 |
+
</Channel>
|
| 605 |
+
<Description>
|
| 606 |
+
ME007E
|
| 607 |
+
</Description>
|
| 608 |
+
<Data-Processing>
|
| 609 |
+
reads were adaptor trimmed using bismark that used a file of adaptor sequences and trimmed three bases back from any detected adaptor to delete the C invorporated and rejecting any reads that were trimmed to less than 10bp
|
| 610 |
+
reads were aligned to the hg19 genome using bismark with the following specifications: a tolerance for one non-bisulfite mismatch per read, the default minimum alignment score (L,O, -02), and with ignore - quals in order to calculate the mismatch penalty by considering the quality value at the mismatched position to be the highest possible
|
| 611 |
+
bam files generated by Bismark alignment were then processed using DMAP to compare control vs. patients with the following specifications: Chi squared test on fragments 40-220bp in length, with the fragment requireing at lest 2 CpGs to have 10 or more sequence reads. The differential methylation file was then annotated with protein coding gene information using the DMAP command identgeneloc. DMAPmatrix.csv file contains this data.
|
| 612 |
+
Genome_build: hg19
|
| 613 |
+
Supplementary_files_format_and_content: Individual .txt files for each sample containing C and T frequency per base and coverage. C012_Full, ME007_Full and ME016_Full are excel files that contain, for the control, patient one, and patient two respectively, information about the per fragment methylation data including, genomic location, gene feature information, CpG relative location and fragment size.
|
| 614 |
+
</Data-Processing>
|
| 615 |
+
<Platform-Ref ref="GPL16791" />
|
| 616 |
+
<Library-Strategy>Bisulfite-Seq</Library-Strategy>
|
| 617 |
+
<Library-Source>genomic</Library-Source>
|
| 618 |
+
<Library-Selection>Reduced Representation</Library-Selection>
|
| 619 |
+
<Instrument-Model>
|
| 620 |
+
<Predefined>Illumina HiSeq 2500</Predefined>
|
| 621 |
+
</Instrument-Model>
|
| 622 |
+
<Contact-Ref ref="contrib1" />
|
| 623 |
+
<Supplementary-Data type="TXT">
|
| 624 |
+
ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5076nnn/GSM5076049/suppl/GSM5076049_ME007E_CpG.txt.gz
|
| 625 |
+
</Supplementary-Data>
|
| 626 |
+
<Relation type="BioSample" target="https://www.ncbi.nlm.nih.gov/biosample/SAMN17862801" />
|
| 627 |
+
<Relation type="SRA" target="https://www.ncbi.nlm.nih.gov/sra?term=SRX10073456" />
|
| 628 |
+
</Sample>
|
| 629 |
+
|
| 630 |
+
<Sample iid="GSM5076050">
|
| 631 |
+
<Status database="GEO">
|
| 632 |
+
<Submission-Date>2021-02-10</Submission-Date>
|
| 633 |
+
<Release-Date>2021-02-11</Release-Date>
|
| 634 |
+
<Last-Update-Date>2021-02-12</Last-Update-Date>
|
| 635 |
+
</Status>
|
| 636 |
+
<Title>Patient_Two_A</Title>
|
| 637 |
+
<Accession database="GEO">GSM5076050</Accession>
|
| 638 |
+
<Type>SRA</Type>
|
| 639 |
+
<Channel-Count>1</Channel-Count>
|
| 640 |
+
<Channel position="1">
|
| 641 |
+
<Source>Peripheral Blood Mononuclear Cells</Source>
|
| 642 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 643 |
+
<Characteristics tag="disease state">
|
| 644 |
+
myalgic encephalomyelitis/chronic fatigue syndrome
|
| 645 |
+
</Characteristics>
|
| 646 |
+
<Characteristics tag="individual">
|
| 647 |
+
Patient_Two
|
| 648 |
+
</Characteristics>
|
| 649 |
+
<Characteristics tag="time point">
|
| 650 |
+
A
|
| 651 |
+
</Characteristics>
|
| 652 |
+
<Characteristics tag="cell type">
|
| 653 |
+
Peripheral Blood Mononuclear Cells
|
| 654 |
+
</Characteristics>
|
| 655 |
+
<Molecule>genomic DNA</Molecule>
|
| 656 |
+
<Extract-Protocol>
|
| 657 |
+
DNA was extracted from 200ul of PBMCs
|
| 658 |
+
MSPI digestion (purify), end repair (purify), A-tialing and adaptor ligation (purify), PCR amplification (purify), Gel size selection and gel extraction (purify)
|
| 659 |
+
</Extract-Protocol>
|
| 660 |
+
</Channel>
|
| 661 |
+
<Description>
|
| 662 |
+
ME016A
|
| 663 |
+
</Description>
|
| 664 |
+
<Data-Processing>
|
| 665 |
+
reads were adaptor trimmed using bismark that used a file of adaptor sequences and trimmed three bases back from any detected adaptor to delete the C invorporated and rejecting any reads that were trimmed to less than 10bp
|
| 666 |
+
reads were aligned to the hg19 genome using bismark with the following specifications: a tolerance for one non-bisulfite mismatch per read, the default minimum alignment score (L,O, -02), and with ignore - quals in order to calculate the mismatch penalty by considering the quality value at the mismatched position to be the highest possible
|
| 667 |
+
bam files generated by Bismark alignment were then processed using DMAP to compare control vs. patients with the following specifications: Chi squared test on fragments 40-220bp in length, with the fragment requireing at lest 2 CpGs to have 10 or more sequence reads. The differential methylation file was then annotated with protein coding gene information using the DMAP command identgeneloc. DMAPmatrix.csv file contains this data.
|
| 668 |
+
Genome_build: hg19
|
| 669 |
+
Supplementary_files_format_and_content: Individual .txt files for each sample containing C and T frequency per base and coverage. C012_Full, ME007_Full and ME016_Full are excel files that contain, for the control, patient one, and patient two respectively, information about the per fragment methylation data including, genomic location, gene feature information, CpG relative location and fragment size.
|
| 670 |
+
</Data-Processing>
|
| 671 |
+
<Platform-Ref ref="GPL16791" />
|
| 672 |
+
<Library-Strategy>Bisulfite-Seq</Library-Strategy>
|
| 673 |
+
<Library-Source>genomic</Library-Source>
|
| 674 |
+
<Library-Selection>Reduced Representation</Library-Selection>
|
| 675 |
+
<Instrument-Model>
|
| 676 |
+
<Predefined>Illumina HiSeq 2500</Predefined>
|
| 677 |
+
</Instrument-Model>
|
| 678 |
+
<Contact-Ref ref="contrib1" />
|
| 679 |
+
<Supplementary-Data type="TXT">
|
| 680 |
+
ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5076nnn/GSM5076050/suppl/GSM5076050_ME016A_CpG.txt.gz
|
| 681 |
+
</Supplementary-Data>
|
| 682 |
+
<Relation type="BioSample" target="https://www.ncbi.nlm.nih.gov/biosample/SAMN17862800" />
|
| 683 |
+
<Relation type="SRA" target="https://www.ncbi.nlm.nih.gov/sra?term=SRX10073457" />
|
| 684 |
+
</Sample>
|
| 685 |
+
|
| 686 |
+
<Sample iid="GSM5076051">
|
| 687 |
+
<Status database="GEO">
|
| 688 |
+
<Submission-Date>2021-02-10</Submission-Date>
|
| 689 |
+
<Release-Date>2021-02-11</Release-Date>
|
| 690 |
+
<Last-Update-Date>2021-02-12</Last-Update-Date>
|
| 691 |
+
</Status>
|
| 692 |
+
<Title>Patient_Two_B</Title>
|
| 693 |
+
<Accession database="GEO">GSM5076051</Accession>
|
| 694 |
+
<Type>SRA</Type>
|
| 695 |
+
<Channel-Count>1</Channel-Count>
|
| 696 |
+
<Channel position="1">
|
| 697 |
+
<Source>Peripheral Blood Mononuclear Cells</Source>
|
| 698 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 699 |
+
<Characteristics tag="disease state">
|
| 700 |
+
myalgic encephalomyelitis/chronic fatigue syndrome
|
| 701 |
+
</Characteristics>
|
| 702 |
+
<Characteristics tag="individual">
|
| 703 |
+
Patient_Two
|
| 704 |
+
</Characteristics>
|
| 705 |
+
<Characteristics tag="time point">
|
| 706 |
+
B
|
| 707 |
+
</Characteristics>
|
| 708 |
+
<Characteristics tag="cell type">
|
| 709 |
+
Peripheral Blood Mononuclear Cells
|
| 710 |
+
</Characteristics>
|
| 711 |
+
<Molecule>genomic DNA</Molecule>
|
| 712 |
+
<Extract-Protocol>
|
| 713 |
+
DNA was extracted from 200ul of PBMCs
|
| 714 |
+
MSPI digestion (purify), end repair (purify), A-tialing and adaptor ligation (purify), PCR amplification (purify), Gel size selection and gel extraction (purify)
|
| 715 |
+
</Extract-Protocol>
|
| 716 |
+
</Channel>
|
| 717 |
+
<Description>
|
| 718 |
+
ME016B
|
| 719 |
+
</Description>
|
| 720 |
+
<Data-Processing>
|
| 721 |
+
reads were adaptor trimmed using bismark that used a file of adaptor sequences and trimmed three bases back from any detected adaptor to delete the C invorporated and rejecting any reads that were trimmed to less than 10bp
|
| 722 |
+
reads were aligned to the hg19 genome using bismark with the following specifications: a tolerance for one non-bisulfite mismatch per read, the default minimum alignment score (L,O, -02), and with ignore - quals in order to calculate the mismatch penalty by considering the quality value at the mismatched position to be the highest possible
|
| 723 |
+
bam files generated by Bismark alignment were then processed using DMAP to compare control vs. patients with the following specifications: Chi squared test on fragments 40-220bp in length, with the fragment requireing at lest 2 CpGs to have 10 or more sequence reads. The differential methylation file was then annotated with protein coding gene information using the DMAP command identgeneloc. DMAPmatrix.csv file contains this data.
|
| 724 |
+
Genome_build: hg19
|
| 725 |
+
Supplementary_files_format_and_content: Individual .txt files for each sample containing C and T frequency per base and coverage. C012_Full, ME007_Full and ME016_Full are excel files that contain, for the control, patient one, and patient two respectively, information about the per fragment methylation data including, genomic location, gene feature information, CpG relative location and fragment size.
|
| 726 |
+
</Data-Processing>
|
| 727 |
+
<Platform-Ref ref="GPL16791" />
|
| 728 |
+
<Library-Strategy>Bisulfite-Seq</Library-Strategy>
|
| 729 |
+
<Library-Source>genomic</Library-Source>
|
| 730 |
+
<Library-Selection>Reduced Representation</Library-Selection>
|
| 731 |
+
<Instrument-Model>
|
| 732 |
+
<Predefined>Illumina HiSeq 2500</Predefined>
|
| 733 |
+
</Instrument-Model>
|
| 734 |
+
<Contact-Ref ref="contrib1" />
|
| 735 |
+
<Supplementary-Data type="TXT">
|
| 736 |
+
ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5076nnn/GSM5076051/suppl/GSM5076051_ME016B_CpG.txt.gz
|
| 737 |
+
</Supplementary-Data>
|
| 738 |
+
<Relation type="BioSample" target="https://www.ncbi.nlm.nih.gov/biosample/SAMN17862799" />
|
| 739 |
+
<Relation type="SRA" target="https://www.ncbi.nlm.nih.gov/sra?term=SRX10073458" />
|
| 740 |
+
</Sample>
|
| 741 |
+
|
| 742 |
+
<Sample iid="GSM5076052">
|
| 743 |
+
<Status database="GEO">
|
| 744 |
+
<Submission-Date>2021-02-10</Submission-Date>
|
| 745 |
+
<Release-Date>2021-02-11</Release-Date>
|
| 746 |
+
<Last-Update-Date>2021-03-17</Last-Update-Date>
|
| 747 |
+
</Status>
|
| 748 |
+
<Title>Patient_Two_C</Title>
|
| 749 |
+
<Accession database="GEO">GSM5076052</Accession>
|
| 750 |
+
<Type>SRA</Type>
|
| 751 |
+
<Channel-Count>1</Channel-Count>
|
| 752 |
+
<Channel position="1">
|
| 753 |
+
<Source>Peripheral Blood Mononuclear Cells</Source>
|
| 754 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 755 |
+
<Characteristics tag="disease state">
|
| 756 |
+
myalgic encephalomyelitis/chronic fatigue syndrome
|
| 757 |
+
</Characteristics>
|
| 758 |
+
<Characteristics tag="individual">
|
| 759 |
+
Patient_Two
|
| 760 |
+
</Characteristics>
|
| 761 |
+
<Characteristics tag="time point">
|
| 762 |
+
C
|
| 763 |
+
</Characteristics>
|
| 764 |
+
<Characteristics tag="cell type">
|
| 765 |
+
Peripheral Blood Mononuclear Cells
|
| 766 |
+
</Characteristics>
|
| 767 |
+
<Molecule>genomic DNA</Molecule>
|
| 768 |
+
<Extract-Protocol>
|
| 769 |
+
DNA was extracted from 200ul of PBMCs
|
| 770 |
+
MSPI digestion (purify), end repair (purify), A-tialing and adaptor ligation (purify), PCR amplification (purify), Gel size selection and gel extraction (purify)
|
| 771 |
+
</Extract-Protocol>
|
| 772 |
+
</Channel>
|
| 773 |
+
<Description>
|
| 774 |
+
ME016C
|
| 775 |
+
</Description>
|
| 776 |
+
<Data-Processing>
|
| 777 |
+
reads were adaptor trimmed using bismark that used a file of adaptor sequences and trimmed three bases back from any detected adaptor to delete the C invorporated and rejecting any reads that were trimmed to less than 10bp
|
| 778 |
+
reads were aligned to the hg19 genome using bismark with the following specifications: a tolerance for one non-bisulfite mismatch per read, the default minimum alignment score (L,O, -02), and with ignore - quals in order to calculate the mismatch penalty by considering the quality value at the mismatched position to be the highest possible
|
| 779 |
+
bam files generated by Bismark alignment were then processed using DMAP to compare control vs. patients with the following specifications: Chi squared test on fragments 40-220bp in length, with the fragment requireing at lest 2 CpGs to have 10 or more sequence reads. The differential methylation file was then annotated with protein coding gene information using the DMAP command identgeneloc. DMAPmatrix.csv file contains this data.
|
| 780 |
+
Genome_build: hg19
|
| 781 |
+
Supplementary_files_format_and_content: Individual .txt files for each sample containing C and T frequency per base and coverage. C012_Full, ME007_Full and ME016_Full are excel files that contain, for the control, patient one, and patient two respectively, information about the per fragment methylation data including, genomic location, gene feature information, CpG relative location and fragment size.
|
| 782 |
+
</Data-Processing>
|
| 783 |
+
<Platform-Ref ref="GPL16791" />
|
| 784 |
+
<Library-Strategy>Bisulfite-Seq</Library-Strategy>
|
| 785 |
+
<Library-Source>genomic</Library-Source>
|
| 786 |
+
<Library-Selection>Reduced Representation</Library-Selection>
|
| 787 |
+
<Instrument-Model>
|
| 788 |
+
<Predefined>Illumina HiSeq 2500</Predefined>
|
| 789 |
+
</Instrument-Model>
|
| 790 |
+
<Contact-Ref ref="contrib1" />
|
| 791 |
+
<Supplementary-Data type="TXT">
|
| 792 |
+
ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5076nnn/GSM5076052/suppl/GSM5076052_ME016C_CpG.txt.gz
|
| 793 |
+
</Supplementary-Data>
|
| 794 |
+
<Relation type="BioSample" target="https://www.ncbi.nlm.nih.gov/biosample/SAMN17862798" />
|
| 795 |
+
<Relation type="SRA" target="https://www.ncbi.nlm.nih.gov/sra?term=SRX10073459" />
|
| 796 |
+
</Sample>
|
| 797 |
+
|
| 798 |
+
<Sample iid="GSM5076053">
|
| 799 |
+
<Status database="GEO">
|
| 800 |
+
<Submission-Date>2021-02-10</Submission-Date>
|
| 801 |
+
<Release-Date>2021-02-11</Release-Date>
|
| 802 |
+
<Last-Update-Date>2021-02-12</Last-Update-Date>
|
| 803 |
+
</Status>
|
| 804 |
+
<Title>Patient_Two_D</Title>
|
| 805 |
+
<Accession database="GEO">GSM5076053</Accession>
|
| 806 |
+
<Type>SRA</Type>
|
| 807 |
+
<Channel-Count>1</Channel-Count>
|
| 808 |
+
<Channel position="1">
|
| 809 |
+
<Source>Peripheral Blood Mononuclear Cells</Source>
|
| 810 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 811 |
+
<Characteristics tag="disease state">
|
| 812 |
+
myalgic encephalomyelitis/chronic fatigue syndrome
|
| 813 |
+
</Characteristics>
|
| 814 |
+
<Characteristics tag="individual">
|
| 815 |
+
Patient_Two
|
| 816 |
+
</Characteristics>
|
| 817 |
+
<Characteristics tag="time point">
|
| 818 |
+
D
|
| 819 |
+
</Characteristics>
|
| 820 |
+
<Characteristics tag="cell type">
|
| 821 |
+
Peripheral Blood Mononuclear Cells
|
| 822 |
+
</Characteristics>
|
| 823 |
+
<Molecule>genomic DNA</Molecule>
|
| 824 |
+
<Extract-Protocol>
|
| 825 |
+
DNA was extracted from 200ul of PBMCs
|
| 826 |
+
MSPI digestion (purify), end repair (purify), A-tialing and adaptor ligation (purify), PCR amplification (purify), Gel size selection and gel extraction (purify)
|
| 827 |
+
</Extract-Protocol>
|
| 828 |
+
</Channel>
|
| 829 |
+
<Description>
|
| 830 |
+
ME016D
|
| 831 |
+
</Description>
|
| 832 |
+
<Data-Processing>
|
| 833 |
+
reads were adaptor trimmed using bismark that used a file of adaptor sequences and trimmed three bases back from any detected adaptor to delete the C invorporated and rejecting any reads that were trimmed to less than 10bp
|
| 834 |
+
reads were aligned to the hg19 genome using bismark with the following specifications: a tolerance for one non-bisulfite mismatch per read, the default minimum alignment score (L,O, -02), and with ignore - quals in order to calculate the mismatch penalty by considering the quality value at the mismatched position to be the highest possible
|
| 835 |
+
bam files generated by Bismark alignment were then processed using DMAP to compare control vs. patients with the following specifications: Chi squared test on fragments 40-220bp in length, with the fragment requireing at lest 2 CpGs to have 10 or more sequence reads. The differential methylation file was then annotated with protein coding gene information using the DMAP command identgeneloc. DMAPmatrix.csv file contains this data.
|
| 836 |
+
Genome_build: hg19
|
| 837 |
+
Supplementary_files_format_and_content: Individual .txt files for each sample containing C and T frequency per base and coverage. C012_Full, ME007_Full and ME016_Full are excel files that contain, for the control, patient one, and patient two respectively, information about the per fragment methylation data including, genomic location, gene feature information, CpG relative location and fragment size.
|
| 838 |
+
</Data-Processing>
|
| 839 |
+
<Platform-Ref ref="GPL16791" />
|
| 840 |
+
<Library-Strategy>Bisulfite-Seq</Library-Strategy>
|
| 841 |
+
<Library-Source>genomic</Library-Source>
|
| 842 |
+
<Library-Selection>Reduced Representation</Library-Selection>
|
| 843 |
+
<Instrument-Model>
|
| 844 |
+
<Predefined>Illumina HiSeq 2500</Predefined>
|
| 845 |
+
</Instrument-Model>
|
| 846 |
+
<Contact-Ref ref="contrib1" />
|
| 847 |
+
<Supplementary-Data type="TXT">
|
| 848 |
+
ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5076nnn/GSM5076053/suppl/GSM5076053_ME016D_CpG.txt.gz
|
| 849 |
+
</Supplementary-Data>
|
| 850 |
+
<Relation type="BioSample" target="https://www.ncbi.nlm.nih.gov/biosample/SAMN17862797" />
|
| 851 |
+
<Relation type="SRA" target="https://www.ncbi.nlm.nih.gov/sra?term=SRX10073460" />
|
| 852 |
+
</Sample>
|
| 853 |
+
|
| 854 |
+
<Sample iid="GSM5076054">
|
| 855 |
+
<Status database="GEO">
|
| 856 |
+
<Submission-Date>2021-02-10</Submission-Date>
|
| 857 |
+
<Release-Date>2021-02-11</Release-Date>
|
| 858 |
+
<Last-Update-Date>2021-02-12</Last-Update-Date>
|
| 859 |
+
</Status>
|
| 860 |
+
<Title>Patient_Two_E</Title>
|
| 861 |
+
<Accession database="GEO">GSM5076054</Accession>
|
| 862 |
+
<Type>SRA</Type>
|
| 863 |
+
<Channel-Count>1</Channel-Count>
|
| 864 |
+
<Channel position="1">
|
| 865 |
+
<Source>Peripheral Blood Mononuclear Cells</Source>
|
| 866 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 867 |
+
<Characteristics tag="disease state">
|
| 868 |
+
myalgic encephalomyelitis/chronic fatigue syndrome
|
| 869 |
+
</Characteristics>
|
| 870 |
+
<Characteristics tag="individual">
|
| 871 |
+
Patient_Two
|
| 872 |
+
</Characteristics>
|
| 873 |
+
<Characteristics tag="time point">
|
| 874 |
+
E
|
| 875 |
+
</Characteristics>
|
| 876 |
+
<Characteristics tag="cell type">
|
| 877 |
+
Peripheral Blood Mononuclear Cells
|
| 878 |
+
</Characteristics>
|
| 879 |
+
<Molecule>genomic DNA</Molecule>
|
| 880 |
+
<Extract-Protocol>
|
| 881 |
+
DNA was extracted from 200ul of PBMCs
|
| 882 |
+
MSPI digestion (purify), end repair (purify), A-tialing and adaptor ligation (purify), PCR amplification (purify), Gel size selection and gel extraction (purify)
|
| 883 |
+
</Extract-Protocol>
|
| 884 |
+
</Channel>
|
| 885 |
+
<Description>
|
| 886 |
+
ME016E
|
| 887 |
+
</Description>
|
| 888 |
+
<Data-Processing>
|
| 889 |
+
reads were adaptor trimmed using bismark that used a file of adaptor sequences and trimmed three bases back from any detected adaptor to delete the C invorporated and rejecting any reads that were trimmed to less than 10bp
|
| 890 |
+
reads were aligned to the hg19 genome using bismark with the following specifications: a tolerance for one non-bisulfite mismatch per read, the default minimum alignment score (L,O, -02), and with ignore - quals in order to calculate the mismatch penalty by considering the quality value at the mismatched position to be the highest possible
|
| 891 |
+
bam files generated by Bismark alignment were then processed using DMAP to compare control vs. patients with the following specifications: Chi squared test on fragments 40-220bp in length, with the fragment requireing at lest 2 CpGs to have 10 or more sequence reads. The differential methylation file was then annotated with protein coding gene information using the DMAP command identgeneloc. DMAPmatrix.csv file contains this data.
|
| 892 |
+
Genome_build: hg19
|
| 893 |
+
Supplementary_files_format_and_content: Individual .txt files for each sample containing C and T frequency per base and coverage. C012_Full, ME007_Full and ME016_Full are excel files that contain, for the control, patient one, and patient two respectively, information about the per fragment methylation data including, genomic location, gene feature information, CpG relative location and fragment size.
|
| 894 |
+
</Data-Processing>
|
| 895 |
+
<Platform-Ref ref="GPL16791" />
|
| 896 |
+
<Library-Strategy>Bisulfite-Seq</Library-Strategy>
|
| 897 |
+
<Library-Source>genomic</Library-Source>
|
| 898 |
+
<Library-Selection>Reduced Representation</Library-Selection>
|
| 899 |
+
<Instrument-Model>
|
| 900 |
+
<Predefined>Illumina HiSeq 2500</Predefined>
|
| 901 |
+
</Instrument-Model>
|
| 902 |
+
<Contact-Ref ref="contrib1" />
|
| 903 |
+
<Supplementary-Data type="TXT">
|
| 904 |
+
ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5076nnn/GSM5076054/suppl/GSM5076054_ME016E_CpG.txt.gz
|
| 905 |
+
</Supplementary-Data>
|
| 906 |
+
<Relation type="BioSample" target="https://www.ncbi.nlm.nih.gov/biosample/SAMN17862796" />
|
| 907 |
+
<Relation type="SRA" target="https://www.ncbi.nlm.nih.gov/sra?term=SRX10073461" />
|
| 908 |
+
</Sample>
|
| 909 |
+
|
| 910 |
+
<Series iid="GSE166592">
|
| 911 |
+
<Status database="GEO">
|
| 912 |
+
<Submission-Date>2021-02-10</Submission-Date>
|
| 913 |
+
<Release-Date>2021-02-11</Release-Date>
|
| 914 |
+
<Last-Update-Date>2021-03-17</Last-Update-Date>
|
| 915 |
+
</Status>
|
| 916 |
+
<Title>Dynamic Epigenetic Changes during a Relapse and Recovery Cycle in Myalgic Encephalomyelitis/Chronic Fatigue Syndrome </Title>
|
| 917 |
+
<Accession database="GEO">GSE166592</Accession>
|
| 918 |
+
<Summary>
|
| 919 |
+
Purpose: ME/CFS is a debilitating and complex disease. The majority of patients exist in a chronic state of health where they are affected by relapse events. Precision medicine following patients can capture changes in the DNA methylation indicative of biological dysfunction
|
| 920 |
+
Methods: DNA was extracted from the PBMCs of 2 ME/CFS patients and a age/gender matched control at five different time points. After performing RRBS the sequence was aligned to hg19 genome using Bismark. The data was analyzed using a Chi squared test through DMAP in order to determine variation between the patient and control groups across 40-220bp fragments of the genome.
|
| 921 |
+
Results: A total of 17 and 14 statistically significant variably methylated fragements were indentified in each patient that strongly associated with a relapse event. These fragements were found on regions of regulatory importance of the genome that associated with immune (primarily inflammatory) and metabolic function.
|
| 922 |
+
Conclusions: Our study represents the first investigation of ME/CFS patients using reduced representation bisulfite sequencing along a longitudinal timeframe. We captured a number of major variably methylated fragments in each patient that associated with their relapse events. Our results identified a number of differentially methylated regulatory elements and gene bodies that highlight the disturbed pathophysiology in ME/CFS. DNA methylation that differentiates disease variability in ongoing ME/CFS may have practical applications for strategies to deacrease the frequency and severity of relapse events.
|
| 923 |
+
</Summary>
|
| 924 |
+
<Overall-Design>
|
| 925 |
+
RRBS Analysis of 2 ME/CFS patients and matched control over eleven months
|
| 926 |
+
</Overall-Design>
|
| 927 |
+
<Type>Methylation profiling by high throughput sequencing</Type>
|
| 928 |
+
<Contributor-Ref ref="contrib1" position="1" />
|
| 929 |
+
<Contributor-Ref ref="contrib3" position="2" />
|
| 930 |
+
<Contributor-Ref ref="contrib4" position="3" />
|
| 931 |
+
<Contributor-Ref ref="contrib5" position="4" />
|
| 932 |
+
<Contributor-Ref ref="contrib6" position="5" />
|
| 933 |
+
<Contact-Ref ref="contrib1" />
|
| 934 |
+
<Sample-Ref ref="GSM5076040" />
|
| 935 |
+
<Sample-Ref ref="GSM5076041" />
|
| 936 |
+
<Sample-Ref ref="GSM5076042" />
|
| 937 |
+
<Sample-Ref ref="GSM5076043" />
|
| 938 |
+
<Sample-Ref ref="GSM5076044" />
|
| 939 |
+
<Sample-Ref ref="GSM5076045" />
|
| 940 |
+
<Sample-Ref ref="GSM5076046" />
|
| 941 |
+
<Sample-Ref ref="GSM5076047" />
|
| 942 |
+
<Sample-Ref ref="GSM5076048" />
|
| 943 |
+
<Sample-Ref ref="GSM5076049" />
|
| 944 |
+
<Sample-Ref ref="GSM5076050" />
|
| 945 |
+
<Sample-Ref ref="GSM5076051" />
|
| 946 |
+
<Sample-Ref ref="GSM5076052" />
|
| 947 |
+
<Sample-Ref ref="GSM5076053" />
|
| 948 |
+
<Sample-Ref ref="GSM5076054" />
|
| 949 |
+
<Supplementary-Data type="XLSX">
|
| 950 |
+
ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE166nnn/GSE166592/suppl/GSE166592_C012_Full.xlsx
|
| 951 |
+
</Supplementary-Data>
|
| 952 |
+
<Supplementary-Data type="XLSX">
|
| 953 |
+
ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE166nnn/GSE166592/suppl/GSE166592_ME007_Full.xlsx
|
| 954 |
+
</Supplementary-Data>
|
| 955 |
+
<Supplementary-Data type="XLSX">
|
| 956 |
+
ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE166nnn/GSE166592/suppl/GSE166592_ME016_Full.xlsx
|
| 957 |
+
</Supplementary-Data>
|
| 958 |
+
<Supplementary-Data type="TAR">
|
| 959 |
+
ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE166nnn/GSE166592/suppl/GSE166592_RAW.tar
|
| 960 |
+
</Supplementary-Data>
|
| 961 |
+
<Relation type="BioProject" target="https://www.ncbi.nlm.nih.gov/bioproject/PRJNA701322" />
|
| 962 |
+
<Relation type="SRA" target="https://www.ncbi.nlm.nih.gov/sra?term=SRP305748" />
|
| 963 |
+
</Series>
|
| 964 |
+
|
| 965 |
+
</MINiML>
|
ME/GSE166592/meta/GSE166592_series_matrix.txt
ADDED
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|
| 1 |
+
!Series_title "Dynamic Epigenetic Changes during a Relapse and Recovery Cycle in Myalgic Encephalomyelitis/Chronic Fatigue Syndrome "
|
| 2 |
+
!Series_geo_accession "GSE166592"
|
| 3 |
+
!Series_status "Public on Feb 11 2021"
|
| 4 |
+
!Series_submission_date "Feb 10 2021"
|
| 5 |
+
!Series_last_update_date "Mar 17 2021"
|
| 6 |
+
!Series_summary "Purpose: ME/CFS is a debilitating and complex disease. The majority of patients exist in a chronic state of health where they are affected by relapse events. Precision medicine following patients can capture changes in the DNA methylation indicative of biological dysfunction"
|
| 7 |
+
!Series_summary "Methods: DNA was extracted from the PBMCs of 2 ME/CFS patients and a age/gender matched control at five different time points. After performing RRBS the sequence was aligned to hg19 genome using Bismark. The data was analyzed using a Chi squared test through DMAP in order to determine variation between the patient and control groups across 40-220bp fragments of the genome."
|
| 8 |
+
!Series_summary "Results: A total of 17 and 14 statistically significant variably methylated fragements were indentified in each patient that strongly associated with a relapse event. These fragements were found on regions of regulatory importance of the genome that associated with immune (primarily inflammatory) and metabolic function."
|
| 9 |
+
!Series_summary "Conclusions: Our study represents the first investigation of ME/CFS patients using reduced representation bisulfite sequencing along a longitudinal timeframe. We captured a number of major variably methylated fragments in each patient that associated with their relapse events. Our results identified a number of differentially methylated regulatory elements and gene bodies that highlight the disturbed pathophysiology in ME/CFS. DNA methylation that differentiates disease variability in ongoing ME/CFS may have practical applications for strategies to deacrease the frequency and severity of relapse events."
|
| 10 |
+
!Series_overall_design "RRBS Analysis of 2 ME/CFS patients and matched control over eleven months"
|
| 11 |
+
!Series_type "Methylation profiling by high throughput sequencing"
|
| 12 |
+
!Series_contributor "Amber,,Helliwell"
|
| 13 |
+
!Series_contributor "Warren,,Tate"
|
| 14 |
+
!Series_contributor "Aniruddha,,Chatterjee"
|
| 15 |
+
!Series_contributor "Peter,,Stockwell"
|
| 16 |
+
!Series_contributor "Tina,,Edgar"
|
| 17 |
+
!Series_sample_id "GSM5076040 GSM5076041 GSM5076042 GSM5076043 GSM5076044 GSM5076045 GSM5076046 GSM5076047 GSM5076048 GSM5076049 GSM5076050 GSM5076051 GSM5076052 GSM5076053 GSM5076054 "
|
| 18 |
+
!Series_contact_name "Amber,,Helliwell"
|
| 19 |
+
!Series_contact_department "Biochemistry Department"
|
| 20 |
+
!Series_contact_institute "University of Otago"
|
| 21 |
+
!Series_contact_address "710 Cumberland Road"
|
| 22 |
+
!Series_contact_city "Dunedin"
|
| 23 |
+
!Series_contact_zip/postal_code "9016"
|
| 24 |
+
!Series_contact_country "New Zealand"
|
| 25 |
+
!Series_supplementary_file "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE166nnn/GSE166592/suppl/GSE166592_C012_Full.xlsx"
|
| 26 |
+
!Series_supplementary_file "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE166nnn/GSE166592/suppl/GSE166592_ME007_Full.xlsx"
|
| 27 |
+
!Series_supplementary_file "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE166nnn/GSE166592/suppl/GSE166592_ME016_Full.xlsx"
|
| 28 |
+
!Series_supplementary_file "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE166nnn/GSE166592/suppl/GSE166592_RAW.tar"
|
| 29 |
+
!Series_platform_id "GPL16791"
|
| 30 |
+
!Series_platform_taxid "9606"
|
| 31 |
+
!Series_sample_taxid "9606"
|
| 32 |
+
!Series_relation "BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA701322"
|
| 33 |
+
!Series_relation "SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP305748"
|
| 34 |
+
|
| 35 |
+
!Sample_title "C012A" "C012B" "C012C" "C012D" "C012E" "Patient_One_A" "Patient_One_B" "Patient_One_C" "Patient_One_D" "Patient_One_E" "Patient_Two_A" "Patient_Two_B" "Patient_Two_C" "Patient_Two_D" "Patient_Two_E"
|
| 36 |
+
!Sample_geo_accession "GSM5076040" "GSM5076041" "GSM5076042" "GSM5076043" "GSM5076044" "GSM5076045" "GSM5076046" "GSM5076047" "GSM5076048" "GSM5076049" "GSM5076050" "GSM5076051" "GSM5076052" "GSM5076053" "GSM5076054"
|
| 37 |
+
!Sample_status "Public on Feb 11 2021" "Public on Feb 11 2021" "Public on Feb 11 2021" "Public on Feb 11 2021" "Public on Feb 11 2021" "Public on Feb 11 2021" "Public on Feb 11 2021" "Public on Feb 11 2021" "Public on Feb 11 2021" "Public on Feb 11 2021" "Public on Feb 11 2021" "Public on Feb 11 2021" "Public on Feb 11 2021" "Public on Feb 11 2021" "Public on Feb 11 2021"
|
| 38 |
+
!Sample_submission_date "Feb 10 2021" "Feb 10 2021" "Feb 10 2021" "Feb 10 2021" "Feb 10 2021" "Feb 10 2021" "Feb 10 2021" "Feb 10 2021" "Feb 10 2021" "Feb 10 2021" "Feb 10 2021" "Feb 10 2021" "Feb 10 2021" "Feb 10 2021" "Feb 10 2021"
|
| 39 |
+
!Sample_last_update_date "Feb 12 2021" "Feb 12 2021" "Feb 12 2021" "Feb 12 2021" "Feb 12 2021" "Mar 17 2021" "Feb 12 2021" "Feb 12 2021" "Feb 12 2021" "Feb 12 2021" "Feb 12 2021" "Feb 12 2021" "Mar 17 2021" "Feb 12 2021" "Feb 12 2021"
|
| 40 |
+
!Sample_type "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "SRA"
|
| 41 |
+
!Sample_channel_count "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1"
|
| 42 |
+
!Sample_source_name_ch1 "Peripheral Blood Mononuclear Cells" "Peripheral Blood Mononuclear Cells" "Peripheral Blood Mononuclear Cells" "Peripheral Blood Mononuclear Cells" "Peripheral Blood Mononuclear Cells" "Peripheral Blood Mononuclear Cells" "Peripheral Blood Mononuclear Cells" "Peripheral Blood Mononuclear Cells" "Peripheral Blood Mononuclear Cells" "Peripheral Blood Mononuclear Cells" "Peripheral Blood Mononuclear Cells" "Peripheral Blood Mononuclear Cells" "Peripheral Blood Mononuclear Cells" "Peripheral Blood Mononuclear Cells" "Peripheral Blood Mononuclear Cells"
|
| 43 |
+
!Sample_organism_ch1 "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens"
|
| 44 |
+
!Sample_characteristics_ch1 "disease state: Control" "disease state: Control" "disease state: Control" "disease state: Control" "disease state: Control" "disease state: myalgic encephalomyelitis/chronic fatigue syndrome" "disease state: myalgic encephalomyelitis/chronic fatigue syndrome" "disease state: myalgic encephalomyelitis/chronic fatigue syndrome" "disease state: myalgic encephalomyelitis/chronic fatigue syndrome" "disease state: myalgic encephalomyelitis/chronic fatigue syndrome" "disease state: myalgic encephalomyelitis/chronic fatigue syndrome" "disease state: myalgic encephalomyelitis/chronic fatigue syndrome" "disease state: myalgic encephalomyelitis/chronic fatigue syndrome" "disease state: myalgic encephalomyelitis/chronic fatigue syndrome" "disease state: myalgic encephalomyelitis/chronic fatigue syndrome"
|
| 45 |
+
!Sample_characteristics_ch1 "individual: C012" "individual: C012" "individual: C012" "individual: C012" "individual: C012" "individual: Patient_One" "individual: Patient_One" "individual: Patient_One" "individual: Patient_One" "individual: Patient_One" "individual: Patient_Two" "individual: Patient_Two" "individual: Patient_Two" "individual: Patient_Two" "individual: Patient_Two"
|
| 46 |
+
!Sample_characteristics_ch1 "time point: A" "time point: B" "time point: C" "time point: D" "time point: E" "time point: A" "time point: B" "time point: C" "time point: D" "time point: E" "time point: A" "time point: B" "time point: C" "time point: D" "time point: E"
|
| 47 |
+
!Sample_characteristics_ch1 "cell type: Peripheral Blood Mononuclear Cells" "cell type: Peripheral Blood Mononuclear Cells" "cell type: Peripheral Blood Mononuclear Cells" "cell type: Peripheral Blood Mononuclear Cells" "cell type: Peripheral Blood Mononuclear Cells" "cell type: Peripheral Blood Mononuclear Cells" "cell type: Peripheral Blood Mononuclear Cells" "cell type: Peripheral Blood Mononuclear Cells" "cell type: Peripheral Blood Mononuclear Cells" "cell type: Peripheral Blood Mononuclear Cells" "cell type: Peripheral Blood Mononuclear Cells" "cell type: Peripheral Blood Mononuclear Cells" "cell type: Peripheral Blood Mononuclear Cells" "cell type: Peripheral Blood Mononuclear Cells" "cell type: Peripheral Blood Mononuclear Cells"
|
| 48 |
+
!Sample_molecule_ch1 "genomic DNA" "genomic DNA" "genomic DNA" "genomic DNA" "genomic DNA" "genomic DNA" "genomic DNA" "genomic DNA" "genomic DNA" "genomic DNA" "genomic DNA" "genomic DNA" "genomic DNA" "genomic DNA" "genomic DNA"
|
| 49 |
+
!Sample_extract_protocol_ch1 "DNA was extracted from 200ul of PBMCs" "DNA was extracted from 200ul of PBMCs" "DNA was extracted from 200ul of PBMCs" "DNA was extracted from 200ul of PBMCs" "DNA was extracted from 200ul of PBMCs" "DNA was extracted from 200ul of PBMCs" "DNA was extracted from 200ul of PBMCs" "DNA was extracted from 200ul of PBMCs" "DNA was extracted from 200ul of PBMCs" "DNA was extracted from 200ul of PBMCs" "DNA was extracted from 200ul of PBMCs" "DNA was extracted from 200ul of PBMCs" "DNA was extracted from 200ul of PBMCs" "DNA was extracted from 200ul of PBMCs" "DNA was extracted from 200ul of PBMCs"
|
| 50 |
+
!Sample_extract_protocol_ch1 "MSPI digestion (purify), end repair (purify), A-tialing and adaptor ligation (purify), PCR amplification (purify), Gel size selection and gel extraction (purify)" "MSPI digestion (purify), end repair (purify), A-tialing and adaptor ligation (purify), PCR amplification (purify), Gel size selection and gel extraction (purify)" "MSPI digestion (purify), end repair (purify), A-tialing and adaptor ligation (purify), PCR amplification (purify), Gel size selection and gel extraction (purify)" "MSPI digestion (purify), end repair (purify), A-tialing and adaptor ligation (purify), PCR amplification (purify), Gel size selection and gel extraction (purify)" "MSPI digestion (purify), end repair (purify), A-tialing and adaptor ligation (purify), PCR amplification (purify), Gel size selection and gel extraction (purify)" "MSPI digestion (purify), end repair (purify), A-tialing and adaptor ligation (purify), PCR amplification (purify), Gel size selection and gel extraction (purify)" "MSPI digestion (purify), end repair (purify), A-tialing and adaptor ligation (purify), PCR amplification (purify), Gel size selection and gel extraction (purify)" "MSPI digestion (purify), end repair (purify), A-tialing and adaptor ligation (purify), PCR amplification (purify), Gel size selection and gel extraction (purify)" "MSPI digestion (purify), end repair (purify), A-tialing and adaptor ligation (purify), PCR amplification (purify), Gel size selection and gel extraction (purify)" "MSPI digestion (purify), end repair (purify), A-tialing and adaptor ligation (purify), PCR amplification (purify), Gel size selection and gel extraction (purify)" "MSPI digestion (purify), end repair (purify), A-tialing and adaptor ligation (purify), PCR amplification (purify), Gel size selection and gel extraction (purify)" "MSPI digestion (purify), end repair (purify), A-tialing and adaptor ligation (purify), PCR amplification (purify), Gel size selection and gel extraction (purify)" "MSPI digestion (purify), end repair (purify), A-tialing and adaptor ligation (purify), PCR amplification (purify), Gel size selection and gel extraction (purify)" "MSPI digestion (purify), end repair (purify), A-tialing and adaptor ligation (purify), PCR amplification (purify), Gel size selection and gel extraction (purify)" "MSPI digestion (purify), end repair (purify), A-tialing and adaptor ligation (purify), PCR amplification (purify), Gel size selection and gel extraction (purify)"
|
| 51 |
+
!Sample_taxid_ch1 "9606" "9606" "9606" "9606" "9606" "9606" "9606" "9606" "9606" "9606" "9606" "9606" "9606" "9606" "9606"
|
| 52 |
+
!Sample_description "C012A" "C012B" "C012C" "C012D" "C012E" "ME007A" "ME007B" "ME007C" "ME007D" "ME007E" "ME016A" "ME016B" "ME016C" "ME016D" "ME016E"
|
| 53 |
+
!Sample_data_processing "reads were adaptor trimmed using bismark that used a file of adaptor sequences and trimmed three bases back from any detected adaptor to delete the C invorporated and rejecting any reads that were trimmed to less than 10bp" "reads were adaptor trimmed using bismark that used a file of adaptor sequences and trimmed three bases back from any detected adaptor to delete the C invorporated and rejecting any reads that were trimmed to less than 10bp" "reads were adaptor trimmed using bismark that used a file of adaptor sequences and trimmed three bases back from any detected adaptor to delete the C invorporated and rejecting any reads that were trimmed to less than 10bp" "reads were adaptor trimmed using bismark that used a file of adaptor sequences and trimmed three bases back from any detected adaptor to delete the C invorporated and rejecting any reads that were trimmed to less than 10bp" "reads were adaptor trimmed using bismark that used a file of adaptor sequences and trimmed three bases back from any detected adaptor to delete the C invorporated and rejecting any reads that were trimmed to less than 10bp" "reads were adaptor trimmed using bismark that used a file of adaptor sequences and trimmed three bases back from any detected adaptor to delete the C invorporated and rejecting any reads that were trimmed to less than 10bp" "reads were adaptor trimmed using bismark that used a file of adaptor sequences and trimmed three bases back from any detected adaptor to delete the C invorporated and rejecting any reads that were trimmed to less than 10bp" "reads were adaptor trimmed using bismark that used a file of adaptor sequences and trimmed three bases back from any detected adaptor to delete the C invorporated and rejecting any reads that were trimmed to less than 10bp" "reads were adaptor trimmed using bismark that used a file of adaptor sequences and trimmed three bases back from any detected adaptor to delete the C invorporated and rejecting any reads that were trimmed to less than 10bp" "reads were adaptor trimmed using bismark that used a file of adaptor sequences and trimmed three bases back from any detected adaptor to delete the C invorporated and rejecting any reads that were trimmed to less than 10bp" "reads were adaptor trimmed using bismark that used a file of adaptor sequences and trimmed three bases back from any detected adaptor to delete the C invorporated and rejecting any reads that were trimmed to less than 10bp" "reads were adaptor trimmed using bismark that used a file of adaptor sequences and trimmed three bases back from any detected adaptor to delete the C invorporated and rejecting any reads that were trimmed to less than 10bp" "reads were adaptor trimmed using bismark that used a file of adaptor sequences and trimmed three bases back from any detected adaptor to delete the C invorporated and rejecting any reads that were trimmed to less than 10bp" "reads were adaptor trimmed using bismark that used a file of adaptor sequences and trimmed three bases back from any detected adaptor to delete the C invorporated and rejecting any reads that were trimmed to less than 10bp" "reads were adaptor trimmed using bismark that used a file of adaptor sequences and trimmed three bases back from any detected adaptor to delete the C invorporated and rejecting any reads that were trimmed to less than 10bp"
|
| 54 |
+
!Sample_data_processing "reads were aligned to the hg19 genome using bismark with the following specifications: a tolerance for one non-bisulfite mismatch per read, the default minimum alignment score (L,O, -02), and with ignore - quals in order to calculate the mismatch penalty by considering the quality value at the mismatched position to be the highest possible" "reads were aligned to the hg19 genome using bismark with the following specifications: a tolerance for one non-bisulfite mismatch per read, the default minimum alignment score (L,O, -02), and with ignore - quals in order to calculate the mismatch penalty by considering the quality value at the mismatched position to be the highest possible" "reads were aligned to the hg19 genome using bismark with the following specifications: a tolerance for one non-bisulfite mismatch per read, the default minimum alignment score (L,O, -02), and with ignore - quals in order to calculate the mismatch penalty by considering the quality value at the mismatched position to be the highest possible" "reads were aligned to the hg19 genome using bismark with the following specifications: a tolerance for one non-bisulfite mismatch per read, the default minimum alignment score (L,O, -02), and with ignore - quals in order to calculate the mismatch penalty by considering the quality value at the mismatched position to be the highest possible" "reads were aligned to the hg19 genome using bismark with the following specifications: a tolerance for one non-bisulfite mismatch per read, the default minimum alignment score (L,O, -02), and with ignore - quals in order to calculate the mismatch penalty by considering the quality value at the mismatched position to be the highest possible" "reads were aligned to the hg19 genome using bismark with the following specifications: a tolerance for one non-bisulfite mismatch per read, the default minimum alignment score (L,O, -02), and with ignore - quals in order to calculate the mismatch penalty by considering the quality value at the mismatched position to be the highest possible" "reads were aligned to the hg19 genome using bismark with the following specifications: a tolerance for one non-bisulfite mismatch per read, the default minimum alignment score (L,O, -02), and with ignore - quals in order to calculate the mismatch penalty by considering the quality value at the mismatched position to be the highest possible" "reads were aligned to the hg19 genome using bismark with the following specifications: a tolerance for one non-bisulfite mismatch per read, the default minimum alignment score (L,O, -02), and with ignore - quals in order to calculate the mismatch penalty by considering the quality value at the mismatched position to be the highest possible" "reads were aligned to the hg19 genome using bismark with the following specifications: a tolerance for one non-bisulfite mismatch per read, the default minimum alignment score (L,O, -02), and with ignore - quals in order to calculate the mismatch penalty by considering the quality value at the mismatched position to be the highest possible" "reads were aligned to the hg19 genome using bismark with the following specifications: a tolerance for one non-bisulfite mismatch per read, the default minimum alignment score (L,O, -02), and with ignore - quals in order to calculate the mismatch penalty by considering the quality value at the mismatched position to be the highest possible" "reads were aligned to the hg19 genome using bismark with the following specifications: a tolerance for one non-bisulfite mismatch per read, the default minimum alignment score (L,O, -02), and with ignore - quals in order to calculate the mismatch penalty by considering the quality value at the mismatched position to be the highest possible" "reads were aligned to the hg19 genome using bismark with the following specifications: a tolerance for one non-bisulfite mismatch per read, the default minimum alignment score (L,O, -02), and with ignore - quals in order to calculate the mismatch penalty by considering the quality value at the mismatched position to be the highest possible" "reads were aligned to the hg19 genome using bismark with the following specifications: a tolerance for one non-bisulfite mismatch per read, the default minimum alignment score (L,O, -02), and with ignore - quals in order to calculate the mismatch penalty by considering the quality value at the mismatched position to be the highest possible" "reads were aligned to the hg19 genome using bismark with the following specifications: a tolerance for one non-bisulfite mismatch per read, the default minimum alignment score (L,O, -02), and with ignore - quals in order to calculate the mismatch penalty by considering the quality value at the mismatched position to be the highest possible" "reads were aligned to the hg19 genome using bismark with the following specifications: a tolerance for one non-bisulfite mismatch per read, the default minimum alignment score (L,O, -02), and with ignore - quals in order to calculate the mismatch penalty by considering the quality value at the mismatched position to be the highest possible"
|
| 55 |
+
!Sample_data_processing "bam files generated by Bismark alignment were then processed using DMAP to compare control vs. patients with the following specifications: Chi squared test on fragments 40-220bp in length, with the fragment requireing at lest 2 CpGs to have 10 or more sequence reads. The differential methylation file was then annotated with protein coding gene information using the DMAP command identgeneloc. DMAPmatrix.csv file contains this data." "bam files generated by Bismark alignment were then processed using DMAP to compare control vs. patients with the following specifications: Chi squared test on fragments 40-220bp in length, with the fragment requireing at lest 2 CpGs to have 10 or more sequence reads. The differential methylation file was then annotated with protein coding gene information using the DMAP command identgeneloc. DMAPmatrix.csv file contains this data." "bam files generated by Bismark alignment were then processed using DMAP to compare control vs. patients with the following specifications: Chi squared test on fragments 40-220bp in length, with the fragment requireing at lest 2 CpGs to have 10 or more sequence reads. The differential methylation file was then annotated with protein coding gene information using the DMAP command identgeneloc. DMAPmatrix.csv file contains this data." "bam files generated by Bismark alignment were then processed using DMAP to compare control vs. patients with the following specifications: Chi squared test on fragments 40-220bp in length, with the fragment requireing at lest 2 CpGs to have 10 or more sequence reads. The differential methylation file was then annotated with protein coding gene information using the DMAP command identgeneloc. DMAPmatrix.csv file contains this data." "bam files generated by Bismark alignment were then processed using DMAP to compare control vs. patients with the following specifications: Chi squared test on fragments 40-220bp in length, with the fragment requireing at lest 2 CpGs to have 10 or more sequence reads. The differential methylation file was then annotated with protein coding gene information using the DMAP command identgeneloc. DMAPmatrix.csv file contains this data." "bam files generated by Bismark alignment were then processed using DMAP to compare control vs. patients with the following specifications: Chi squared test on fragments 40-220bp in length, with the fragment requireing at lest 2 CpGs to have 10 or more sequence reads. The differential methylation file was then annotated with protein coding gene information using the DMAP command identgeneloc. DMAPmatrix.csv file contains this data." "bam files generated by Bismark alignment were then processed using DMAP to compare control vs. patients with the following specifications: Chi squared test on fragments 40-220bp in length, with the fragment requireing at lest 2 CpGs to have 10 or more sequence reads. The differential methylation file was then annotated with protein coding gene information using the DMAP command identgeneloc. DMAPmatrix.csv file contains this data." "bam files generated by Bismark alignment were then processed using DMAP to compare control vs. patients with the following specifications: Chi squared test on fragments 40-220bp in length, with the fragment requireing at lest 2 CpGs to have 10 or more sequence reads. The differential methylation file was then annotated with protein coding gene information using the DMAP command identgeneloc. DMAPmatrix.csv file contains this data." "bam files generated by Bismark alignment were then processed using DMAP to compare control vs. patients with the following specifications: Chi squared test on fragments 40-220bp in length, with the fragment requireing at lest 2 CpGs to have 10 or more sequence reads. The differential methylation file was then annotated with protein coding gene information using the DMAP command identgeneloc. DMAPmatrix.csv file contains this data." "bam files generated by Bismark alignment were then processed using DMAP to compare control vs. patients with the following specifications: Chi squared test on fragments 40-220bp in length, with the fragment requireing at lest 2 CpGs to have 10 or more sequence reads. The differential methylation file was then annotated with protein coding gene information using the DMAP command identgeneloc. DMAPmatrix.csv file contains this data." "bam files generated by Bismark alignment were then processed using DMAP to compare control vs. patients with the following specifications: Chi squared test on fragments 40-220bp in length, with the fragment requireing at lest 2 CpGs to have 10 or more sequence reads. The differential methylation file was then annotated with protein coding gene information using the DMAP command identgeneloc. DMAPmatrix.csv file contains this data." "bam files generated by Bismark alignment were then processed using DMAP to compare control vs. patients with the following specifications: Chi squared test on fragments 40-220bp in length, with the fragment requireing at lest 2 CpGs to have 10 or more sequence reads. The differential methylation file was then annotated with protein coding gene information using the DMAP command identgeneloc. DMAPmatrix.csv file contains this data." "bam files generated by Bismark alignment were then processed using DMAP to compare control vs. patients with the following specifications: Chi squared test on fragments 40-220bp in length, with the fragment requireing at lest 2 CpGs to have 10 or more sequence reads. The differential methylation file was then annotated with protein coding gene information using the DMAP command identgeneloc. DMAPmatrix.csv file contains this data." "bam files generated by Bismark alignment were then processed using DMAP to compare control vs. patients with the following specifications: Chi squared test on fragments 40-220bp in length, with the fragment requireing at lest 2 CpGs to have 10 or more sequence reads. The differential methylation file was then annotated with protein coding gene information using the DMAP command identgeneloc. DMAPmatrix.csv file contains this data." "bam files generated by Bismark alignment were then processed using DMAP to compare control vs. patients with the following specifications: Chi squared test on fragments 40-220bp in length, with the fragment requireing at lest 2 CpGs to have 10 or more sequence reads. The differential methylation file was then annotated with protein coding gene information using the DMAP command identgeneloc. DMAPmatrix.csv file contains this data."
|
| 56 |
+
!Sample_data_processing "Genome_build: hg19" "Genome_build: hg19" "Genome_build: hg19" "Genome_build: hg19" "Genome_build: hg19" "Genome_build: hg19" "Genome_build: hg19" "Genome_build: hg19" "Genome_build: hg19" "Genome_build: hg19" "Genome_build: hg19" "Genome_build: hg19" "Genome_build: hg19" "Genome_build: hg19" "Genome_build: hg19"
|
| 57 |
+
!Sample_data_processing "Supplementary_files_format_and_content: Individual .txt files for each sample containing C and T frequency per base and coverage. C012_Full, ME007_Full and ME016_Full are excel files that contain, for the control, patient one, and patient two respectively, information about the per fragment methylation data including, genomic location, gene feature information, CpG relative location and fragment size." "Supplementary_files_format_and_content: Individual .txt files for each sample containing C and T frequency per base and coverage. C012_Full, ME007_Full and ME016_Full are excel files that contain, for the control, patient one, and patient two respectively, information about the per fragment methylation data including, genomic location, gene feature information, CpG relative location and fragment size." "Supplementary_files_format_and_content: Individual .txt files for each sample containing C and T frequency per base and coverage. C012_Full, ME007_Full and ME016_Full are excel files that contain, for the control, patient one, and patient two respectively, information about the per fragment methylation data including, genomic location, gene feature information, CpG relative location and fragment size." "Supplementary_files_format_and_content: Individual .txt files for each sample containing C and T frequency per base and coverage. C012_Full, ME007_Full and ME016_Full are excel files that contain, for the control, patient one, and patient two respectively, information about the per fragment methylation data including, genomic location, gene feature information, CpG relative location and fragment size." "Supplementary_files_format_and_content: Individual .txt files for each sample containing C and T frequency per base and coverage. C012_Full, ME007_Full and ME016_Full are excel files that contain, for the control, patient one, and patient two respectively, information about the per fragment methylation data including, genomic location, gene feature information, CpG relative location and fragment size." "Supplementary_files_format_and_content: Individual .txt files for each sample containing C and T frequency per base and coverage. C012_Full, ME007_Full and ME016_Full are excel files that contain, for the control, patient one, and patient two respectively, information about the per fragment methylation data including, genomic location, gene feature information, CpG relative location and fragment size." "Supplementary_files_format_and_content: Individual .txt files for each sample containing C and T frequency per base and coverage. C012_Full, ME007_Full and ME016_Full are excel files that contain, for the control, patient one, and patient two respectively, information about the per fragment methylation data including, genomic location, gene feature information, CpG relative location and fragment size." "Supplementary_files_format_and_content: Individual .txt files for each sample containing C and T frequency per base and coverage. C012_Full, ME007_Full and ME016_Full are excel files that contain, for the control, patient one, and patient two respectively, information about the per fragment methylation data including, genomic location, gene feature information, CpG relative location and fragment size." "Supplementary_files_format_and_content: Individual .txt files for each sample containing C and T frequency per base and coverage. C012_Full, ME007_Full and ME016_Full are excel files that contain, for the control, patient one, and patient two respectively, information about the per fragment methylation data including, genomic location, gene feature information, CpG relative location and fragment size." "Supplementary_files_format_and_content: Individual .txt files for each sample containing C and T frequency per base and coverage. C012_Full, ME007_Full and ME016_Full are excel files that contain, for the control, patient one, and patient two respectively, information about the per fragment methylation data including, genomic location, gene feature information, CpG relative location and fragment size." "Supplementary_files_format_and_content: Individual .txt files for each sample containing C and T frequency per base and coverage. C012_Full, ME007_Full and ME016_Full are excel files that contain, for the control, patient one, and patient two respectively, information about the per fragment methylation data including, genomic location, gene feature information, CpG relative location and fragment size." "Supplementary_files_format_and_content: Individual .txt files for each sample containing C and T frequency per base and coverage. C012_Full, ME007_Full and ME016_Full are excel files that contain, for the control, patient one, and patient two respectively, information about the per fragment methylation data including, genomic location, gene feature information, CpG relative location and fragment size." "Supplementary_files_format_and_content: Individual .txt files for each sample containing C and T frequency per base and coverage. C012_Full, ME007_Full and ME016_Full are excel files that contain, for the control, patient one, and patient two respectively, information about the per fragment methylation data including, genomic location, gene feature information, CpG relative location and fragment size." "Supplementary_files_format_and_content: Individual .txt files for each sample containing C and T frequency per base and coverage. C012_Full, ME007_Full and ME016_Full are excel files that contain, for the control, patient one, and patient two respectively, information about the per fragment methylation data including, genomic location, gene feature information, CpG relative location and fragment size." "Supplementary_files_format_and_content: Individual .txt files for each sample containing C and T frequency per base and coverage. C012_Full, ME007_Full and ME016_Full are excel files that contain, for the control, patient one, and patient two respectively, information about the per fragment methylation data including, genomic location, gene feature information, CpG relative location and fragment size."
|
| 58 |
+
!Sample_platform_id "GPL16791" "GPL16791" "GPL16791" "GPL16791" "GPL16791" "GPL16791" "GPL16791" "GPL16791" "GPL16791" "GPL16791" "GPL16791" "GPL16791" "GPL16791" "GPL16791" "GPL16791"
|
| 59 |
+
!Sample_contact_name "Amber,,Helliwell" "Amber,,Helliwell" "Amber,,Helliwell" "Amber,,Helliwell" "Amber,,Helliwell" "Amber,,Helliwell" "Amber,,Helliwell" "Amber,,Helliwell" "Amber,,Helliwell" "Amber,,Helliwell" "Amber,,Helliwell" "Amber,,Helliwell" "Amber,,Helliwell" "Amber,,Helliwell" "Amber,,Helliwell"
|
| 60 |
+
!Sample_contact_department "Biochemistry Department" "Biochemistry Department" "Biochemistry Department" "Biochemistry Department" "Biochemistry Department" "Biochemistry Department" "Biochemistry Department" "Biochemistry Department" "Biochemistry Department" "Biochemistry Department" "Biochemistry Department" "Biochemistry Department" "Biochemistry Department" "Biochemistry Department" "Biochemistry Department"
|
| 61 |
+
!Sample_contact_institute "University of Otago" "University of Otago" "University of Otago" "University of Otago" "University of Otago" "University of Otago" "University of Otago" "University of Otago" "University of Otago" "University of Otago" "University of Otago" "University of Otago" "University of Otago" "University of Otago" "University of Otago"
|
| 62 |
+
!Sample_contact_address "710 Cumberland Road" "710 Cumberland Road" "710 Cumberland Road" "710 Cumberland Road" "710 Cumberland Road" "710 Cumberland Road" "710 Cumberland Road" "710 Cumberland Road" "710 Cumberland Road" "710 Cumberland Road" "710 Cumberland Road" "710 Cumberland Road" "710 Cumberland Road" "710 Cumberland Road" "710 Cumberland Road"
|
| 63 |
+
!Sample_contact_city "Dunedin" "Dunedin" "Dunedin" "Dunedin" "Dunedin" "Dunedin" "Dunedin" "Dunedin" "Dunedin" "Dunedin" "Dunedin" "Dunedin" "Dunedin" "Dunedin" "Dunedin"
|
| 64 |
+
!Sample_contact_zip/postal_code "9016" "9016" "9016" "9016" "9016" "9016" "9016" "9016" "9016" "9016" "9016" "9016" "9016" "9016" "9016"
|
| 65 |
+
!Sample_contact_country "New Zealand" "New Zealand" "New Zealand" "New Zealand" "New Zealand" "New Zealand" "New Zealand" "New Zealand" "New Zealand" "New Zealand" "New Zealand" "New Zealand" "New Zealand" "New Zealand" "New Zealand"
|
| 66 |
+
!Sample_data_row_count "0" "0" "0" "0" "0" "0" "0" "0" "0" "0" "0" "0" "0" "0" "0"
|
| 67 |
+
!Sample_instrument_model "Illumina HiSeq 2500" "Illumina HiSeq 2500" "Illumina HiSeq 2500" "Illumina HiSeq 2500" "Illumina HiSeq 2500" "Illumina HiSeq 2500" "Illumina HiSeq 2500" "Illumina HiSeq 2500" "Illumina HiSeq 2500" "Illumina HiSeq 2500" "Illumina HiSeq 2500" "Illumina HiSeq 2500" "Illumina HiSeq 2500" "Illumina HiSeq 2500" "Illumina HiSeq 2500"
|
| 68 |
+
!Sample_library_selection "Reduced Representation" "Reduced Representation" "Reduced Representation" "Reduced Representation" "Reduced Representation" "Reduced Representation" "Reduced Representation" "Reduced Representation" "Reduced Representation" "Reduced Representation" "Reduced Representation" "Reduced Representation" "Reduced Representation" "Reduced Representation" "Reduced Representation"
|
| 69 |
+
!Sample_library_source "genomic" "genomic" "genomic" "genomic" "genomic" "genomic" "genomic" "genomic" "genomic" "genomic" "genomic" "genomic" "genomic" "genomic" "genomic"
|
| 70 |
+
!Sample_library_strategy "Bisulfite-Seq" "Bisulfite-Seq" "Bisulfite-Seq" "Bisulfite-Seq" "Bisulfite-Seq" "Bisulfite-Seq" "Bisulfite-Seq" "Bisulfite-Seq" "Bisulfite-Seq" "Bisulfite-Seq" "Bisulfite-Seq" "Bisulfite-Seq" "Bisulfite-Seq" "Bisulfite-Seq" "Bisulfite-Seq"
|
| 71 |
+
!Sample_relation "BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN17862810" "BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN17862809" "BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN17862808" "BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN17862807" "BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN17862806" "BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN17862805" "BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN17862804" "BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN17862803" "BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN17862802" "BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN17862801" "BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN17862800" "BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN17862799" "BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN17862798" "BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN17862797" "BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN17862796"
|
| 72 |
+
!Sample_relation "SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10073447" "SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10073448" "SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10073449" "SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10073450" "SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10073451" "SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10073452" "SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10073453" "SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10073454" "SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10073455" "SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10073456" "SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10073457" "SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10073458" "SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10073459" "SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10073460" "SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10073461"
|
| 73 |
+
!Sample_supplementary_file_1 "ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5076nnn/GSM5076040/suppl/GSM5076040_C012A_CpG.txt.gz" "ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5076nnn/GSM5076041/suppl/GSM5076041_C012B_CpG.txt.gz" "ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5076nnn/GSM5076042/suppl/GSM5076042_C012C_CpG.txt.gz" "ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5076nnn/GSM5076043/suppl/GSM5076043_C012D_CpG.txt.gz" "ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5076nnn/GSM5076044/suppl/GSM5076044_C012E_CpG.txt.gz" "ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5076nnn/GSM5076045/suppl/GSM5076045_ME007A_CpG.txt.gz" "ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5076nnn/GSM5076046/suppl/GSM5076046_ME007B_CpG.txt.gz" "ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5076nnn/GSM5076047/suppl/GSM5076047_ME007C_CpG.txt.gz" "ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5076nnn/GSM5076048/suppl/GSM5076048_ME007D_CpG.txt.gz" "ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5076nnn/GSM5076049/suppl/GSM5076049_ME007E_CpG.txt.gz" "ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5076nnn/GSM5076050/suppl/GSM5076050_ME016A_CpG.txt.gz" "ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5076nnn/GSM5076051/suppl/GSM5076051_ME016B_CpG.txt.gz" "ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5076nnn/GSM5076052/suppl/GSM5076052_ME016C_CpG.txt.gz" "ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5076nnn/GSM5076053/suppl/GSM5076053_ME016D_CpG.txt.gz" "ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5076nnn/GSM5076054/suppl/GSM5076054_ME016E_CpG.txt.gz"
|
| 74 |
+
!series_matrix_table_begin
|
| 75 |
+
"ID_REF" "GSM5076040" "GSM5076041" "GSM5076042" "GSM5076043" "GSM5076044" "GSM5076045" "GSM5076046" "GSM5076047" "GSM5076048" "GSM5076049" "GSM5076050" "GSM5076051" "GSM5076052" "GSM5076053" "GSM5076054"
|
| 76 |
+
!series_matrix_table_end
|
ME/GSE59489/GSE59489_RAW/GPL13534_450K_Manifest_header_Descriptions.xlsx
ADDED
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ME/GSE59489/meta/._GSE59489_family.soft
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ME/GSE59489/meta/._GSE59489_family.xml
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ME/GSE59489/meta/._GSE59489_series_matrix.txt
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ME/GSE59489/meta/GSE59489_family.xml/._GPL13534-tbl-1.txt
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ME/GSE59489/meta/GSE59489_family.xml/._GSE59489_family.xml
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ME/GSE59489/meta/GSE59489_family.xml/._GSM1437759-tbl-1.txt
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ME/GSE59489/meta/GSE59489_family.xml/._GSM1437761-tbl-1.txt
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ME/GSE59489/meta/GSE59489_family.xml/._GSM1437762-tbl-1.txt
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ME/GSE59489/meta/GSE59489_family.xml/._GSM1437763-tbl-1.txt
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ME/GSE59489/meta/GSE59489_family.xml/._GSM1437764-tbl-1.txt
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ME/GSE59489/meta/GSE59489_family.xml/._GSM1437765-tbl-1.txt
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ME/GSE59489/meta/GSE59489_family.xml/._GSM1437766-tbl-1.txt
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ME/GSE59489/meta/GSE59489_family.xml/._GSM1437767-tbl-1.txt
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ME/GSE59489/meta/GSE59489_family.xml/._GSM1437768-tbl-1.txt
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ME/GSE59489/meta/GSE59489_family.xml/._GSM1437769-tbl-1.txt
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ME/GSE59489/meta/GSE59489_family.xml/._GSM1437770-tbl-1.txt
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ME/GSE59489/meta/GSE59489_family.xml/._GSM1437771-tbl-1.txt
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ME/GSE59489/meta/GSE59489_family.xml/._GSM1437772-tbl-1.txt
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ME/GSE59489/meta/GSE59489_family.xml/._GSM1437773-tbl-1.txt
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ME/GSE59489/meta/GSE59489_family.xml/._GSM1437775-tbl-1.txt
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ME/GSE59489/meta/GSE59489_family.xml/._GSM1437776-tbl-1.txt
ADDED
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ME/GSE59489/meta/GSE59489_family.xml/._GSM1437777-tbl-1.txt
ADDED
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ME/GSE59489/meta/GSE59489_family.xml/._GSM1437778-tbl-1.txt
ADDED
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Binary file (4.1 kB). View file
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ME/GSE59489/meta/GSE59489_family.xml/._GSM1437780-tbl-1.txt
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ME/GSE59489/meta/GSE59489_family.xml/._GSM1437781-tbl-1.txt
ADDED
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Binary file (4.1 kB). View file
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ME/GSE59489/meta/GSE59489_family.xml/._GSM1437782-tbl-1.txt
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ME/GSE59489/meta/GSE59489_family.xml/GSE59489_family.xml
ADDED
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|
| 1 |
+
<?xml version="1.0" encoding="UTF-8" standalone="no"?>
|
| 2 |
+
|
| 3 |
+
<MINiML
|
| 4 |
+
xmlns="http://www.ncbi.nlm.nih.gov/geo/info/MINiML"
|
| 5 |
+
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
|
| 6 |
+
xsi:schemaLocation="http://www.ncbi.nlm.nih.gov/geo/info/MINiML http://www.ncbi.nlm.nih.gov/geo/info/MINiML.xsd"
|
| 7 |
+
version="0.5.0" >
|
| 8 |
+
|
| 9 |
+
<Contributor iid="contrib1">
|
| 10 |
+
<Person><First>Patrick</First><Last>McGowan</Last></Person>
|
| 11 |
+
<Email>patrick.mcgowan@utoronto.ca</Email>
|
| 12 |
+
<Laboratory>SW326</Laboratory>
|
| 13 |
+
<Department>Biological Sciences</Department>
|
| 14 |
+
<Organization>University of Toronto Scarborough</Organization>
|
| 15 |
+
<Address>
|
| 16 |
+
<Line>1265 Military Trail</Line>
|
| 17 |
+
<City>Toronto</City>
|
| 18 |
+
<State>Ontario</State>
|
| 19 |
+
<Postal-Code>M1C 1A4</Postal-Code>
|
| 20 |
+
<Country>Canada</Country>
|
| 21 |
+
</Address>
|
| 22 |
+
</Contributor>
|
| 23 |
+
|
| 24 |
+
<Contributor iid="contrib2">
|
| 25 |
+
<Organization>Illumina Inc.</Organization>
|
| 26 |
+
<Email>expression@illumina.com, techsupport@illumina.com</Email>
|
| 27 |
+
<Phone>1 800 809 4566 </Phone>
|
| 28 |
+
<Organization>Illumina Inc.</Organization>
|
| 29 |
+
<Address>
|
| 30 |
+
<Line>9885 Towne Centre Drive</Line>
|
| 31 |
+
<City>San Diego</City>
|
| 32 |
+
<State>CA</State>
|
| 33 |
+
<Zip-Code>92121</Zip-Code>
|
| 34 |
+
<Country>USA</Country>
|
| 35 |
+
</Address>
|
| 36 |
+
<Web-Link>www.illumina.com</Web-Link>
|
| 37 |
+
</Contributor>
|
| 38 |
+
|
| 39 |
+
<Contributor iid="contrib3">
|
| 40 |
+
<Person><First>Wilfred</First><Middle>C</Middle><Last>de Vega</Last></Person>
|
| 41 |
+
</Contributor>
|
| 42 |
+
|
| 43 |
+
<Contributor iid="contrib4">
|
| 44 |
+
<Person><First>Suzanne</First><Middle>D</Middle><Last>Vernon</Last></Person>
|
| 45 |
+
</Contributor>
|
| 46 |
+
|
| 47 |
+
<Contributor iid="contrib5">
|
| 48 |
+
<Person><First>Patrick</First><Middle>O</Middle><Last>McGowan</Last></Person>
|
| 49 |
+
</Contributor>
|
| 50 |
+
|
| 51 |
+
<Database iid="GEO">
|
| 52 |
+
<Name>Gene Expression Omnibus (GEO)</Name>
|
| 53 |
+
<Public-ID>GEO</Public-ID>
|
| 54 |
+
<Organization>NCBI NLM NIH</Organization>
|
| 55 |
+
<Web-Link>http://www.ncbi.nlm.nih.gov/geo</Web-Link>
|
| 56 |
+
<Email>geo@ncbi.nlm.nih.gov</Email>
|
| 57 |
+
</Database>
|
| 58 |
+
|
| 59 |
+
<Platform iid="GPL13534">
|
| 60 |
+
<Status database="GEO">
|
| 61 |
+
<Submission-Date>2011-05-13</Submission-Date>
|
| 62 |
+
<Release-Date>2011-05-13</Release-Date>
|
| 63 |
+
<Last-Update-Date>2019-03-22</Last-Update-Date>
|
| 64 |
+
</Status>
|
| 65 |
+
<Title>Illumina HumanMethylation450 BeadChip (HumanMethylation450_15017482)</Title>
|
| 66 |
+
<Accession database="GEO">GPL13534</Accession>
|
| 67 |
+
<Technology>oligonucleotide beads</Technology>
|
| 68 |
+
<Distribution>commercial</Distribution>
|
| 69 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 70 |
+
<Manufacturer>Illumina, Inc.</Manufacturer>
|
| 71 |
+
<Manufacture-Protocol>
|
| 72 |
+
See manufacturer's website
|
| 73 |
+
</Manufacture-Protocol>
|
| 74 |
+
<Description>
|
| 75 |
+
1 difference between HumanMethylation450_15017482_v.1.1.bpm and HumanMethylation450_15017482_v.1.2.bpm:
|
| 76 |
+
|
| 77 |
+
1.1:
|
| 78 |
+
|
| 79 |
+
41636384,NEGATIVE,-99,Negative 604
|
| 80 |
+
|
| 81 |
+
1.2:
|
| 82 |
+
|
| 83 |
+
41636384,RESTORATION,Green,Restore
|
| 84 |
+
</Description>
|
| 85 |
+
<Contact-Ref ref="contrib2" />
|
| 86 |
+
<Supplementary-Data type="XLSX">
|
| 87 |
+
ftp://ftp.ncbi.nlm.nih.gov/geo/platforms/GPL13nnn/GPL13534/suppl/GPL13534_450K_Manifest_header_Descriptions.xlsx.gz
|
| 88 |
+
</Supplementary-Data>
|
| 89 |
+
<Supplementary-Data type="TXT">
|
| 90 |
+
ftp://ftp.ncbi.nlm.nih.gov/geo/platforms/GPL13nnn/GPL13534/suppl/GPL13534_HumanMethylation450_15017482_v.1.1.bpm.txt.gz
|
| 91 |
+
</Supplementary-Data>
|
| 92 |
+
<Supplementary-Data type="CSV">
|
| 93 |
+
ftp://ftp.ncbi.nlm.nih.gov/geo/platforms/GPL13nnn/GPL13534/suppl/GPL13534_HumanMethylation450_15017482_v.1.1.csv.gz
|
| 94 |
+
</Supplementary-Data>
|
| 95 |
+
<Supplementary-Data type="BPM">
|
| 96 |
+
ftp://ftp.ncbi.nlm.nih.gov/geo/platforms/GPL13nnn/GPL13534/suppl/GPL13534_HumanMethylation450_15017482_v.1.2.bpm.gz
|
| 97 |
+
</Supplementary-Data>
|
| 98 |
+
<Relation type="Alternative to" target="GPL16304" />
|
| 99 |
+
<Data-Table>
|
| 100 |
+
<Column position="1">
|
| 101 |
+
<Name>ID</Name>
|
| 102 |
+
</Column>
|
| 103 |
+
<Column position="2">
|
| 104 |
+
<Name>Name</Name>
|
| 105 |
+
</Column>
|
| 106 |
+
<Column position="3">
|
| 107 |
+
<Name>AddressA_ID</Name>
|
| 108 |
+
</Column>
|
| 109 |
+
<Column position="4">
|
| 110 |
+
<Name>AlleleA_ProbeSeq</Name>
|
| 111 |
+
</Column>
|
| 112 |
+
<Column position="5">
|
| 113 |
+
<Name>AddressB_ID</Name>
|
| 114 |
+
</Column>
|
| 115 |
+
<Column position="6">
|
| 116 |
+
<Name>AlleleB_ProbeSeq</Name>
|
| 117 |
+
</Column>
|
| 118 |
+
<Column position="7">
|
| 119 |
+
<Name>Infinium_Design_Type</Name>
|
| 120 |
+
</Column>
|
| 121 |
+
<Column position="8">
|
| 122 |
+
<Name>Next_Base</Name>
|
| 123 |
+
</Column>
|
| 124 |
+
<Column position="9">
|
| 125 |
+
<Name>Color_Channel</Name>
|
| 126 |
+
</Column>
|
| 127 |
+
<Column position="10">
|
| 128 |
+
<Name>Forward_Sequence</Name>
|
| 129 |
+
</Column>
|
| 130 |
+
<Column position="11">
|
| 131 |
+
<Name>Genome_Build</Name>
|
| 132 |
+
</Column>
|
| 133 |
+
<Column position="12">
|
| 134 |
+
<Name>CHR</Name>
|
| 135 |
+
</Column>
|
| 136 |
+
<Column position="13">
|
| 137 |
+
<Name>MAPINFO</Name>
|
| 138 |
+
</Column>
|
| 139 |
+
<Column position="14">
|
| 140 |
+
<Name>SourceSeq</Name>
|
| 141 |
+
</Column>
|
| 142 |
+
<Column position="15">
|
| 143 |
+
<Name>Chromosome_36</Name>
|
| 144 |
+
</Column>
|
| 145 |
+
<Column position="16">
|
| 146 |
+
<Name>Coordinate_36</Name>
|
| 147 |
+
</Column>
|
| 148 |
+
<Column position="17">
|
| 149 |
+
<Name>Strand</Name>
|
| 150 |
+
</Column>
|
| 151 |
+
<Column position="18">
|
| 152 |
+
<Name>Probe_SNPs</Name>
|
| 153 |
+
</Column>
|
| 154 |
+
<Column position="19">
|
| 155 |
+
<Name>Probe_SNPs_10</Name>
|
| 156 |
+
</Column>
|
| 157 |
+
<Column position="20">
|
| 158 |
+
<Name>Random_Loci</Name>
|
| 159 |
+
</Column>
|
| 160 |
+
<Column position="21">
|
| 161 |
+
<Name>Methyl27_Loci</Name>
|
| 162 |
+
</Column>
|
| 163 |
+
<Column position="22">
|
| 164 |
+
<Name>UCSC_RefGene_Name</Name>
|
| 165 |
+
</Column>
|
| 166 |
+
<Column position="23">
|
| 167 |
+
<Name>UCSC_RefGene_Accession</Name>
|
| 168 |
+
</Column>
|
| 169 |
+
<Column position="24">
|
| 170 |
+
<Name>UCSC_RefGene_Group</Name>
|
| 171 |
+
</Column>
|
| 172 |
+
<Column position="25">
|
| 173 |
+
<Name>UCSC_CpG_Islands_Name</Name>
|
| 174 |
+
</Column>
|
| 175 |
+
<Column position="26">
|
| 176 |
+
<Name>Relation_to_UCSC_CpG_Island</Name>
|
| 177 |
+
</Column>
|
| 178 |
+
<Column position="27">
|
| 179 |
+
<Name>Phantom</Name>
|
| 180 |
+
</Column>
|
| 181 |
+
<Column position="28">
|
| 182 |
+
<Name>DMR</Name>
|
| 183 |
+
</Column>
|
| 184 |
+
<Column position="29">
|
| 185 |
+
<Name>Enhancer</Name>
|
| 186 |
+
</Column>
|
| 187 |
+
<Column position="30">
|
| 188 |
+
<Name>HMM_Island</Name>
|
| 189 |
+
</Column>
|
| 190 |
+
<Column position="31">
|
| 191 |
+
<Name>Regulatory_Feature_Name</Name>
|
| 192 |
+
</Column>
|
| 193 |
+
<Column position="32">
|
| 194 |
+
<Name>Regulatory_Feature_Group</Name>
|
| 195 |
+
</Column>
|
| 196 |
+
<Column position="33">
|
| 197 |
+
<Name>DHS</Name>
|
| 198 |
+
</Column>
|
| 199 |
+
<Column position="34">
|
| 200 |
+
<Name>RANGE_START</Name>
|
| 201 |
+
</Column>
|
| 202 |
+
<Column position="35">
|
| 203 |
+
<Name>RANGE_END</Name>
|
| 204 |
+
</Column>
|
| 205 |
+
<Column position="36">
|
| 206 |
+
<Name>RANGE_GB</Name>
|
| 207 |
+
</Column>
|
| 208 |
+
<Column position="37">
|
| 209 |
+
<Name>SPOT_ID</Name>
|
| 210 |
+
</Column>
|
| 211 |
+
<External-Data rows="485577">
|
| 212 |
+
GPL13534-tbl-1.txt
|
| 213 |
+
</External-Data>
|
| 214 |
+
</Data-Table>
|
| 215 |
+
</Platform>
|
| 216 |
+
|
| 217 |
+
<Sample iid="GSM1437759">
|
| 218 |
+
<Status database="GEO">
|
| 219 |
+
<Submission-Date>2014-07-16</Submission-Date>
|
| 220 |
+
<Release-Date>2014-08-12</Release-Date>
|
| 221 |
+
<Last-Update-Date>2014-08-12</Last-Update-Date>
|
| 222 |
+
</Status>
|
| 223 |
+
<Title>PBMC genomic DNA_CFS1</Title>
|
| 224 |
+
<Accession database="GEO">GSM1437759</Accession>
|
| 225 |
+
<Type>genomic</Type>
|
| 226 |
+
<Channel-Count>1</Channel-Count>
|
| 227 |
+
<Channel position="1">
|
| 228 |
+
<Source>CFS PBMC</Source>
|
| 229 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 230 |
+
<Characteristics tag="gender">
|
| 231 |
+
female
|
| 232 |
+
</Characteristics>
|
| 233 |
+
<Characteristics tag="subject id">
|
| 234 |
+
CFS subject 1
|
| 235 |
+
</Characteristics>
|
| 236 |
+
<Characteristics tag="disease state">
|
| 237 |
+
Chronic Fatigue Syndrome (CFS)
|
| 238 |
+
</Characteristics>
|
| 239 |
+
<Characteristics tag="cell type">
|
| 240 |
+
peripheral blood mononuclear cells (PBMC)
|
| 241 |
+
</Characteristics>
|
| 242 |
+
<Molecule>genomic DNA</Molecule>
|
| 243 |
+
<Extract-Protocol>
|
| 244 |
+
Omega EZNA Tissue DNA Kit; Qiagen MinElute Reaction Cleanup Kit; Genome Quebec sample processing protocols
|
| 245 |
+
</Extract-Protocol>
|
| 246 |
+
<Label>Cy3,Cy5</Label>
|
| 247 |
+
<Label-Protocol>
|
| 248 |
+
Standard Illumina Protocol
|
| 249 |
+
</Label-Protocol>
|
| 250 |
+
</Channel>
|
| 251 |
+
<Hybridization-Protocol>
|
| 252 |
+
Standard Illumina Protocol
|
| 253 |
+
</Hybridization-Protocol>
|
| 254 |
+
<Scan-Protocol>
|
| 255 |
+
Standard Illumina Protocol
|
| 256 |
+
</Scan-Protocol>
|
| 257 |
+
<Description>
|
| 258 |
+
PBMC genomic DNA from CFS subject 1
|
| 259 |
+
7985#WG0153568-DNA#A01#G00061
|
| 260 |
+
</Description>
|
| 261 |
+
<Data-Processing>
|
| 262 |
+
Illumina Genome Studio; the non_normalized.txt contains unmethylated (A) and methylated (B) signal intensities.
|
| 263 |
+
</Data-Processing>
|
| 264 |
+
<Platform-Ref ref="GPL13534" />
|
| 265 |
+
<Contact-Ref ref="contrib1" />
|
| 266 |
+
<Supplementary-Data type="unknown">
|
| 267 |
+
NONE
|
| 268 |
+
</Supplementary-Data>
|
| 269 |
+
<Data-Table>
|
| 270 |
+
<Column position="1">
|
| 271 |
+
<Name>ID_REF</Name>
|
| 272 |
+
</Column>
|
| 273 |
+
<Column position="2">
|
| 274 |
+
<Name>VALUE</Name>
|
| 275 |
+
<Description>Average Beta</Description>
|
| 276 |
+
</Column>
|
| 277 |
+
<Column position="3">
|
| 278 |
+
<Name>Detection Pval</Name>
|
| 279 |
+
</Column>
|
| 280 |
+
<External-Data rows="485577">
|
| 281 |
+
GSM1437759-tbl-1.txt
|
| 282 |
+
</External-Data>
|
| 283 |
+
</Data-Table>
|
| 284 |
+
</Sample>
|
| 285 |
+
|
| 286 |
+
<Sample iid="GSM1437760">
|
| 287 |
+
<Status database="GEO">
|
| 288 |
+
<Submission-Date>2014-07-16</Submission-Date>
|
| 289 |
+
<Release-Date>2014-08-12</Release-Date>
|
| 290 |
+
<Last-Update-Date>2014-08-12</Last-Update-Date>
|
| 291 |
+
</Status>
|
| 292 |
+
<Title>PBMC genomic DNA_CFS2</Title>
|
| 293 |
+
<Accession database="GEO">GSM1437760</Accession>
|
| 294 |
+
<Type>genomic</Type>
|
| 295 |
+
<Channel-Count>1</Channel-Count>
|
| 296 |
+
<Channel position="1">
|
| 297 |
+
<Source>CFS PBMC</Source>
|
| 298 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 299 |
+
<Characteristics tag="gender">
|
| 300 |
+
female
|
| 301 |
+
</Characteristics>
|
| 302 |
+
<Characteristics tag="subject id">
|
| 303 |
+
CFS subject 2
|
| 304 |
+
</Characteristics>
|
| 305 |
+
<Characteristics tag="disease state">
|
| 306 |
+
Chronic Fatigue Syndrome (CFS)
|
| 307 |
+
</Characteristics>
|
| 308 |
+
<Characteristics tag="cell type">
|
| 309 |
+
peripheral blood mononuclear cells (PBMC)
|
| 310 |
+
</Characteristics>
|
| 311 |
+
<Molecule>genomic DNA</Molecule>
|
| 312 |
+
<Extract-Protocol>
|
| 313 |
+
Omega EZNA Tissue DNA Kit; Qiagen MinElute Reaction Cleanup Kit; Genome Quebec sample processing protocols
|
| 314 |
+
</Extract-Protocol>
|
| 315 |
+
<Label>Cy3,Cy5</Label>
|
| 316 |
+
<Label-Protocol>
|
| 317 |
+
Standard Illumina Protocol
|
| 318 |
+
</Label-Protocol>
|
| 319 |
+
</Channel>
|
| 320 |
+
<Hybridization-Protocol>
|
| 321 |
+
Standard Illumina Protocol
|
| 322 |
+
</Hybridization-Protocol>
|
| 323 |
+
<Scan-Protocol>
|
| 324 |
+
Standard Illumina Protocol
|
| 325 |
+
</Scan-Protocol>
|
| 326 |
+
<Description>
|
| 327 |
+
PBMC genomic DNA from CFS subject 2
|
| 328 |
+
7985#WG0153568-DNA#A02#G00062
|
| 329 |
+
</Description>
|
| 330 |
+
<Data-Processing>
|
| 331 |
+
Illumina Genome Studio; the non_normalized.txt contains unmethylated (A) and methylated (B) signal intensities.
|
| 332 |
+
</Data-Processing>
|
| 333 |
+
<Platform-Ref ref="GPL13534" />
|
| 334 |
+
<Contact-Ref ref="contrib1" />
|
| 335 |
+
<Supplementary-Data type="unknown">
|
| 336 |
+
NONE
|
| 337 |
+
</Supplementary-Data>
|
| 338 |
+
<Data-Table>
|
| 339 |
+
<Column position="1">
|
| 340 |
+
<Name>ID_REF</Name>
|
| 341 |
+
</Column>
|
| 342 |
+
<Column position="2">
|
| 343 |
+
<Name>VALUE</Name>
|
| 344 |
+
<Description>Average Beta</Description>
|
| 345 |
+
</Column>
|
| 346 |
+
<Column position="3">
|
| 347 |
+
<Name>Detection Pval</Name>
|
| 348 |
+
</Column>
|
| 349 |
+
<External-Data rows="485577">
|
| 350 |
+
GSM1437760-tbl-1.txt
|
| 351 |
+
</External-Data>
|
| 352 |
+
</Data-Table>
|
| 353 |
+
</Sample>
|
| 354 |
+
|
| 355 |
+
<Sample iid="GSM1437761">
|
| 356 |
+
<Status database="GEO">
|
| 357 |
+
<Submission-Date>2014-07-16</Submission-Date>
|
| 358 |
+
<Release-Date>2014-08-12</Release-Date>
|
| 359 |
+
<Last-Update-Date>2014-08-12</Last-Update-Date>
|
| 360 |
+
</Status>
|
| 361 |
+
<Title>PBMC genomic DNA_CFS3</Title>
|
| 362 |
+
<Accession database="GEO">GSM1437761</Accession>
|
| 363 |
+
<Type>genomic</Type>
|
| 364 |
+
<Channel-Count>1</Channel-Count>
|
| 365 |
+
<Channel position="1">
|
| 366 |
+
<Source>CFS PBMC</Source>
|
| 367 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 368 |
+
<Characteristics tag="gender">
|
| 369 |
+
female
|
| 370 |
+
</Characteristics>
|
| 371 |
+
<Characteristics tag="subject id">
|
| 372 |
+
CFS subject 3
|
| 373 |
+
</Characteristics>
|
| 374 |
+
<Characteristics tag="disease state">
|
| 375 |
+
Chronic Fatigue Syndrome (CFS)
|
| 376 |
+
</Characteristics>
|
| 377 |
+
<Characteristics tag="cell type">
|
| 378 |
+
peripheral blood mononuclear cells (PBMC)
|
| 379 |
+
</Characteristics>
|
| 380 |
+
<Molecule>genomic DNA</Molecule>
|
| 381 |
+
<Extract-Protocol>
|
| 382 |
+
Omega EZNA Tissue DNA Kit; Qiagen MinElute Reaction Cleanup Kit; Genome Quebec sample processing protocols
|
| 383 |
+
</Extract-Protocol>
|
| 384 |
+
<Label>Cy3,Cy5</Label>
|
| 385 |
+
<Label-Protocol>
|
| 386 |
+
Standard Illumina Protocol
|
| 387 |
+
</Label-Protocol>
|
| 388 |
+
</Channel>
|
| 389 |
+
<Hybridization-Protocol>
|
| 390 |
+
Standard Illumina Protocol
|
| 391 |
+
</Hybridization-Protocol>
|
| 392 |
+
<Scan-Protocol>
|
| 393 |
+
Standard Illumina Protocol
|
| 394 |
+
</Scan-Protocol>
|
| 395 |
+
<Description>
|
| 396 |
+
PBMC genomic DNA from CFS subject 3
|
| 397 |
+
7985#WG0153568-DNA#A03#G00055
|
| 398 |
+
</Description>
|
| 399 |
+
<Data-Processing>
|
| 400 |
+
Illumina Genome Studio; the non_normalized.txt contains unmethylated (A) and methylated (B) signal intensities.
|
| 401 |
+
</Data-Processing>
|
| 402 |
+
<Platform-Ref ref="GPL13534" />
|
| 403 |
+
<Contact-Ref ref="contrib1" />
|
| 404 |
+
<Supplementary-Data type="unknown">
|
| 405 |
+
NONE
|
| 406 |
+
</Supplementary-Data>
|
| 407 |
+
<Data-Table>
|
| 408 |
+
<Column position="1">
|
| 409 |
+
<Name>ID_REF</Name>
|
| 410 |
+
</Column>
|
| 411 |
+
<Column position="2">
|
| 412 |
+
<Name>VALUE</Name>
|
| 413 |
+
<Description>Average Beta</Description>
|
| 414 |
+
</Column>
|
| 415 |
+
<Column position="3">
|
| 416 |
+
<Name>Detection Pval</Name>
|
| 417 |
+
</Column>
|
| 418 |
+
<External-Data rows="485577">
|
| 419 |
+
GSM1437761-tbl-1.txt
|
| 420 |
+
</External-Data>
|
| 421 |
+
</Data-Table>
|
| 422 |
+
</Sample>
|
| 423 |
+
|
| 424 |
+
<Sample iid="GSM1437762">
|
| 425 |
+
<Status database="GEO">
|
| 426 |
+
<Submission-Date>2014-07-16</Submission-Date>
|
| 427 |
+
<Release-Date>2014-08-12</Release-Date>
|
| 428 |
+
<Last-Update-Date>2014-08-12</Last-Update-Date>
|
| 429 |
+
</Status>
|
| 430 |
+
<Title>PBMC genomic DNA_CFS4</Title>
|
| 431 |
+
<Accession database="GEO">GSM1437762</Accession>
|
| 432 |
+
<Type>genomic</Type>
|
| 433 |
+
<Channel-Count>1</Channel-Count>
|
| 434 |
+
<Channel position="1">
|
| 435 |
+
<Source>CFS PBMC</Source>
|
| 436 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 437 |
+
<Characteristics tag="gender">
|
| 438 |
+
female
|
| 439 |
+
</Characteristics>
|
| 440 |
+
<Characteristics tag="subject id">
|
| 441 |
+
CFS subject 4
|
| 442 |
+
</Characteristics>
|
| 443 |
+
<Characteristics tag="disease state">
|
| 444 |
+
Chronic Fatigue Syndrome (CFS)
|
| 445 |
+
</Characteristics>
|
| 446 |
+
<Characteristics tag="cell type">
|
| 447 |
+
peripheral blood mononuclear cells (PBMC)
|
| 448 |
+
</Characteristics>
|
| 449 |
+
<Molecule>genomic DNA</Molecule>
|
| 450 |
+
<Extract-Protocol>
|
| 451 |
+
Omega EZNA Tissue DNA Kit; Qiagen MinElute Reaction Cleanup Kit; Genome Quebec sample processing protocols
|
| 452 |
+
</Extract-Protocol>
|
| 453 |
+
<Label>Cy3,Cy5</Label>
|
| 454 |
+
<Label-Protocol>
|
| 455 |
+
Standard Illumina Protocol
|
| 456 |
+
</Label-Protocol>
|
| 457 |
+
</Channel>
|
| 458 |
+
<Hybridization-Protocol>
|
| 459 |
+
Standard Illumina Protocol
|
| 460 |
+
</Hybridization-Protocol>
|
| 461 |
+
<Scan-Protocol>
|
| 462 |
+
Standard Illumina Protocol
|
| 463 |
+
</Scan-Protocol>
|
| 464 |
+
<Description>
|
| 465 |
+
PBMC genomic DNA from CFS subject 4
|
| 466 |
+
7985#WG0153568-DNA#A04#G00042
|
| 467 |
+
</Description>
|
| 468 |
+
<Data-Processing>
|
| 469 |
+
Illumina Genome Studio; the non_normalized.txt contains unmethylated (A) and methylated (B) signal intensities.
|
| 470 |
+
</Data-Processing>
|
| 471 |
+
<Platform-Ref ref="GPL13534" />
|
| 472 |
+
<Contact-Ref ref="contrib1" />
|
| 473 |
+
<Supplementary-Data type="unknown">
|
| 474 |
+
NONE
|
| 475 |
+
</Supplementary-Data>
|
| 476 |
+
<Data-Table>
|
| 477 |
+
<Column position="1">
|
| 478 |
+
<Name>ID_REF</Name>
|
| 479 |
+
</Column>
|
| 480 |
+
<Column position="2">
|
| 481 |
+
<Name>VALUE</Name>
|
| 482 |
+
<Description>Average Beta</Description>
|
| 483 |
+
</Column>
|
| 484 |
+
<Column position="3">
|
| 485 |
+
<Name>Detection Pval</Name>
|
| 486 |
+
</Column>
|
| 487 |
+
<External-Data rows="485577">
|
| 488 |
+
GSM1437762-tbl-1.txt
|
| 489 |
+
</External-Data>
|
| 490 |
+
</Data-Table>
|
| 491 |
+
</Sample>
|
| 492 |
+
|
| 493 |
+
<Sample iid="GSM1437763">
|
| 494 |
+
<Status database="GEO">
|
| 495 |
+
<Submission-Date>2014-07-16</Submission-Date>
|
| 496 |
+
<Release-Date>2014-08-12</Release-Date>
|
| 497 |
+
<Last-Update-Date>2014-08-12</Last-Update-Date>
|
| 498 |
+
</Status>
|
| 499 |
+
<Title>PBMC genomic DNA_CFS5</Title>
|
| 500 |
+
<Accession database="GEO">GSM1437763</Accession>
|
| 501 |
+
<Type>genomic</Type>
|
| 502 |
+
<Channel-Count>1</Channel-Count>
|
| 503 |
+
<Channel position="1">
|
| 504 |
+
<Source>CFS PBMC</Source>
|
| 505 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 506 |
+
<Characteristics tag="gender">
|
| 507 |
+
female
|
| 508 |
+
</Characteristics>
|
| 509 |
+
<Characteristics tag="subject id">
|
| 510 |
+
CFS subject 5
|
| 511 |
+
</Characteristics>
|
| 512 |
+
<Characteristics tag="disease state">
|
| 513 |
+
Chronic Fatigue Syndrome (CFS)
|
| 514 |
+
</Characteristics>
|
| 515 |
+
<Characteristics tag="cell type">
|
| 516 |
+
peripheral blood mononuclear cells (PBMC)
|
| 517 |
+
</Characteristics>
|
| 518 |
+
<Molecule>genomic DNA</Molecule>
|
| 519 |
+
<Extract-Protocol>
|
| 520 |
+
Omega EZNA Tissue DNA Kit; Qiagen MinElute Reaction Cleanup Kit; Genome Quebec sample processing protocols
|
| 521 |
+
</Extract-Protocol>
|
| 522 |
+
<Label>Cy3,Cy5</Label>
|
| 523 |
+
<Label-Protocol>
|
| 524 |
+
Standard Illumina Protocol
|
| 525 |
+
</Label-Protocol>
|
| 526 |
+
</Channel>
|
| 527 |
+
<Hybridization-Protocol>
|
| 528 |
+
Standard Illumina Protocol
|
| 529 |
+
</Hybridization-Protocol>
|
| 530 |
+
<Scan-Protocol>
|
| 531 |
+
Standard Illumina Protocol
|
| 532 |
+
</Scan-Protocol>
|
| 533 |
+
<Description>
|
| 534 |
+
PBMC genomic DNA from CFS subject 5
|
| 535 |
+
7985#WG0153568-DNA#A05#G00080
|
| 536 |
+
</Description>
|
| 537 |
+
<Data-Processing>
|
| 538 |
+
Illumina Genome Studio; the non_normalized.txt contains unmethylated (A) and methylated (B) signal intensities.
|
| 539 |
+
</Data-Processing>
|
| 540 |
+
<Platform-Ref ref="GPL13534" />
|
| 541 |
+
<Contact-Ref ref="contrib1" />
|
| 542 |
+
<Supplementary-Data type="unknown">
|
| 543 |
+
NONE
|
| 544 |
+
</Supplementary-Data>
|
| 545 |
+
<Data-Table>
|
| 546 |
+
<Column position="1">
|
| 547 |
+
<Name>ID_REF</Name>
|
| 548 |
+
</Column>
|
| 549 |
+
<Column position="2">
|
| 550 |
+
<Name>VALUE</Name>
|
| 551 |
+
<Description>Average Beta</Description>
|
| 552 |
+
</Column>
|
| 553 |
+
<Column position="3">
|
| 554 |
+
<Name>Detection Pval</Name>
|
| 555 |
+
</Column>
|
| 556 |
+
<External-Data rows="485577">
|
| 557 |
+
GSM1437763-tbl-1.txt
|
| 558 |
+
</External-Data>
|
| 559 |
+
</Data-Table>
|
| 560 |
+
</Sample>
|
| 561 |
+
|
| 562 |
+
<Sample iid="GSM1437764">
|
| 563 |
+
<Status database="GEO">
|
| 564 |
+
<Submission-Date>2014-07-16</Submission-Date>
|
| 565 |
+
<Release-Date>2014-08-12</Release-Date>
|
| 566 |
+
<Last-Update-Date>2014-08-12</Last-Update-Date>
|
| 567 |
+
</Status>
|
| 568 |
+
<Title>PBMC genomic DNA_CFS6</Title>
|
| 569 |
+
<Accession database="GEO">GSM1437764</Accession>
|
| 570 |
+
<Type>genomic</Type>
|
| 571 |
+
<Channel-Count>1</Channel-Count>
|
| 572 |
+
<Channel position="1">
|
| 573 |
+
<Source>CFS PBMC</Source>
|
| 574 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 575 |
+
<Characteristics tag="gender">
|
| 576 |
+
female
|
| 577 |
+
</Characteristics>
|
| 578 |
+
<Characteristics tag="subject id">
|
| 579 |
+
CFS subject 6
|
| 580 |
+
</Characteristics>
|
| 581 |
+
<Characteristics tag="disease state">
|
| 582 |
+
Chronic Fatigue Syndrome (CFS)
|
| 583 |
+
</Characteristics>
|
| 584 |
+
<Characteristics tag="cell type">
|
| 585 |
+
peripheral blood mononuclear cells (PBMC)
|
| 586 |
+
</Characteristics>
|
| 587 |
+
<Molecule>genomic DNA</Molecule>
|
| 588 |
+
<Extract-Protocol>
|
| 589 |
+
Omega EZNA Tissue DNA Kit; Qiagen MinElute Reaction Cleanup Kit; Genome Quebec sample processing protocols
|
| 590 |
+
</Extract-Protocol>
|
| 591 |
+
<Label>Cy3,Cy5</Label>
|
| 592 |
+
<Label-Protocol>
|
| 593 |
+
Standard Illumina Protocol
|
| 594 |
+
</Label-Protocol>
|
| 595 |
+
</Channel>
|
| 596 |
+
<Hybridization-Protocol>
|
| 597 |
+
Standard Illumina Protocol
|
| 598 |
+
</Hybridization-Protocol>
|
| 599 |
+
<Scan-Protocol>
|
| 600 |
+
Standard Illumina Protocol
|
| 601 |
+
</Scan-Protocol>
|
| 602 |
+
<Description>
|
| 603 |
+
PBMC genomic DNA from CFS subject 6
|
| 604 |
+
7985#WG0153568-DNA#A06#G00200
|
| 605 |
+
</Description>
|
| 606 |
+
<Data-Processing>
|
| 607 |
+
Illumina Genome Studio; the non_normalized.txt contains unmethylated (A) and methylated (B) signal intensities.
|
| 608 |
+
</Data-Processing>
|
| 609 |
+
<Platform-Ref ref="GPL13534" />
|
| 610 |
+
<Contact-Ref ref="contrib1" />
|
| 611 |
+
<Supplementary-Data type="unknown">
|
| 612 |
+
NONE
|
| 613 |
+
</Supplementary-Data>
|
| 614 |
+
<Data-Table>
|
| 615 |
+
<Column position="1">
|
| 616 |
+
<Name>ID_REF</Name>
|
| 617 |
+
</Column>
|
| 618 |
+
<Column position="2">
|
| 619 |
+
<Name>VALUE</Name>
|
| 620 |
+
<Description>Average Beta</Description>
|
| 621 |
+
</Column>
|
| 622 |
+
<Column position="3">
|
| 623 |
+
<Name>Detection Pval</Name>
|
| 624 |
+
</Column>
|
| 625 |
+
<External-Data rows="485577">
|
| 626 |
+
GSM1437764-tbl-1.txt
|
| 627 |
+
</External-Data>
|
| 628 |
+
</Data-Table>
|
| 629 |
+
</Sample>
|
| 630 |
+
|
| 631 |
+
<Sample iid="GSM1437765">
|
| 632 |
+
<Status database="GEO">
|
| 633 |
+
<Submission-Date>2014-07-16</Submission-Date>
|
| 634 |
+
<Release-Date>2014-08-12</Release-Date>
|
| 635 |
+
<Last-Update-Date>2014-08-12</Last-Update-Date>
|
| 636 |
+
</Status>
|
| 637 |
+
<Title>PBMC genomic DNA_Control1</Title>
|
| 638 |
+
<Accession database="GEO">GSM1437765</Accession>
|
| 639 |
+
<Type>genomic</Type>
|
| 640 |
+
<Channel-Count>1</Channel-Count>
|
| 641 |
+
<Channel position="1">
|
| 642 |
+
<Source>Control PBMC</Source>
|
| 643 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 644 |
+
<Characteristics tag="gender">
|
| 645 |
+
female
|
| 646 |
+
</Characteristics>
|
| 647 |
+
<Characteristics tag="subject id">
|
| 648 |
+
Control subject 1
|
| 649 |
+
</Characteristics>
|
| 650 |
+
<Characteristics tag="disease state">
|
| 651 |
+
Control
|
| 652 |
+
</Characteristics>
|
| 653 |
+
<Characteristics tag="cell type">
|
| 654 |
+
peripheral blood mononuclear cells (PBMC)
|
| 655 |
+
</Characteristics>
|
| 656 |
+
<Molecule>genomic DNA</Molecule>
|
| 657 |
+
<Extract-Protocol>
|
| 658 |
+
Omega EZNA Tissue DNA Kit; Qiagen MinElute Reaction Cleanup Kit; Genome Quebec sample processing protocols
|
| 659 |
+
</Extract-Protocol>
|
| 660 |
+
<Label>Cy3,Cy5</Label>
|
| 661 |
+
<Label-Protocol>
|
| 662 |
+
Standard Illumina Protocol
|
| 663 |
+
</Label-Protocol>
|
| 664 |
+
</Channel>
|
| 665 |
+
<Hybridization-Protocol>
|
| 666 |
+
Standard Illumina Protocol
|
| 667 |
+
</Hybridization-Protocol>
|
| 668 |
+
<Scan-Protocol>
|
| 669 |
+
Standard Illumina Protocol
|
| 670 |
+
</Scan-Protocol>
|
| 671 |
+
<Description>
|
| 672 |
+
PBMC genomic DNA from Control subject 1
|
| 673 |
+
7985#WG0153568-DNA#A07#G00211
|
| 674 |
+
</Description>
|
| 675 |
+
<Data-Processing>
|
| 676 |
+
Illumina Genome Studio; the non_normalized.txt contains unmethylated (A) and methylated (B) signal intensities.
|
| 677 |
+
</Data-Processing>
|
| 678 |
+
<Platform-Ref ref="GPL13534" />
|
| 679 |
+
<Contact-Ref ref="contrib1" />
|
| 680 |
+
<Supplementary-Data type="unknown">
|
| 681 |
+
NONE
|
| 682 |
+
</Supplementary-Data>
|
| 683 |
+
<Data-Table>
|
| 684 |
+
<Column position="1">
|
| 685 |
+
<Name>ID_REF</Name>
|
| 686 |
+
</Column>
|
| 687 |
+
<Column position="2">
|
| 688 |
+
<Name>VALUE</Name>
|
| 689 |
+
<Description>Average Beta</Description>
|
| 690 |
+
</Column>
|
| 691 |
+
<Column position="3">
|
| 692 |
+
<Name>Detection Pval</Name>
|
| 693 |
+
</Column>
|
| 694 |
+
<External-Data rows="485577">
|
| 695 |
+
GSM1437765-tbl-1.txt
|
| 696 |
+
</External-Data>
|
| 697 |
+
</Data-Table>
|
| 698 |
+
</Sample>
|
| 699 |
+
|
| 700 |
+
<Sample iid="GSM1437766">
|
| 701 |
+
<Status database="GEO">
|
| 702 |
+
<Submission-Date>2014-07-16</Submission-Date>
|
| 703 |
+
<Release-Date>2014-08-12</Release-Date>
|
| 704 |
+
<Last-Update-Date>2014-08-12</Last-Update-Date>
|
| 705 |
+
</Status>
|
| 706 |
+
<Title>PBMC genomic DNA_Control2</Title>
|
| 707 |
+
<Accession database="GEO">GSM1437766</Accession>
|
| 708 |
+
<Type>genomic</Type>
|
| 709 |
+
<Channel-Count>1</Channel-Count>
|
| 710 |
+
<Channel position="1">
|
| 711 |
+
<Source>Control PBMC</Source>
|
| 712 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 713 |
+
<Characteristics tag="gender">
|
| 714 |
+
female
|
| 715 |
+
</Characteristics>
|
| 716 |
+
<Characteristics tag="subject id">
|
| 717 |
+
Control subject 2
|
| 718 |
+
</Characteristics>
|
| 719 |
+
<Characteristics tag="disease state">
|
| 720 |
+
Control
|
| 721 |
+
</Characteristics>
|
| 722 |
+
<Characteristics tag="cell type">
|
| 723 |
+
peripheral blood mononuclear cells (PBMC)
|
| 724 |
+
</Characteristics>
|
| 725 |
+
<Molecule>genomic DNA</Molecule>
|
| 726 |
+
<Extract-Protocol>
|
| 727 |
+
Omega EZNA Tissue DNA Kit; Qiagen MinElute Reaction Cleanup Kit; Genome Quebec sample processing protocols
|
| 728 |
+
</Extract-Protocol>
|
| 729 |
+
<Label>Cy3,Cy5</Label>
|
| 730 |
+
<Label-Protocol>
|
| 731 |
+
Standard Illumina Protocol
|
| 732 |
+
</Label-Protocol>
|
| 733 |
+
</Channel>
|
| 734 |
+
<Hybridization-Protocol>
|
| 735 |
+
Standard Illumina Protocol
|
| 736 |
+
</Hybridization-Protocol>
|
| 737 |
+
<Scan-Protocol>
|
| 738 |
+
Standard Illumina Protocol
|
| 739 |
+
</Scan-Protocol>
|
| 740 |
+
<Description>
|
| 741 |
+
PBMC genomic DNA from Control subject 2
|
| 742 |
+
7985#WG0153568-DNA#A08#G00140
|
| 743 |
+
</Description>
|
| 744 |
+
<Data-Processing>
|
| 745 |
+
Illumina Genome Studio; the non_normalized.txt contains unmethylated (A) and methylated (B) signal intensities.
|
| 746 |
+
</Data-Processing>
|
| 747 |
+
<Platform-Ref ref="GPL13534" />
|
| 748 |
+
<Contact-Ref ref="contrib1" />
|
| 749 |
+
<Supplementary-Data type="unknown">
|
| 750 |
+
NONE
|
| 751 |
+
</Supplementary-Data>
|
| 752 |
+
<Data-Table>
|
| 753 |
+
<Column position="1">
|
| 754 |
+
<Name>ID_REF</Name>
|
| 755 |
+
</Column>
|
| 756 |
+
<Column position="2">
|
| 757 |
+
<Name>VALUE</Name>
|
| 758 |
+
<Description>Average Beta</Description>
|
| 759 |
+
</Column>
|
| 760 |
+
<Column position="3">
|
| 761 |
+
<Name>Detection Pval</Name>
|
| 762 |
+
</Column>
|
| 763 |
+
<External-Data rows="485577">
|
| 764 |
+
GSM1437766-tbl-1.txt
|
| 765 |
+
</External-Data>
|
| 766 |
+
</Data-Table>
|
| 767 |
+
</Sample>
|
| 768 |
+
|
| 769 |
+
<Sample iid="GSM1437767">
|
| 770 |
+
<Status database="GEO">
|
| 771 |
+
<Submission-Date>2014-07-16</Submission-Date>
|
| 772 |
+
<Release-Date>2014-08-12</Release-Date>
|
| 773 |
+
<Last-Update-Date>2014-08-12</Last-Update-Date>
|
| 774 |
+
</Status>
|
| 775 |
+
<Title>PBMC genomic DNA_Control3</Title>
|
| 776 |
+
<Accession database="GEO">GSM1437767</Accession>
|
| 777 |
+
<Type>genomic</Type>
|
| 778 |
+
<Channel-Count>1</Channel-Count>
|
| 779 |
+
<Channel position="1">
|
| 780 |
+
<Source>Control PBMC</Source>
|
| 781 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 782 |
+
<Characteristics tag="gender">
|
| 783 |
+
female
|
| 784 |
+
</Characteristics>
|
| 785 |
+
<Characteristics tag="subject id">
|
| 786 |
+
Control subject 3
|
| 787 |
+
</Characteristics>
|
| 788 |
+
<Characteristics tag="disease state">
|
| 789 |
+
Control
|
| 790 |
+
</Characteristics>
|
| 791 |
+
<Characteristics tag="cell type">
|
| 792 |
+
peripheral blood mononuclear cells (PBMC)
|
| 793 |
+
</Characteristics>
|
| 794 |
+
<Molecule>genomic DNA</Molecule>
|
| 795 |
+
<Extract-Protocol>
|
| 796 |
+
Omega EZNA Tissue DNA Kit; Qiagen MinElute Reaction Cleanup Kit; Genome Quebec sample processing protocols
|
| 797 |
+
</Extract-Protocol>
|
| 798 |
+
<Label>Cy3,Cy5</Label>
|
| 799 |
+
<Label-Protocol>
|
| 800 |
+
Standard Illumina Protocol
|
| 801 |
+
</Label-Protocol>
|
| 802 |
+
</Channel>
|
| 803 |
+
<Hybridization-Protocol>
|
| 804 |
+
Standard Illumina Protocol
|
| 805 |
+
</Hybridization-Protocol>
|
| 806 |
+
<Scan-Protocol>
|
| 807 |
+
Standard Illumina Protocol
|
| 808 |
+
</Scan-Protocol>
|
| 809 |
+
<Description>
|
| 810 |
+
PBMC genomic DNA from Control subject 3
|
| 811 |
+
7985#WG0153568-DNA#A09#G00158
|
| 812 |
+
</Description>
|
| 813 |
+
<Data-Processing>
|
| 814 |
+
Illumina Genome Studio; the non_normalized.txt contains unmethylated (A) and methylated (B) signal intensities.
|
| 815 |
+
</Data-Processing>
|
| 816 |
+
<Platform-Ref ref="GPL13534" />
|
| 817 |
+
<Contact-Ref ref="contrib1" />
|
| 818 |
+
<Supplementary-Data type="unknown">
|
| 819 |
+
NONE
|
| 820 |
+
</Supplementary-Data>
|
| 821 |
+
<Data-Table>
|
| 822 |
+
<Column position="1">
|
| 823 |
+
<Name>ID_REF</Name>
|
| 824 |
+
</Column>
|
| 825 |
+
<Column position="2">
|
| 826 |
+
<Name>VALUE</Name>
|
| 827 |
+
<Description>Average Beta</Description>
|
| 828 |
+
</Column>
|
| 829 |
+
<Column position="3">
|
| 830 |
+
<Name>Detection Pval</Name>
|
| 831 |
+
</Column>
|
| 832 |
+
<External-Data rows="485577">
|
| 833 |
+
GSM1437767-tbl-1.txt
|
| 834 |
+
</External-Data>
|
| 835 |
+
</Data-Table>
|
| 836 |
+
</Sample>
|
| 837 |
+
|
| 838 |
+
<Sample iid="GSM1437768">
|
| 839 |
+
<Status database="GEO">
|
| 840 |
+
<Submission-Date>2014-07-16</Submission-Date>
|
| 841 |
+
<Release-Date>2014-08-12</Release-Date>
|
| 842 |
+
<Last-Update-Date>2014-08-12</Last-Update-Date>
|
| 843 |
+
</Status>
|
| 844 |
+
<Title>PBMC genomic DNA_Control4</Title>
|
| 845 |
+
<Accession database="GEO">GSM1437768</Accession>
|
| 846 |
+
<Type>genomic</Type>
|
| 847 |
+
<Channel-Count>1</Channel-Count>
|
| 848 |
+
<Channel position="1">
|
| 849 |
+
<Source>Control PBMC</Source>
|
| 850 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 851 |
+
<Characteristics tag="gender">
|
| 852 |
+
female
|
| 853 |
+
</Characteristics>
|
| 854 |
+
<Characteristics tag="subject id">
|
| 855 |
+
Control subject 4
|
| 856 |
+
</Characteristics>
|
| 857 |
+
<Characteristics tag="disease state">
|
| 858 |
+
Control
|
| 859 |
+
</Characteristics>
|
| 860 |
+
<Characteristics tag="cell type">
|
| 861 |
+
peripheral blood mononuclear cells (PBMC)
|
| 862 |
+
</Characteristics>
|
| 863 |
+
<Molecule>genomic DNA</Molecule>
|
| 864 |
+
<Extract-Protocol>
|
| 865 |
+
Omega EZNA Tissue DNA Kit; Qiagen MinElute Reaction Cleanup Kit; Genome Quebec sample processing protocols
|
| 866 |
+
</Extract-Protocol>
|
| 867 |
+
<Label>Cy3,Cy5</Label>
|
| 868 |
+
<Label-Protocol>
|
| 869 |
+
Standard Illumina Protocol
|
| 870 |
+
</Label-Protocol>
|
| 871 |
+
</Channel>
|
| 872 |
+
<Hybridization-Protocol>
|
| 873 |
+
Standard Illumina Protocol
|
| 874 |
+
</Hybridization-Protocol>
|
| 875 |
+
<Scan-Protocol>
|
| 876 |
+
Standard Illumina Protocol
|
| 877 |
+
</Scan-Protocol>
|
| 878 |
+
<Description>
|
| 879 |
+
PBMC genomic DNA from Control subject 4
|
| 880 |
+
7985#WG0153568-DNA#A10#G00212
|
| 881 |
+
</Description>
|
| 882 |
+
<Data-Processing>
|
| 883 |
+
Illumina Genome Studio; the non_normalized.txt contains unmethylated (A) and methylated (B) signal intensities.
|
| 884 |
+
</Data-Processing>
|
| 885 |
+
<Platform-Ref ref="GPL13534" />
|
| 886 |
+
<Contact-Ref ref="contrib1" />
|
| 887 |
+
<Supplementary-Data type="unknown">
|
| 888 |
+
NONE
|
| 889 |
+
</Supplementary-Data>
|
| 890 |
+
<Data-Table>
|
| 891 |
+
<Column position="1">
|
| 892 |
+
<Name>ID_REF</Name>
|
| 893 |
+
</Column>
|
| 894 |
+
<Column position="2">
|
| 895 |
+
<Name>VALUE</Name>
|
| 896 |
+
<Description>Average Beta</Description>
|
| 897 |
+
</Column>
|
| 898 |
+
<Column position="3">
|
| 899 |
+
<Name>Detection Pval</Name>
|
| 900 |
+
</Column>
|
| 901 |
+
<External-Data rows="485577">
|
| 902 |
+
GSM1437768-tbl-1.txt
|
| 903 |
+
</External-Data>
|
| 904 |
+
</Data-Table>
|
| 905 |
+
</Sample>
|
| 906 |
+
|
| 907 |
+
<Sample iid="GSM1437769">
|
| 908 |
+
<Status database="GEO">
|
| 909 |
+
<Submission-Date>2014-07-16</Submission-Date>
|
| 910 |
+
<Release-Date>2014-08-12</Release-Date>
|
| 911 |
+
<Last-Update-Date>2014-08-12</Last-Update-Date>
|
| 912 |
+
</Status>
|
| 913 |
+
<Title>PBMC genomic DNA_Control5</Title>
|
| 914 |
+
<Accession database="GEO">GSM1437769</Accession>
|
| 915 |
+
<Type>genomic</Type>
|
| 916 |
+
<Channel-Count>1</Channel-Count>
|
| 917 |
+
<Channel position="1">
|
| 918 |
+
<Source>Control PBMC</Source>
|
| 919 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 920 |
+
<Characteristics tag="gender">
|
| 921 |
+
female
|
| 922 |
+
</Characteristics>
|
| 923 |
+
<Characteristics tag="subject id">
|
| 924 |
+
Control subject 5
|
| 925 |
+
</Characteristics>
|
| 926 |
+
<Characteristics tag="disease state">
|
| 927 |
+
Control
|
| 928 |
+
</Characteristics>
|
| 929 |
+
<Characteristics tag="cell type">
|
| 930 |
+
peripheral blood mononuclear cells (PBMC)
|
| 931 |
+
</Characteristics>
|
| 932 |
+
<Molecule>genomic DNA</Molecule>
|
| 933 |
+
<Extract-Protocol>
|
| 934 |
+
Omega EZNA Tissue DNA Kit; Qiagen MinElute Reaction Cleanup Kit; Genome Quebec sample processing protocols
|
| 935 |
+
</Extract-Protocol>
|
| 936 |
+
<Label>Cy3,Cy5</Label>
|
| 937 |
+
<Label-Protocol>
|
| 938 |
+
Standard Illumina Protocol
|
| 939 |
+
</Label-Protocol>
|
| 940 |
+
</Channel>
|
| 941 |
+
<Hybridization-Protocol>
|
| 942 |
+
Standard Illumina Protocol
|
| 943 |
+
</Hybridization-Protocol>
|
| 944 |
+
<Scan-Protocol>
|
| 945 |
+
Standard Illumina Protocol
|
| 946 |
+
</Scan-Protocol>
|
| 947 |
+
<Description>
|
| 948 |
+
PBMC genomic DNA from Control subject 5
|
| 949 |
+
7985#WG0153568-DNA#A11#G00135
|
| 950 |
+
</Description>
|
| 951 |
+
<Data-Processing>
|
| 952 |
+
Illumina Genome Studio; the non_normalized.txt contains unmethylated (A) and methylated (B) signal intensities.
|
| 953 |
+
</Data-Processing>
|
| 954 |
+
<Platform-Ref ref="GPL13534" />
|
| 955 |
+
<Contact-Ref ref="contrib1" />
|
| 956 |
+
<Supplementary-Data type="unknown">
|
| 957 |
+
NONE
|
| 958 |
+
</Supplementary-Data>
|
| 959 |
+
<Data-Table>
|
| 960 |
+
<Column position="1">
|
| 961 |
+
<Name>ID_REF</Name>
|
| 962 |
+
</Column>
|
| 963 |
+
<Column position="2">
|
| 964 |
+
<Name>VALUE</Name>
|
| 965 |
+
<Description>Average Beta</Description>
|
| 966 |
+
</Column>
|
| 967 |
+
<Column position="3">
|
| 968 |
+
<Name>Detection Pval</Name>
|
| 969 |
+
</Column>
|
| 970 |
+
<External-Data rows="485577">
|
| 971 |
+
GSM1437769-tbl-1.txt
|
| 972 |
+
</External-Data>
|
| 973 |
+
</Data-Table>
|
| 974 |
+
</Sample>
|
| 975 |
+
|
| 976 |
+
<Sample iid="GSM1437770">
|
| 977 |
+
<Status database="GEO">
|
| 978 |
+
<Submission-Date>2014-07-16</Submission-Date>
|
| 979 |
+
<Release-Date>2014-08-12</Release-Date>
|
| 980 |
+
<Last-Update-Date>2014-08-12</Last-Update-Date>
|
| 981 |
+
</Status>
|
| 982 |
+
<Title>PBMC genomic DNA_Control6</Title>
|
| 983 |
+
<Accession database="GEO">GSM1437770</Accession>
|
| 984 |
+
<Type>genomic</Type>
|
| 985 |
+
<Channel-Count>1</Channel-Count>
|
| 986 |
+
<Channel position="1">
|
| 987 |
+
<Source>Control PBMC</Source>
|
| 988 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 989 |
+
<Characteristics tag="gender">
|
| 990 |
+
female
|
| 991 |
+
</Characteristics>
|
| 992 |
+
<Characteristics tag="subject id">
|
| 993 |
+
Control subject 6
|
| 994 |
+
</Characteristics>
|
| 995 |
+
<Characteristics tag="disease state">
|
| 996 |
+
Control
|
| 997 |
+
</Characteristics>
|
| 998 |
+
<Characteristics tag="cell type">
|
| 999 |
+
peripheral blood mononuclear cells (PBMC)
|
| 1000 |
+
</Characteristics>
|
| 1001 |
+
<Molecule>genomic DNA</Molecule>
|
| 1002 |
+
<Extract-Protocol>
|
| 1003 |
+
Omega EZNA Tissue DNA Kit; Qiagen MinElute Reaction Cleanup Kit; Genome Quebec sample processing protocols
|
| 1004 |
+
</Extract-Protocol>
|
| 1005 |
+
<Label>Cy3,Cy5</Label>
|
| 1006 |
+
<Label-Protocol>
|
| 1007 |
+
Standard Illumina Protocol
|
| 1008 |
+
</Label-Protocol>
|
| 1009 |
+
</Channel>
|
| 1010 |
+
<Hybridization-Protocol>
|
| 1011 |
+
Standard Illumina Protocol
|
| 1012 |
+
</Hybridization-Protocol>
|
| 1013 |
+
<Scan-Protocol>
|
| 1014 |
+
Standard Illumina Protocol
|
| 1015 |
+
</Scan-Protocol>
|
| 1016 |
+
<Description>
|
| 1017 |
+
PBMC genomic DNA from Control subject 6
|
| 1018 |
+
7985#WG0153568-DNA#A12#G00213
|
| 1019 |
+
</Description>
|
| 1020 |
+
<Data-Processing>
|
| 1021 |
+
Illumina Genome Studio; the non_normalized.txt contains unmethylated (A) and methylated (B) signal intensities.
|
| 1022 |
+
</Data-Processing>
|
| 1023 |
+
<Platform-Ref ref="GPL13534" />
|
| 1024 |
+
<Contact-Ref ref="contrib1" />
|
| 1025 |
+
<Supplementary-Data type="unknown">
|
| 1026 |
+
NONE
|
| 1027 |
+
</Supplementary-Data>
|
| 1028 |
+
<Data-Table>
|
| 1029 |
+
<Column position="1">
|
| 1030 |
+
<Name>ID_REF</Name>
|
| 1031 |
+
</Column>
|
| 1032 |
+
<Column position="2">
|
| 1033 |
+
<Name>VALUE</Name>
|
| 1034 |
+
<Description>Average Beta</Description>
|
| 1035 |
+
</Column>
|
| 1036 |
+
<Column position="3">
|
| 1037 |
+
<Name>Detection Pval</Name>
|
| 1038 |
+
</Column>
|
| 1039 |
+
<External-Data rows="485577">
|
| 1040 |
+
GSM1437770-tbl-1.txt
|
| 1041 |
+
</External-Data>
|
| 1042 |
+
</Data-Table>
|
| 1043 |
+
</Sample>
|
| 1044 |
+
|
| 1045 |
+
<Sample iid="GSM1437771">
|
| 1046 |
+
<Status database="GEO">
|
| 1047 |
+
<Submission-Date>2014-07-16</Submission-Date>
|
| 1048 |
+
<Release-Date>2014-08-12</Release-Date>
|
| 1049 |
+
<Last-Update-Date>2014-08-12</Last-Update-Date>
|
| 1050 |
+
</Status>
|
| 1051 |
+
<Title>PBMC genomic DNA_CFS7</Title>
|
| 1052 |
+
<Accession database="GEO">GSM1437771</Accession>
|
| 1053 |
+
<Type>genomic</Type>
|
| 1054 |
+
<Channel-Count>1</Channel-Count>
|
| 1055 |
+
<Channel position="1">
|
| 1056 |
+
<Source>CFS PBMC</Source>
|
| 1057 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 1058 |
+
<Characteristics tag="gender">
|
| 1059 |
+
female
|
| 1060 |
+
</Characteristics>
|
| 1061 |
+
<Characteristics tag="subject id">
|
| 1062 |
+
CFS subject 7
|
| 1063 |
+
</Characteristics>
|
| 1064 |
+
<Characteristics tag="disease state">
|
| 1065 |
+
Chronic Fatigue Syndrome (CFS)
|
| 1066 |
+
</Characteristics>
|
| 1067 |
+
<Characteristics tag="cell type">
|
| 1068 |
+
peripheral blood mononuclear cells (PBMC)
|
| 1069 |
+
</Characteristics>
|
| 1070 |
+
<Molecule>genomic DNA</Molecule>
|
| 1071 |
+
<Extract-Protocol>
|
| 1072 |
+
Omega EZNA Tissue DNA Kit; Qiagen MinElute Reaction Cleanup Kit; Genome Quebec sample processing protocols
|
| 1073 |
+
</Extract-Protocol>
|
| 1074 |
+
<Label>Cy3,Cy5</Label>
|
| 1075 |
+
<Label-Protocol>
|
| 1076 |
+
Standard Illumina Protocol
|
| 1077 |
+
</Label-Protocol>
|
| 1078 |
+
</Channel>
|
| 1079 |
+
<Hybridization-Protocol>
|
| 1080 |
+
Standard Illumina Protocol
|
| 1081 |
+
</Hybridization-Protocol>
|
| 1082 |
+
<Scan-Protocol>
|
| 1083 |
+
Standard Illumina Protocol
|
| 1084 |
+
</Scan-Protocol>
|
| 1085 |
+
<Description>
|
| 1086 |
+
PBMC genomic DNA from CFS subject 7
|
| 1087 |
+
7985#WG0153568-DNA#B01#G00021
|
| 1088 |
+
</Description>
|
| 1089 |
+
<Data-Processing>
|
| 1090 |
+
Illumina Genome Studio; the non_normalized.txt contains unmethylated (A) and methylated (B) signal intensities.
|
| 1091 |
+
</Data-Processing>
|
| 1092 |
+
<Platform-Ref ref="GPL13534" />
|
| 1093 |
+
<Contact-Ref ref="contrib1" />
|
| 1094 |
+
<Supplementary-Data type="unknown">
|
| 1095 |
+
NONE
|
| 1096 |
+
</Supplementary-Data>
|
| 1097 |
+
<Data-Table>
|
| 1098 |
+
<Column position="1">
|
| 1099 |
+
<Name>ID_REF</Name>
|
| 1100 |
+
</Column>
|
| 1101 |
+
<Column position="2">
|
| 1102 |
+
<Name>VALUE</Name>
|
| 1103 |
+
<Description>Average Beta</Description>
|
| 1104 |
+
</Column>
|
| 1105 |
+
<Column position="3">
|
| 1106 |
+
<Name>Detection Pval</Name>
|
| 1107 |
+
</Column>
|
| 1108 |
+
<External-Data rows="485577">
|
| 1109 |
+
GSM1437771-tbl-1.txt
|
| 1110 |
+
</External-Data>
|
| 1111 |
+
</Data-Table>
|
| 1112 |
+
</Sample>
|
| 1113 |
+
|
| 1114 |
+
<Sample iid="GSM1437772">
|
| 1115 |
+
<Status database="GEO">
|
| 1116 |
+
<Submission-Date>2014-07-16</Submission-Date>
|
| 1117 |
+
<Release-Date>2014-08-12</Release-Date>
|
| 1118 |
+
<Last-Update-Date>2014-08-12</Last-Update-Date>
|
| 1119 |
+
</Status>
|
| 1120 |
+
<Title>PBMC genomic DNA_CFS8</Title>
|
| 1121 |
+
<Accession database="GEO">GSM1437772</Accession>
|
| 1122 |
+
<Type>genomic</Type>
|
| 1123 |
+
<Channel-Count>1</Channel-Count>
|
| 1124 |
+
<Channel position="1">
|
| 1125 |
+
<Source>CFS PBMC</Source>
|
| 1126 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 1127 |
+
<Characteristics tag="gender">
|
| 1128 |
+
female
|
| 1129 |
+
</Characteristics>
|
| 1130 |
+
<Characteristics tag="subject id">
|
| 1131 |
+
CFS subject 8
|
| 1132 |
+
</Characteristics>
|
| 1133 |
+
<Characteristics tag="disease state">
|
| 1134 |
+
Chronic Fatigue Syndrome (CFS)
|
| 1135 |
+
</Characteristics>
|
| 1136 |
+
<Characteristics tag="cell type">
|
| 1137 |
+
peripheral blood mononuclear cells (PBMC)
|
| 1138 |
+
</Characteristics>
|
| 1139 |
+
<Molecule>genomic DNA</Molecule>
|
| 1140 |
+
<Extract-Protocol>
|
| 1141 |
+
Omega EZNA Tissue DNA Kit; Qiagen MinElute Reaction Cleanup Kit; Genome Quebec sample processing protocols
|
| 1142 |
+
</Extract-Protocol>
|
| 1143 |
+
<Label>Cy3,Cy5</Label>
|
| 1144 |
+
<Label-Protocol>
|
| 1145 |
+
Standard Illumina Protocol
|
| 1146 |
+
</Label-Protocol>
|
| 1147 |
+
</Channel>
|
| 1148 |
+
<Hybridization-Protocol>
|
| 1149 |
+
Standard Illumina Protocol
|
| 1150 |
+
</Hybridization-Protocol>
|
| 1151 |
+
<Scan-Protocol>
|
| 1152 |
+
Standard Illumina Protocol
|
| 1153 |
+
</Scan-Protocol>
|
| 1154 |
+
<Description>
|
| 1155 |
+
PBMC genomic DNA from CFS subject 8
|
| 1156 |
+
7985#WG0153568-DNA#B02#G00059
|
| 1157 |
+
</Description>
|
| 1158 |
+
<Data-Processing>
|
| 1159 |
+
Illumina Genome Studio; the non_normalized.txt contains unmethylated (A) and methylated (B) signal intensities.
|
| 1160 |
+
</Data-Processing>
|
| 1161 |
+
<Platform-Ref ref="GPL13534" />
|
| 1162 |
+
<Contact-Ref ref="contrib1" />
|
| 1163 |
+
<Supplementary-Data type="unknown">
|
| 1164 |
+
NONE
|
| 1165 |
+
</Supplementary-Data>
|
| 1166 |
+
<Data-Table>
|
| 1167 |
+
<Column position="1">
|
| 1168 |
+
<Name>ID_REF</Name>
|
| 1169 |
+
</Column>
|
| 1170 |
+
<Column position="2">
|
| 1171 |
+
<Name>VALUE</Name>
|
| 1172 |
+
<Description>Average Beta</Description>
|
| 1173 |
+
</Column>
|
| 1174 |
+
<Column position="3">
|
| 1175 |
+
<Name>Detection Pval</Name>
|
| 1176 |
+
</Column>
|
| 1177 |
+
<External-Data rows="485577">
|
| 1178 |
+
GSM1437772-tbl-1.txt
|
| 1179 |
+
</External-Data>
|
| 1180 |
+
</Data-Table>
|
| 1181 |
+
</Sample>
|
| 1182 |
+
|
| 1183 |
+
<Sample iid="GSM1437773">
|
| 1184 |
+
<Status database="GEO">
|
| 1185 |
+
<Submission-Date>2014-07-16</Submission-Date>
|
| 1186 |
+
<Release-Date>2014-08-12</Release-Date>
|
| 1187 |
+
<Last-Update-Date>2014-08-12</Last-Update-Date>
|
| 1188 |
+
</Status>
|
| 1189 |
+
<Title>PBMC genomic DNA_CFS9</Title>
|
| 1190 |
+
<Accession database="GEO">GSM1437773</Accession>
|
| 1191 |
+
<Type>genomic</Type>
|
| 1192 |
+
<Channel-Count>1</Channel-Count>
|
| 1193 |
+
<Channel position="1">
|
| 1194 |
+
<Source>CFS PBMC</Source>
|
| 1195 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 1196 |
+
<Characteristics tag="gender">
|
| 1197 |
+
female
|
| 1198 |
+
</Characteristics>
|
| 1199 |
+
<Characteristics tag="subject id">
|
| 1200 |
+
CFS subject 9
|
| 1201 |
+
</Characteristics>
|
| 1202 |
+
<Characteristics tag="disease state">
|
| 1203 |
+
Chronic Fatigue Syndrome (CFS)
|
| 1204 |
+
</Characteristics>
|
| 1205 |
+
<Characteristics tag="cell type">
|
| 1206 |
+
peripheral blood mononuclear cells (PBMC)
|
| 1207 |
+
</Characteristics>
|
| 1208 |
+
<Molecule>genomic DNA</Molecule>
|
| 1209 |
+
<Extract-Protocol>
|
| 1210 |
+
Omega EZNA Tissue DNA Kit; Qiagen MinElute Reaction Cleanup Kit; Genome Quebec sample processing protocols
|
| 1211 |
+
</Extract-Protocol>
|
| 1212 |
+
<Label>Cy3,Cy5</Label>
|
| 1213 |
+
<Label-Protocol>
|
| 1214 |
+
Standard Illumina Protocol
|
| 1215 |
+
</Label-Protocol>
|
| 1216 |
+
</Channel>
|
| 1217 |
+
<Hybridization-Protocol>
|
| 1218 |
+
Standard Illumina Protocol
|
| 1219 |
+
</Hybridization-Protocol>
|
| 1220 |
+
<Scan-Protocol>
|
| 1221 |
+
Standard Illumina Protocol
|
| 1222 |
+
</Scan-Protocol>
|
| 1223 |
+
<Description>
|
| 1224 |
+
PBMC genomic DNA from CFS subject 9
|
| 1225 |
+
7985#WG0153568-DNA#B03#G00054
|
| 1226 |
+
</Description>
|
| 1227 |
+
<Data-Processing>
|
| 1228 |
+
Illumina Genome Studio; the non_normalized.txt contains unmethylated (A) and methylated (B) signal intensities.
|
| 1229 |
+
</Data-Processing>
|
| 1230 |
+
<Platform-Ref ref="GPL13534" />
|
| 1231 |
+
<Contact-Ref ref="contrib1" />
|
| 1232 |
+
<Supplementary-Data type="unknown">
|
| 1233 |
+
NONE
|
| 1234 |
+
</Supplementary-Data>
|
| 1235 |
+
<Data-Table>
|
| 1236 |
+
<Column position="1">
|
| 1237 |
+
<Name>ID_REF</Name>
|
| 1238 |
+
</Column>
|
| 1239 |
+
<Column position="2">
|
| 1240 |
+
<Name>VALUE</Name>
|
| 1241 |
+
<Description>Average Beta</Description>
|
| 1242 |
+
</Column>
|
| 1243 |
+
<Column position="3">
|
| 1244 |
+
<Name>Detection Pval</Name>
|
| 1245 |
+
</Column>
|
| 1246 |
+
<External-Data rows="485577">
|
| 1247 |
+
GSM1437773-tbl-1.txt
|
| 1248 |
+
</External-Data>
|
| 1249 |
+
</Data-Table>
|
| 1250 |
+
</Sample>
|
| 1251 |
+
|
| 1252 |
+
<Sample iid="GSM1437774">
|
| 1253 |
+
<Status database="GEO">
|
| 1254 |
+
<Submission-Date>2014-07-16</Submission-Date>
|
| 1255 |
+
<Release-Date>2014-08-12</Release-Date>
|
| 1256 |
+
<Last-Update-Date>2014-08-12</Last-Update-Date>
|
| 1257 |
+
</Status>
|
| 1258 |
+
<Title>PBMC genomic DNA_CFS10</Title>
|
| 1259 |
+
<Accession database="GEO">GSM1437774</Accession>
|
| 1260 |
+
<Type>genomic</Type>
|
| 1261 |
+
<Channel-Count>1</Channel-Count>
|
| 1262 |
+
<Channel position="1">
|
| 1263 |
+
<Source>CFS PBMC</Source>
|
| 1264 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 1265 |
+
<Characteristics tag="gender">
|
| 1266 |
+
female
|
| 1267 |
+
</Characteristics>
|
| 1268 |
+
<Characteristics tag="subject id">
|
| 1269 |
+
CFS subject 10
|
| 1270 |
+
</Characteristics>
|
| 1271 |
+
<Characteristics tag="disease state">
|
| 1272 |
+
Chronic Fatigue Syndrome (CFS)
|
| 1273 |
+
</Characteristics>
|
| 1274 |
+
<Characteristics tag="cell type">
|
| 1275 |
+
peripheral blood mononuclear cells (PBMC)
|
| 1276 |
+
</Characteristics>
|
| 1277 |
+
<Molecule>genomic DNA</Molecule>
|
| 1278 |
+
<Extract-Protocol>
|
| 1279 |
+
Omega EZNA Tissue DNA Kit; Qiagen MinElute Reaction Cleanup Kit; Genome Quebec sample processing protocols
|
| 1280 |
+
</Extract-Protocol>
|
| 1281 |
+
<Label>Cy3,Cy5</Label>
|
| 1282 |
+
<Label-Protocol>
|
| 1283 |
+
Standard Illumina Protocol
|
| 1284 |
+
</Label-Protocol>
|
| 1285 |
+
</Channel>
|
| 1286 |
+
<Hybridization-Protocol>
|
| 1287 |
+
Standard Illumina Protocol
|
| 1288 |
+
</Hybridization-Protocol>
|
| 1289 |
+
<Scan-Protocol>
|
| 1290 |
+
Standard Illumina Protocol
|
| 1291 |
+
</Scan-Protocol>
|
| 1292 |
+
<Description>
|
| 1293 |
+
PBMC genomic DNA from CFS subject 10
|
| 1294 |
+
7985#WG0153568-DNA#B04#G00030
|
| 1295 |
+
</Description>
|
| 1296 |
+
<Data-Processing>
|
| 1297 |
+
Illumina Genome Studio; the non_normalized.txt contains unmethylated (A) and methylated (B) signal intensities.
|
| 1298 |
+
</Data-Processing>
|
| 1299 |
+
<Platform-Ref ref="GPL13534" />
|
| 1300 |
+
<Contact-Ref ref="contrib1" />
|
| 1301 |
+
<Supplementary-Data type="unknown">
|
| 1302 |
+
NONE
|
| 1303 |
+
</Supplementary-Data>
|
| 1304 |
+
<Data-Table>
|
| 1305 |
+
<Column position="1">
|
| 1306 |
+
<Name>ID_REF</Name>
|
| 1307 |
+
</Column>
|
| 1308 |
+
<Column position="2">
|
| 1309 |
+
<Name>VALUE</Name>
|
| 1310 |
+
<Description>Average Beta</Description>
|
| 1311 |
+
</Column>
|
| 1312 |
+
<Column position="3">
|
| 1313 |
+
<Name>Detection Pval</Name>
|
| 1314 |
+
</Column>
|
| 1315 |
+
<External-Data rows="485577">
|
| 1316 |
+
GSM1437774-tbl-1.txt
|
| 1317 |
+
</External-Data>
|
| 1318 |
+
</Data-Table>
|
| 1319 |
+
</Sample>
|
| 1320 |
+
|
| 1321 |
+
<Sample iid="GSM1437775">
|
| 1322 |
+
<Status database="GEO">
|
| 1323 |
+
<Submission-Date>2014-07-16</Submission-Date>
|
| 1324 |
+
<Release-Date>2014-08-12</Release-Date>
|
| 1325 |
+
<Last-Update-Date>2014-08-12</Last-Update-Date>
|
| 1326 |
+
</Status>
|
| 1327 |
+
<Title>PBMC genomic DNA_CFS11</Title>
|
| 1328 |
+
<Accession database="GEO">GSM1437775</Accession>
|
| 1329 |
+
<Type>genomic</Type>
|
| 1330 |
+
<Channel-Count>1</Channel-Count>
|
| 1331 |
+
<Channel position="1">
|
| 1332 |
+
<Source>CFS PBMC</Source>
|
| 1333 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 1334 |
+
<Characteristics tag="gender">
|
| 1335 |
+
female
|
| 1336 |
+
</Characteristics>
|
| 1337 |
+
<Characteristics tag="subject id">
|
| 1338 |
+
CFS subject 11
|
| 1339 |
+
</Characteristics>
|
| 1340 |
+
<Characteristics tag="disease state">
|
| 1341 |
+
Chronic Fatigue Syndrome (CFS)
|
| 1342 |
+
</Characteristics>
|
| 1343 |
+
<Characteristics tag="cell type">
|
| 1344 |
+
peripheral blood mononuclear cells (PBMC)
|
| 1345 |
+
</Characteristics>
|
| 1346 |
+
<Molecule>genomic DNA</Molecule>
|
| 1347 |
+
<Extract-Protocol>
|
| 1348 |
+
Omega EZNA Tissue DNA Kit; Qiagen MinElute Reaction Cleanup Kit; Genome Quebec sample processing protocols
|
| 1349 |
+
</Extract-Protocol>
|
| 1350 |
+
<Label>Cy3,Cy5</Label>
|
| 1351 |
+
<Label-Protocol>
|
| 1352 |
+
Standard Illumina Protocol
|
| 1353 |
+
</Label-Protocol>
|
| 1354 |
+
</Channel>
|
| 1355 |
+
<Hybridization-Protocol>
|
| 1356 |
+
Standard Illumina Protocol
|
| 1357 |
+
</Hybridization-Protocol>
|
| 1358 |
+
<Scan-Protocol>
|
| 1359 |
+
Standard Illumina Protocol
|
| 1360 |
+
</Scan-Protocol>
|
| 1361 |
+
<Description>
|
| 1362 |
+
PBMC genomic DNA from CFS subject 11
|
| 1363 |
+
7985#WG0153568-DNA#B05#G00121
|
| 1364 |
+
</Description>
|
| 1365 |
+
<Data-Processing>
|
| 1366 |
+
Illumina Genome Studio; the non_normalized.txt contains unmethylated (A) and methylated (B) signal intensities.
|
| 1367 |
+
</Data-Processing>
|
| 1368 |
+
<Platform-Ref ref="GPL13534" />
|
| 1369 |
+
<Contact-Ref ref="contrib1" />
|
| 1370 |
+
<Supplementary-Data type="unknown">
|
| 1371 |
+
NONE
|
| 1372 |
+
</Supplementary-Data>
|
| 1373 |
+
<Data-Table>
|
| 1374 |
+
<Column position="1">
|
| 1375 |
+
<Name>ID_REF</Name>
|
| 1376 |
+
</Column>
|
| 1377 |
+
<Column position="2">
|
| 1378 |
+
<Name>VALUE</Name>
|
| 1379 |
+
<Description>Average Beta</Description>
|
| 1380 |
+
</Column>
|
| 1381 |
+
<Column position="3">
|
| 1382 |
+
<Name>Detection Pval</Name>
|
| 1383 |
+
</Column>
|
| 1384 |
+
<External-Data rows="485577">
|
| 1385 |
+
GSM1437775-tbl-1.txt
|
| 1386 |
+
</External-Data>
|
| 1387 |
+
</Data-Table>
|
| 1388 |
+
</Sample>
|
| 1389 |
+
|
| 1390 |
+
<Sample iid="GSM1437776">
|
| 1391 |
+
<Status database="GEO">
|
| 1392 |
+
<Submission-Date>2014-07-16</Submission-Date>
|
| 1393 |
+
<Release-Date>2014-08-12</Release-Date>
|
| 1394 |
+
<Last-Update-Date>2014-08-12</Last-Update-Date>
|
| 1395 |
+
</Status>
|
| 1396 |
+
<Title>PBMC genomic DNA_CFS12</Title>
|
| 1397 |
+
<Accession database="GEO">GSM1437776</Accession>
|
| 1398 |
+
<Type>genomic</Type>
|
| 1399 |
+
<Channel-Count>1</Channel-Count>
|
| 1400 |
+
<Channel position="1">
|
| 1401 |
+
<Source>CFS PBMC</Source>
|
| 1402 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 1403 |
+
<Characteristics tag="gender">
|
| 1404 |
+
female
|
| 1405 |
+
</Characteristics>
|
| 1406 |
+
<Characteristics tag="subject id">
|
| 1407 |
+
CFS subject 12
|
| 1408 |
+
</Characteristics>
|
| 1409 |
+
<Characteristics tag="disease state">
|
| 1410 |
+
Chronic Fatigue Syndrome (CFS)
|
| 1411 |
+
</Characteristics>
|
| 1412 |
+
<Characteristics tag="cell type">
|
| 1413 |
+
peripheral blood mononuclear cells (PBMC)
|
| 1414 |
+
</Characteristics>
|
| 1415 |
+
<Molecule>genomic DNA</Molecule>
|
| 1416 |
+
<Extract-Protocol>
|
| 1417 |
+
Omega EZNA Tissue DNA Kit; Qiagen MinElute Reaction Cleanup Kit; Genome Quebec sample processing protocols
|
| 1418 |
+
</Extract-Protocol>
|
| 1419 |
+
<Label>Cy3,Cy5</Label>
|
| 1420 |
+
<Label-Protocol>
|
| 1421 |
+
Standard Illumina Protocol
|
| 1422 |
+
</Label-Protocol>
|
| 1423 |
+
</Channel>
|
| 1424 |
+
<Hybridization-Protocol>
|
| 1425 |
+
Standard Illumina Protocol
|
| 1426 |
+
</Hybridization-Protocol>
|
| 1427 |
+
<Scan-Protocol>
|
| 1428 |
+
Standard Illumina Protocol
|
| 1429 |
+
</Scan-Protocol>
|
| 1430 |
+
<Description>
|
| 1431 |
+
PBMC genomic DNA from CFS subject 12
|
| 1432 |
+
7985#WG0153568-DNA#B06#G00113
|
| 1433 |
+
</Description>
|
| 1434 |
+
<Data-Processing>
|
| 1435 |
+
Illumina Genome Studio; the non_normalized.txt contains unmethylated (A) and methylated (B) signal intensities.
|
| 1436 |
+
</Data-Processing>
|
| 1437 |
+
<Platform-Ref ref="GPL13534" />
|
| 1438 |
+
<Contact-Ref ref="contrib1" />
|
| 1439 |
+
<Supplementary-Data type="unknown">
|
| 1440 |
+
NONE
|
| 1441 |
+
</Supplementary-Data>
|
| 1442 |
+
<Data-Table>
|
| 1443 |
+
<Column position="1">
|
| 1444 |
+
<Name>ID_REF</Name>
|
| 1445 |
+
</Column>
|
| 1446 |
+
<Column position="2">
|
| 1447 |
+
<Name>VALUE</Name>
|
| 1448 |
+
<Description>Average Beta</Description>
|
| 1449 |
+
</Column>
|
| 1450 |
+
<Column position="3">
|
| 1451 |
+
<Name>Detection Pval</Name>
|
| 1452 |
+
</Column>
|
| 1453 |
+
<External-Data rows="485577">
|
| 1454 |
+
GSM1437776-tbl-1.txt
|
| 1455 |
+
</External-Data>
|
| 1456 |
+
</Data-Table>
|
| 1457 |
+
</Sample>
|
| 1458 |
+
|
| 1459 |
+
<Sample iid="GSM1437777">
|
| 1460 |
+
<Status database="GEO">
|
| 1461 |
+
<Submission-Date>2014-07-16</Submission-Date>
|
| 1462 |
+
<Release-Date>2014-08-12</Release-Date>
|
| 1463 |
+
<Last-Update-Date>2014-08-12</Last-Update-Date>
|
| 1464 |
+
</Status>
|
| 1465 |
+
<Title>PBMC genomic DNA_Control7</Title>
|
| 1466 |
+
<Accession database="GEO">GSM1437777</Accession>
|
| 1467 |
+
<Type>genomic</Type>
|
| 1468 |
+
<Channel-Count>1</Channel-Count>
|
| 1469 |
+
<Channel position="1">
|
| 1470 |
+
<Source>Control PBMC</Source>
|
| 1471 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 1472 |
+
<Characteristics tag="gender">
|
| 1473 |
+
female
|
| 1474 |
+
</Characteristics>
|
| 1475 |
+
<Characteristics tag="subject id">
|
| 1476 |
+
Control subject 7
|
| 1477 |
+
</Characteristics>
|
| 1478 |
+
<Characteristics tag="disease state">
|
| 1479 |
+
Control
|
| 1480 |
+
</Characteristics>
|
| 1481 |
+
<Characteristics tag="cell type">
|
| 1482 |
+
peripheral blood mononuclear cells (PBMC)
|
| 1483 |
+
</Characteristics>
|
| 1484 |
+
<Molecule>genomic DNA</Molecule>
|
| 1485 |
+
<Extract-Protocol>
|
| 1486 |
+
Omega EZNA Tissue DNA Kit; Qiagen MinElute Reaction Cleanup Kit; Genome Quebec sample processing protocols
|
| 1487 |
+
</Extract-Protocol>
|
| 1488 |
+
<Label>Cy3,Cy5</Label>
|
| 1489 |
+
<Label-Protocol>
|
| 1490 |
+
Standard Illumina Protocol
|
| 1491 |
+
</Label-Protocol>
|
| 1492 |
+
</Channel>
|
| 1493 |
+
<Hybridization-Protocol>
|
| 1494 |
+
Standard Illumina Protocol
|
| 1495 |
+
</Hybridization-Protocol>
|
| 1496 |
+
<Scan-Protocol>
|
| 1497 |
+
Standard Illumina Protocol
|
| 1498 |
+
</Scan-Protocol>
|
| 1499 |
+
<Description>
|
| 1500 |
+
PBMC genomic DNA from Control subject 7
|
| 1501 |
+
7985#WG0153568-DNA#B07#G00162
|
| 1502 |
+
</Description>
|
| 1503 |
+
<Data-Processing>
|
| 1504 |
+
Illumina Genome Studio; the non_normalized.txt contains unmethylated (A) and methylated (B) signal intensities.
|
| 1505 |
+
</Data-Processing>
|
| 1506 |
+
<Platform-Ref ref="GPL13534" />
|
| 1507 |
+
<Contact-Ref ref="contrib1" />
|
| 1508 |
+
<Supplementary-Data type="unknown">
|
| 1509 |
+
NONE
|
| 1510 |
+
</Supplementary-Data>
|
| 1511 |
+
<Data-Table>
|
| 1512 |
+
<Column position="1">
|
| 1513 |
+
<Name>ID_REF</Name>
|
| 1514 |
+
</Column>
|
| 1515 |
+
<Column position="2">
|
| 1516 |
+
<Name>VALUE</Name>
|
| 1517 |
+
<Description>Average Beta</Description>
|
| 1518 |
+
</Column>
|
| 1519 |
+
<Column position="3">
|
| 1520 |
+
<Name>Detection Pval</Name>
|
| 1521 |
+
</Column>
|
| 1522 |
+
<External-Data rows="485577">
|
| 1523 |
+
GSM1437777-tbl-1.txt
|
| 1524 |
+
</External-Data>
|
| 1525 |
+
</Data-Table>
|
| 1526 |
+
</Sample>
|
| 1527 |
+
|
| 1528 |
+
<Sample iid="GSM1437778">
|
| 1529 |
+
<Status database="GEO">
|
| 1530 |
+
<Submission-Date>2014-07-16</Submission-Date>
|
| 1531 |
+
<Release-Date>2014-08-12</Release-Date>
|
| 1532 |
+
<Last-Update-Date>2014-08-12</Last-Update-Date>
|
| 1533 |
+
</Status>
|
| 1534 |
+
<Title>PBMC genomic DNA_Control8</Title>
|
| 1535 |
+
<Accession database="GEO">GSM1437778</Accession>
|
| 1536 |
+
<Type>genomic</Type>
|
| 1537 |
+
<Channel-Count>1</Channel-Count>
|
| 1538 |
+
<Channel position="1">
|
| 1539 |
+
<Source>Control PBMC</Source>
|
| 1540 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 1541 |
+
<Characteristics tag="gender">
|
| 1542 |
+
female
|
| 1543 |
+
</Characteristics>
|
| 1544 |
+
<Characteristics tag="subject id">
|
| 1545 |
+
Control subject 8
|
| 1546 |
+
</Characteristics>
|
| 1547 |
+
<Characteristics tag="disease state">
|
| 1548 |
+
Control
|
| 1549 |
+
</Characteristics>
|
| 1550 |
+
<Characteristics tag="cell type">
|
| 1551 |
+
peripheral blood mononuclear cells (PBMC)
|
| 1552 |
+
</Characteristics>
|
| 1553 |
+
<Molecule>genomic DNA</Molecule>
|
| 1554 |
+
<Extract-Protocol>
|
| 1555 |
+
Omega EZNA Tissue DNA Kit; Qiagen MinElute Reaction Cleanup Kit; Genome Quebec sample processing protocols
|
| 1556 |
+
</Extract-Protocol>
|
| 1557 |
+
<Label>Cy3,Cy5</Label>
|
| 1558 |
+
<Label-Protocol>
|
| 1559 |
+
Standard Illumina Protocol
|
| 1560 |
+
</Label-Protocol>
|
| 1561 |
+
</Channel>
|
| 1562 |
+
<Hybridization-Protocol>
|
| 1563 |
+
Standard Illumina Protocol
|
| 1564 |
+
</Hybridization-Protocol>
|
| 1565 |
+
<Scan-Protocol>
|
| 1566 |
+
Standard Illumina Protocol
|
| 1567 |
+
</Scan-Protocol>
|
| 1568 |
+
<Description>
|
| 1569 |
+
PBMC genomic DNA from Control subject 8
|
| 1570 |
+
7985#WG0153568-DNA#B08#G00208
|
| 1571 |
+
</Description>
|
| 1572 |
+
<Data-Processing>
|
| 1573 |
+
Illumina Genome Studio; the non_normalized.txt contains unmethylated (A) and methylated (B) signal intensities.
|
| 1574 |
+
</Data-Processing>
|
| 1575 |
+
<Platform-Ref ref="GPL13534" />
|
| 1576 |
+
<Contact-Ref ref="contrib1" />
|
| 1577 |
+
<Supplementary-Data type="unknown">
|
| 1578 |
+
NONE
|
| 1579 |
+
</Supplementary-Data>
|
| 1580 |
+
<Data-Table>
|
| 1581 |
+
<Column position="1">
|
| 1582 |
+
<Name>ID_REF</Name>
|
| 1583 |
+
</Column>
|
| 1584 |
+
<Column position="2">
|
| 1585 |
+
<Name>VALUE</Name>
|
| 1586 |
+
<Description>Average Beta</Description>
|
| 1587 |
+
</Column>
|
| 1588 |
+
<Column position="3">
|
| 1589 |
+
<Name>Detection Pval</Name>
|
| 1590 |
+
</Column>
|
| 1591 |
+
<External-Data rows="485577">
|
| 1592 |
+
GSM1437778-tbl-1.txt
|
| 1593 |
+
</External-Data>
|
| 1594 |
+
</Data-Table>
|
| 1595 |
+
</Sample>
|
| 1596 |
+
|
| 1597 |
+
<Sample iid="GSM1437779">
|
| 1598 |
+
<Status database="GEO">
|
| 1599 |
+
<Submission-Date>2014-07-16</Submission-Date>
|
| 1600 |
+
<Release-Date>2014-08-12</Release-Date>
|
| 1601 |
+
<Last-Update-Date>2014-08-12</Last-Update-Date>
|
| 1602 |
+
</Status>
|
| 1603 |
+
<Title>PBMC genomic DNA_Control9</Title>
|
| 1604 |
+
<Accession database="GEO">GSM1437779</Accession>
|
| 1605 |
+
<Type>genomic</Type>
|
| 1606 |
+
<Channel-Count>1</Channel-Count>
|
| 1607 |
+
<Channel position="1">
|
| 1608 |
+
<Source>Control PBMC</Source>
|
| 1609 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 1610 |
+
<Characteristics tag="gender">
|
| 1611 |
+
female
|
| 1612 |
+
</Characteristics>
|
| 1613 |
+
<Characteristics tag="subject id">
|
| 1614 |
+
Control subject 9
|
| 1615 |
+
</Characteristics>
|
| 1616 |
+
<Characteristics tag="disease state">
|
| 1617 |
+
Control
|
| 1618 |
+
</Characteristics>
|
| 1619 |
+
<Characteristics tag="cell type">
|
| 1620 |
+
peripheral blood mononuclear cells (PBMC)
|
| 1621 |
+
</Characteristics>
|
| 1622 |
+
<Molecule>genomic DNA</Molecule>
|
| 1623 |
+
<Extract-Protocol>
|
| 1624 |
+
Omega EZNA Tissue DNA Kit; Qiagen MinElute Reaction Cleanup Kit; Genome Quebec sample processing protocols
|
| 1625 |
+
</Extract-Protocol>
|
| 1626 |
+
<Label>Cy3,Cy5</Label>
|
| 1627 |
+
<Label-Protocol>
|
| 1628 |
+
Standard Illumina Protocol
|
| 1629 |
+
</Label-Protocol>
|
| 1630 |
+
</Channel>
|
| 1631 |
+
<Hybridization-Protocol>
|
| 1632 |
+
Standard Illumina Protocol
|
| 1633 |
+
</Hybridization-Protocol>
|
| 1634 |
+
<Scan-Protocol>
|
| 1635 |
+
Standard Illumina Protocol
|
| 1636 |
+
</Scan-Protocol>
|
| 1637 |
+
<Description>
|
| 1638 |
+
PBMC genomic DNA from Control subject 9
|
| 1639 |
+
7985#WG0153568-DNA#B09#G00150
|
| 1640 |
+
</Description>
|
| 1641 |
+
<Data-Processing>
|
| 1642 |
+
Illumina Genome Studio; the non_normalized.txt contains unmethylated (A) and methylated (B) signal intensities.
|
| 1643 |
+
</Data-Processing>
|
| 1644 |
+
<Platform-Ref ref="GPL13534" />
|
| 1645 |
+
<Contact-Ref ref="contrib1" />
|
| 1646 |
+
<Supplementary-Data type="unknown">
|
| 1647 |
+
NONE
|
| 1648 |
+
</Supplementary-Data>
|
| 1649 |
+
<Data-Table>
|
| 1650 |
+
<Column position="1">
|
| 1651 |
+
<Name>ID_REF</Name>
|
| 1652 |
+
</Column>
|
| 1653 |
+
<Column position="2">
|
| 1654 |
+
<Name>VALUE</Name>
|
| 1655 |
+
<Description>Average Beta</Description>
|
| 1656 |
+
</Column>
|
| 1657 |
+
<Column position="3">
|
| 1658 |
+
<Name>Detection Pval</Name>
|
| 1659 |
+
</Column>
|
| 1660 |
+
<External-Data rows="485577">
|
| 1661 |
+
GSM1437779-tbl-1.txt
|
| 1662 |
+
</External-Data>
|
| 1663 |
+
</Data-Table>
|
| 1664 |
+
</Sample>
|
| 1665 |
+
|
| 1666 |
+
<Sample iid="GSM1437780">
|
| 1667 |
+
<Status database="GEO">
|
| 1668 |
+
<Submission-Date>2014-07-16</Submission-Date>
|
| 1669 |
+
<Release-Date>2014-08-12</Release-Date>
|
| 1670 |
+
<Last-Update-Date>2014-08-12</Last-Update-Date>
|
| 1671 |
+
</Status>
|
| 1672 |
+
<Title>PBMC genomic DNA_Control10</Title>
|
| 1673 |
+
<Accession database="GEO">GSM1437780</Accession>
|
| 1674 |
+
<Type>genomic</Type>
|
| 1675 |
+
<Channel-Count>1</Channel-Count>
|
| 1676 |
+
<Channel position="1">
|
| 1677 |
+
<Source>Control PBMC</Source>
|
| 1678 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 1679 |
+
<Characteristics tag="gender">
|
| 1680 |
+
female
|
| 1681 |
+
</Characteristics>
|
| 1682 |
+
<Characteristics tag="subject id">
|
| 1683 |
+
Control subject 10
|
| 1684 |
+
</Characteristics>
|
| 1685 |
+
<Characteristics tag="disease state">
|
| 1686 |
+
Control
|
| 1687 |
+
</Characteristics>
|
| 1688 |
+
<Characteristics tag="cell type">
|
| 1689 |
+
peripheral blood mononuclear cells (PBMC)
|
| 1690 |
+
</Characteristics>
|
| 1691 |
+
<Molecule>genomic DNA</Molecule>
|
| 1692 |
+
<Extract-Protocol>
|
| 1693 |
+
Omega EZNA Tissue DNA Kit; Qiagen MinElute Reaction Cleanup Kit; Genome Quebec sample processing protocols
|
| 1694 |
+
</Extract-Protocol>
|
| 1695 |
+
<Label>Cy3,Cy5</Label>
|
| 1696 |
+
<Label-Protocol>
|
| 1697 |
+
Standard Illumina Protocol
|
| 1698 |
+
</Label-Protocol>
|
| 1699 |
+
</Channel>
|
| 1700 |
+
<Hybridization-Protocol>
|
| 1701 |
+
Standard Illumina Protocol
|
| 1702 |
+
</Hybridization-Protocol>
|
| 1703 |
+
<Scan-Protocol>
|
| 1704 |
+
Standard Illumina Protocol
|
| 1705 |
+
</Scan-Protocol>
|
| 1706 |
+
<Description>
|
| 1707 |
+
PBMC genomic DNA from Control subject 10
|
| 1708 |
+
7985#WG0153568-DNA#B10#G00199
|
| 1709 |
+
</Description>
|
| 1710 |
+
<Data-Processing>
|
| 1711 |
+
Illumina Genome Studio; the non_normalized.txt contains unmethylated (A) and methylated (B) signal intensities.
|
| 1712 |
+
</Data-Processing>
|
| 1713 |
+
<Platform-Ref ref="GPL13534" />
|
| 1714 |
+
<Contact-Ref ref="contrib1" />
|
| 1715 |
+
<Supplementary-Data type="unknown">
|
| 1716 |
+
NONE
|
| 1717 |
+
</Supplementary-Data>
|
| 1718 |
+
<Data-Table>
|
| 1719 |
+
<Column position="1">
|
| 1720 |
+
<Name>ID_REF</Name>
|
| 1721 |
+
</Column>
|
| 1722 |
+
<Column position="2">
|
| 1723 |
+
<Name>VALUE</Name>
|
| 1724 |
+
<Description>Average Beta</Description>
|
| 1725 |
+
</Column>
|
| 1726 |
+
<Column position="3">
|
| 1727 |
+
<Name>Detection Pval</Name>
|
| 1728 |
+
</Column>
|
| 1729 |
+
<External-Data rows="485577">
|
| 1730 |
+
GSM1437780-tbl-1.txt
|
| 1731 |
+
</External-Data>
|
| 1732 |
+
</Data-Table>
|
| 1733 |
+
</Sample>
|
| 1734 |
+
|
| 1735 |
+
<Sample iid="GSM1437781">
|
| 1736 |
+
<Status database="GEO">
|
| 1737 |
+
<Submission-Date>2014-07-16</Submission-Date>
|
| 1738 |
+
<Release-Date>2014-08-12</Release-Date>
|
| 1739 |
+
<Last-Update-Date>2014-08-12</Last-Update-Date>
|
| 1740 |
+
</Status>
|
| 1741 |
+
<Title>PBMC genomic DNA_Control11</Title>
|
| 1742 |
+
<Accession database="GEO">GSM1437781</Accession>
|
| 1743 |
+
<Type>genomic</Type>
|
| 1744 |
+
<Channel-Count>1</Channel-Count>
|
| 1745 |
+
<Channel position="1">
|
| 1746 |
+
<Source>Control PBMC</Source>
|
| 1747 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 1748 |
+
<Characteristics tag="gender">
|
| 1749 |
+
female
|
| 1750 |
+
</Characteristics>
|
| 1751 |
+
<Characteristics tag="subject id">
|
| 1752 |
+
Control subject 11
|
| 1753 |
+
</Characteristics>
|
| 1754 |
+
<Characteristics tag="disease state">
|
| 1755 |
+
Control
|
| 1756 |
+
</Characteristics>
|
| 1757 |
+
<Characteristics tag="cell type">
|
| 1758 |
+
peripheral blood mononuclear cells (PBMC)
|
| 1759 |
+
</Characteristics>
|
| 1760 |
+
<Molecule>genomic DNA</Molecule>
|
| 1761 |
+
<Extract-Protocol>
|
| 1762 |
+
Omega EZNA Tissue DNA Kit; Qiagen MinElute Reaction Cleanup Kit; Genome Quebec sample processing protocols
|
| 1763 |
+
</Extract-Protocol>
|
| 1764 |
+
<Label>Cy3,Cy5</Label>
|
| 1765 |
+
<Label-Protocol>
|
| 1766 |
+
Standard Illumina Protocol
|
| 1767 |
+
</Label-Protocol>
|
| 1768 |
+
</Channel>
|
| 1769 |
+
<Hybridization-Protocol>
|
| 1770 |
+
Standard Illumina Protocol
|
| 1771 |
+
</Hybridization-Protocol>
|
| 1772 |
+
<Scan-Protocol>
|
| 1773 |
+
Standard Illumina Protocol
|
| 1774 |
+
</Scan-Protocol>
|
| 1775 |
+
<Description>
|
| 1776 |
+
PBMC genomic DNA from Control subject 11
|
| 1777 |
+
7985#WG0153568-DNA#B11#G00216
|
| 1778 |
+
</Description>
|
| 1779 |
+
<Data-Processing>
|
| 1780 |
+
Illumina Genome Studio; the non_normalized.txt contains unmethylated (A) and methylated (B) signal intensities.
|
| 1781 |
+
</Data-Processing>
|
| 1782 |
+
<Platform-Ref ref="GPL13534" />
|
| 1783 |
+
<Contact-Ref ref="contrib1" />
|
| 1784 |
+
<Supplementary-Data type="unknown">
|
| 1785 |
+
NONE
|
| 1786 |
+
</Supplementary-Data>
|
| 1787 |
+
<Data-Table>
|
| 1788 |
+
<Column position="1">
|
| 1789 |
+
<Name>ID_REF</Name>
|
| 1790 |
+
</Column>
|
| 1791 |
+
<Column position="2">
|
| 1792 |
+
<Name>VALUE</Name>
|
| 1793 |
+
<Description>Average Beta</Description>
|
| 1794 |
+
</Column>
|
| 1795 |
+
<Column position="3">
|
| 1796 |
+
<Name>Detection Pval</Name>
|
| 1797 |
+
</Column>
|
| 1798 |
+
<External-Data rows="485577">
|
| 1799 |
+
GSM1437781-tbl-1.txt
|
| 1800 |
+
</External-Data>
|
| 1801 |
+
</Data-Table>
|
| 1802 |
+
</Sample>
|
| 1803 |
+
|
| 1804 |
+
<Sample iid="GSM1437782">
|
| 1805 |
+
<Status database="GEO">
|
| 1806 |
+
<Submission-Date>2014-07-16</Submission-Date>
|
| 1807 |
+
<Release-Date>2014-08-12</Release-Date>
|
| 1808 |
+
<Last-Update-Date>2014-08-12</Last-Update-Date>
|
| 1809 |
+
</Status>
|
| 1810 |
+
<Title>PBMC genomic DNA_Control12</Title>
|
| 1811 |
+
<Accession database="GEO">GSM1437782</Accession>
|
| 1812 |
+
<Type>genomic</Type>
|
| 1813 |
+
<Channel-Count>1</Channel-Count>
|
| 1814 |
+
<Channel position="1">
|
| 1815 |
+
<Source>Control PBMC</Source>
|
| 1816 |
+
<Organism taxid="9606">Homo sapiens</Organism>
|
| 1817 |
+
<Characteristics tag="gender">
|
| 1818 |
+
female
|
| 1819 |
+
</Characteristics>
|
| 1820 |
+
<Characteristics tag="subject id">
|
| 1821 |
+
Control subject 12
|
| 1822 |
+
</Characteristics>
|
| 1823 |
+
<Characteristics tag="disease state">
|
| 1824 |
+
Control
|
| 1825 |
+
</Characteristics>
|
| 1826 |
+
<Characteristics tag="cell type">
|
| 1827 |
+
peripheral blood mononuclear cells (PBMC)
|
| 1828 |
+
</Characteristics>
|
| 1829 |
+
<Molecule>genomic DNA</Molecule>
|
| 1830 |
+
<Extract-Protocol>
|
| 1831 |
+
Omega EZNA Tissue DNA Kit; Qiagen MinElute Reaction Cleanup Kit; Genome Quebec sample processing protocols
|
| 1832 |
+
</Extract-Protocol>
|
| 1833 |
+
<Label>Cy3,Cy5</Label>
|
| 1834 |
+
<Label-Protocol>
|
| 1835 |
+
Standard Illumina Protocol
|
| 1836 |
+
</Label-Protocol>
|
| 1837 |
+
</Channel>
|
| 1838 |
+
<Hybridization-Protocol>
|
| 1839 |
+
Standard Illumina Protocol
|
| 1840 |
+
</Hybridization-Protocol>
|
| 1841 |
+
<Scan-Protocol>
|
| 1842 |
+
Standard Illumina Protocol
|
| 1843 |
+
</Scan-Protocol>
|
| 1844 |
+
<Description>
|
| 1845 |
+
PBMC genomic DNA from Control subject 12
|
| 1846 |
+
7985#WG0153568-DNA#B12#G00143
|
| 1847 |
+
</Description>
|
| 1848 |
+
<Data-Processing>
|
| 1849 |
+
Illumina Genome Studio; the non_normalized.txt contains unmethylated (A) and methylated (B) signal intensities.
|
| 1850 |
+
</Data-Processing>
|
| 1851 |
+
<Platform-Ref ref="GPL13534" />
|
| 1852 |
+
<Contact-Ref ref="contrib1" />
|
| 1853 |
+
<Supplementary-Data type="unknown">
|
| 1854 |
+
NONE
|
| 1855 |
+
</Supplementary-Data>
|
| 1856 |
+
<Data-Table>
|
| 1857 |
+
<Column position="1">
|
| 1858 |
+
<Name>ID_REF</Name>
|
| 1859 |
+
</Column>
|
| 1860 |
+
<Column position="2">
|
| 1861 |
+
<Name>VALUE</Name>
|
| 1862 |
+
<Description>Average Beta</Description>
|
| 1863 |
+
</Column>
|
| 1864 |
+
<Column position="3">
|
| 1865 |
+
<Name>Detection Pval</Name>
|
| 1866 |
+
</Column>
|
| 1867 |
+
<External-Data rows="485577">
|
| 1868 |
+
GSM1437782-tbl-1.txt
|
| 1869 |
+
</External-Data>
|
| 1870 |
+
</Data-Table>
|
| 1871 |
+
</Sample>
|
| 1872 |
+
|
| 1873 |
+
<Series iid="GSE59489">
|
| 1874 |
+
<Status database="GEO">
|
| 1875 |
+
<Submission-Date>2014-07-16</Submission-Date>
|
| 1876 |
+
<Release-Date>2014-08-12</Release-Date>
|
| 1877 |
+
<Last-Update-Date>2019-03-22</Last-Update-Date>
|
| 1878 |
+
</Status>
|
| 1879 |
+
<Title>DNA methylation modifications associated with Chronic Fatigue Syndrome</Title>
|
| 1880 |
+
<Accession database="GEO">GSE59489</Accession>
|
| 1881 |
+
<Pubmed-ID>25111603</Pubmed-ID>
|
| 1882 |
+
<Summary>
|
| 1883 |
+
Chronic Fatigue Syndrome (CFS), also known as myalgic encephalomyelitis, is a complex multifactorial disease that is characterized by the persistent presence of fatigue and other particular symptoms for a minimum of 6 months. Symptoms fail to dissipate after sufficient rest and have major effects on the daily functioning of CFS sufferers. CFS is a multi-system disease with a heterogeneous patient population showing a wide variety of functional disabilities and its biological basis remains poorly understood. Stable alterations in gene function in the immune system have been reported in several studies of CFS. Epigenetic modifications have been implicated in long-term effects on gene function, however, to our knowledge, genome-wide epigenetic modifications associated with CFS have not been explored. We examined the DNA methylome in peripheral blood mononuclear cells isolated from CFS patients and healthy controls using the Illumina HumanMethylation450 BeadChip array, controlling for invariant probes and probes overlapping polymorphic sequences.
|
| 1884 |
+
</Summary>
|
| 1885 |
+
<Overall-Design>
|
| 1886 |
+
Genomic DNA from 24 peripheral blood mononuclear cells (PBMC) samples (12 CFS, 12 controls) were bisulfite-converted and hybridised to the Illumina Infinium HumanMethylation450 BeadChip. GenomeStudio files were generated and the data was analyzed using the Illumina Methylation Analyzer R package.
|
| 1887 |
+
</Overall-Design>
|
| 1888 |
+
<Type>Methylation profiling by genome tiling array</Type>
|
| 1889 |
+
<Contributor-Ref ref="contrib3" position="1" />
|
| 1890 |
+
<Contributor-Ref ref="contrib4" position="2" />
|
| 1891 |
+
<Contributor-Ref ref="contrib5" position="3" />
|
| 1892 |
+
<Contact-Ref ref="contrib1" />
|
| 1893 |
+
<Sample-Ref ref="GSM1437759" />
|
| 1894 |
+
<Sample-Ref ref="GSM1437760" />
|
| 1895 |
+
<Sample-Ref ref="GSM1437761" />
|
| 1896 |
+
<Sample-Ref ref="GSM1437762" />
|
| 1897 |
+
<Sample-Ref ref="GSM1437763" />
|
| 1898 |
+
<Sample-Ref ref="GSM1437764" />
|
| 1899 |
+
<Sample-Ref ref="GSM1437765" />
|
| 1900 |
+
<Sample-Ref ref="GSM1437766" />
|
| 1901 |
+
<Sample-Ref ref="GSM1437767" />
|
| 1902 |
+
<Sample-Ref ref="GSM1437768" />
|
| 1903 |
+
<Sample-Ref ref="GSM1437769" />
|
| 1904 |
+
<Sample-Ref ref="GSM1437770" />
|
| 1905 |
+
<Sample-Ref ref="GSM1437771" />
|
| 1906 |
+
<Sample-Ref ref="GSM1437772" />
|
| 1907 |
+
<Sample-Ref ref="GSM1437773" />
|
| 1908 |
+
<Sample-Ref ref="GSM1437774" />
|
| 1909 |
+
<Sample-Ref ref="GSM1437775" />
|
| 1910 |
+
<Sample-Ref ref="GSM1437776" />
|
| 1911 |
+
<Sample-Ref ref="GSM1437777" />
|
| 1912 |
+
<Sample-Ref ref="GSM1437778" />
|
| 1913 |
+
<Sample-Ref ref="GSM1437779" />
|
| 1914 |
+
<Sample-Ref ref="GSM1437780" />
|
| 1915 |
+
<Sample-Ref ref="GSM1437781" />
|
| 1916 |
+
<Sample-Ref ref="GSM1437782" />
|
| 1917 |
+
<Supplementary-Data type="TAR">
|
| 1918 |
+
ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE59nnn/GSE59489/suppl/GSE59489_RAW.tar
|
| 1919 |
+
</Supplementary-Data>
|
| 1920 |
+
<Supplementary-Data type="TXT">
|
| 1921 |
+
ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE59nnn/GSE59489/suppl/GSE59489_non_normalized.txt.gz
|
| 1922 |
+
</Supplementary-Data>
|
| 1923 |
+
<Relation type="BioProject" target="https://www.ncbi.nlm.nih.gov/bioproject/PRJNA255437" />
|
| 1924 |
+
</Series>
|
| 1925 |
+
|
| 1926 |
+
</MINiML>
|