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b/LC/GSE161678/meta/GSE161678_family.xml/._GSM4912601-tbl-1.txt differ diff --git a/LC/GSE161678/meta/GSE161678_family.xml/GSE161678_family.xml b/LC/GSE161678/meta/GSE161678_family.xml/GSE161678_family.xml new file mode 100644 index 0000000000000000000000000000000000000000..e728f9dc7f8626ad801da0e0a4f1bb079266d166 --- /dev/null +++ b/LC/GSE161678/meta/GSE161678_family.xml/GSE161678_family.xml @@ -0,0 +1,1811 @@ + + + + + + NehaMishra + n.mishra@ikmb.uni-kiel.de + Cell biology Lab + Institute of Clinical Molecular Biology +
+ Rosalind-Franklin-Str. 12 + Kiel + 24105 + Germany +
+ + + + Illumina Inc. + expression@illumina.com, techsupport@illumina.com + 1 800 809 4566 + Illumina Inc. +
+ 9885 Towne Centre Drive + San Diego + CA + 92121 + USA +
+ www.illumina.com + + + + FlorianTran + + + + JohannaIBlase + + + + PhilipRosentiel + + + + Gene Expression Omnibus (GEO) + GEO + NCBI NLM NIH + http://www.ncbi.nlm.nih.gov/geo + geo@ncbi.nlm.nih.gov + + + + + 2015-11-16 + 2015-11-16 + 2019-01-20 + + Infinium MethylationEPIC + GPL21145 + oligonucleotide beads + commercial + Homo sapiens + Illumina, Inc. + +See manufacturer's website + + + +ftp://ftp.ncbi.nlm.nih.gov/geo/platforms/GPL21nnn/GPL21145/suppl/GPL21145_MethylationEPIC_15073387_v-1-0.csv.gz + + + + + ID + IlmnID + + + SPOT_ID + + + AddressA_ID + + + AlleleA_ProbeSeq + + + AddressB_ID + + + AlleleB_ProbeSeq + + + Infinium_Design_Type + + + Next_Base + + + Color_Channel + + + Forward_Sequence + + + Genome_Build + + + CHR + + + MAPINFO + + + SourceSeq + + +GPL21145-tbl-1.txt + + + + + + + 2020-11-17 + 2020-12-11 + 2020-12-11 + + PC_1_EPIC_TA + GSM4912578 + genomic + 1 + + Peripheral Whole Blood + Homo sapiens + +Remission + + +80 + + +4 + + +1 + + genomic DNA + +Blood (2.7 mL) was taken from each patient into an Ethylenediaminetetraacetic acid (EDTA) monovette (Sarstedt) to decelerate blood coagulation. The monovette was centrifuged for 15 min at 3000 rpm and the buffy coat was frozen in micronic tubes at -80°C. DNA was extracted using the QIAamp DNA Blood Mini Kit (Qiagen) according to manufacturer’s protocol with a QIACube (Qiagen). + + + +Standard Illumina Protocol + + + +Standard Illumina Protocol + + +The Infinium© MethylationEPIC BeadChip was used to measure the DNA methylation levels. The Infinium© MethylationEPIC BeadChip targets the following regions: CpG islands, CpG sites, open chromatin, transcription factor binding sites, enhancer and miRNA promoter regions. The EPIC arrays were processed according to Illumina recommendations. + + +DNA methylation data was analysed using the Bioconductor package RnBeads (version 1.12.1). Sites that overlapped with SNPs and had unreliable measurements were filtered resulting in the removal of 17,371 sites and 19,745 probes. 2,977 Context-specific probes, 18,976 probes on the sex chromosomes, and 4 probes with missing values were also removed. In total 41,702 out of 866,895 probes were filtered. + + + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4912nnn/GSM4912578/suppl/GSM4912578_204088010047_R02C01_Grn.idat.gz + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4912nnn/GSM4912578/suppl/GSM4912578_204088010047_R02C01_Red.idat.gz + + + + ID_REF + + + VALUE + The signal intensity values were normalized using the dasen method. + + + Detection Pval + + +GSM4912578-tbl-1.txt + + + + + + + 2020-11-17 + 2020-12-11 + 2020-12-11 + + PC_1_EPIC_TA2 + GSM4912579 + genomic + 1 + + Peripheral Whole Blood + Homo sapiens + +Remission + + +80 + + +4 + + +1 + + genomic DNA + +Blood (2.7 mL) was taken from each patient into an Ethylenediaminetetraacetic acid (EDTA) monovette (Sarstedt) to decelerate blood coagulation. The monovette was centrifuged for 15 min at 3000 rpm and the buffy coat was frozen in micronic tubes at -80°C. DNA was extracted using the QIAamp DNA Blood Mini Kit (Qiagen) according to manufacturer’s protocol with a QIACube (Qiagen). + + + +Standard Illumina Protocol + + + +Standard Illumina Protocol + + +The Infinium© MethylationEPIC BeadChip was used to measure the DNA methylation levels. The Infinium© MethylationEPIC BeadChip targets the following regions: CpG islands, CpG sites, open chromatin, transcription factor binding sites, enhancer and miRNA promoter regions. The EPIC arrays were processed according to Illumina recommendations. + + +DNA methylation data was analysed using the Bioconductor package RnBeads (version 1.12.1). Sites that overlapped with SNPs and had unreliable measurements were filtered resulting in the removal of 17,371 sites and 19,745 probes. 2,977 Context-specific probes, 18,976 probes on the sex chromosomes, and 4 probes with missing values were also removed. In total 41,702 out of 866,895 probes were filtered. + + + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4912nnn/GSM4912579/suppl/GSM4912579_203991470114_R07C01_Grn.idat.gz + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4912nnn/GSM4912579/suppl/GSM4912579_203991470114_R07C01_Red.idat.gz + + + + ID_REF + + + VALUE + The signal intensity values were normalized using the dasen method. + + + Detection Pval + + +GSM4912579-tbl-1.txt + + + + + + + 2020-11-17 + 2020-12-11 + 2020-12-11 + + PC_1_EPIC_TB + GSM4912580 + genomic + 1 + + Peripheral Whole Blood + Homo sapiens + +Remission + + +80 + + +5 + + +1 + + genomic DNA + +Blood (2.7 mL) was taken from each patient into an Ethylenediaminetetraacetic acid (EDTA) monovette (Sarstedt) to decelerate blood coagulation. The monovette was centrifuged for 15 min at 3000 rpm and the buffy coat was frozen in micronic tubes at -80°C. DNA was extracted using the QIAamp DNA Blood Mini Kit (Qiagen) according to manufacturer’s protocol with a QIACube (Qiagen). + + + +Standard Illumina Protocol + + + +Standard Illumina Protocol + + +The Infinium© MethylationEPIC BeadChip was used to measure the DNA methylation levels. The Infinium© MethylationEPIC BeadChip targets the following regions: CpG islands, CpG sites, open chromatin, transcription factor binding sites, enhancer and miRNA promoter regions. The EPIC arrays were processed according to Illumina recommendations. + + +DNA methylation data was analysed using the Bioconductor package RnBeads (version 1.12.1). Sites that overlapped with SNPs and had unreliable measurements were filtered resulting in the removal of 17,371 sites and 19,745 probes. 2,977 Context-specific probes, 18,976 probes on the sex chromosomes, and 4 probes with missing values were also removed. In total 41,702 out of 866,895 probes were filtered. + + + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4912nnn/GSM4912580/suppl/GSM4912580_204088010077_R02C01_Grn.idat.gz + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4912nnn/GSM4912580/suppl/GSM4912580_204088010077_R02C01_Red.idat.gz + + + + ID_REF + + + VALUE + The signal intensity values were normalized using the dasen method. + + + Detection Pval + + +GSM4912580-tbl-1.txt + + + + + + + 2020-11-17 + 2020-12-11 + 2020-12-11 + + PC_1_EPIC_TB2 + GSM4912581 + genomic + 1 + + Peripheral Whole Blood + Homo sapiens + +Remission + + +80 + + +6 + + +1 + + genomic DNA + +Blood (2.7 mL) was taken from each patient into an Ethylenediaminetetraacetic acid (EDTA) monovette (Sarstedt) to decelerate blood coagulation. The monovette was centrifuged for 15 min at 3000 rpm and the buffy coat was frozen in micronic tubes at -80°C. DNA was extracted using the QIAamp DNA Blood Mini Kit (Qiagen) according to manufacturer’s protocol with a QIACube (Qiagen). + + + +Standard Illumina Protocol + + + +Standard Illumina Protocol + + +The Infinium© MethylationEPIC BeadChip was used to measure the DNA methylation levels. The Infinium© MethylationEPIC BeadChip targets the following regions: CpG islands, CpG sites, open chromatin, transcription factor binding sites, enhancer and miRNA promoter regions. The EPIC arrays were processed according to Illumina recommendations. + + +DNA methylation data was analysed using the Bioconductor package RnBeads (version 1.12.1). Sites that overlapped with SNPs and had unreliable measurements were filtered resulting in the removal of 17,371 sites and 19,745 probes. 2,977 Context-specific probes, 18,976 probes on the sex chromosomes, and 4 probes with missing values were also removed. In total 41,702 out of 866,895 probes were filtered. + + + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4912nnn/GSM4912581/suppl/GSM4912581_204088010047_R03C01_Grn.idat.gz + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4912nnn/GSM4912581/suppl/GSM4912581_204088010047_R03C01_Red.idat.gz + + + + ID_REF + + + VALUE + The signal intensity values were normalized using the dasen method. + + + Detection Pval + + +GSM4912581-tbl-1.txt + + + + + + + 2020-11-17 + 2020-12-11 + 2020-12-11 + + PC_1_EPIC_TC + GSM4912582 + genomic + 1 + + Peripheral Whole Blood + Homo sapiens + +Remission + + +80 + + +6 + + +1 + + genomic DNA + +Blood (2.7 mL) was taken from each patient into an Ethylenediaminetetraacetic acid (EDTA) monovette (Sarstedt) to decelerate blood coagulation. The monovette was centrifuged for 15 min at 3000 rpm and the buffy coat was frozen in micronic tubes at -80°C. DNA was extracted using the QIAamp DNA Blood Mini Kit (Qiagen) according to manufacturer’s protocol with a QIACube (Qiagen). + + + +Standard Illumina Protocol + + + +Standard Illumina Protocol + + +The Infinium© MethylationEPIC BeadChip was used to measure the DNA methylation levels. The Infinium© MethylationEPIC BeadChip targets the following regions: CpG islands, CpG sites, open chromatin, transcription factor binding sites, enhancer and miRNA promoter regions. The EPIC arrays were processed according to Illumina recommendations. + + +DNA methylation data was analysed using the Bioconductor package RnBeads (version 1.12.1). Sites that overlapped with SNPs and had unreliable measurements were filtered resulting in the removal of 17,371 sites and 19,745 probes. 2,977 Context-specific probes, 18,976 probes on the sex chromosomes, and 4 probes with missing values were also removed. In total 41,702 out of 866,895 probes were filtered. + + + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4912nnn/GSM4912582/suppl/GSM4912582_204088010047_R06C01_Grn.idat.gz + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4912nnn/GSM4912582/suppl/GSM4912582_204088010047_R06C01_Red.idat.gz + + + + ID_REF + + + VALUE + The signal intensity values were normalized using the dasen method. + + + Detection Pval + + +GSM4912582-tbl-1.txt + + + + + + + 2020-11-17 + 2020-12-11 + 2020-12-11 + + PC_2_EPIC_TA + GSM4912583 + genomic + 1 + + Peripheral Whole Blood + Homo sapiens + +No Remssion + + +57 + + +1 + + +2 + + genomic DNA + +Blood (2.7 mL) was taken from each patient into an Ethylenediaminetetraacetic acid (EDTA) monovette (Sarstedt) to decelerate blood coagulation. The monovette was centrifuged for 15 min at 3000 rpm and the buffy coat was frozen in micronic tubes at -80°C. DNA was extracted using the QIAamp DNA Blood Mini Kit (Qiagen) according to manufacturer’s protocol with a QIACube (Qiagen). + + + +Standard Illumina Protocol + + + +Standard Illumina Protocol + + +The Infinium© MethylationEPIC BeadChip was used to measure the DNA methylation levels. The Infinium© MethylationEPIC BeadChip targets the following regions: CpG islands, CpG sites, open chromatin, transcription factor binding sites, enhancer and miRNA promoter regions. The EPIC arrays were processed according to Illumina recommendations. + + +DNA methylation data was analysed using the Bioconductor package RnBeads (version 1.12.1). Sites that overlapped with SNPs and had unreliable measurements were filtered resulting in the removal of 17,371 sites and 19,745 probes. 2,977 Context-specific probes, 18,976 probes on the sex chromosomes, and 4 probes with missing values were also removed. In total 41,702 out of 866,895 probes were filtered. + + + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4912nnn/GSM4912583/suppl/GSM4912583_204088010047_R04C01_Grn.idat.gz + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4912nnn/GSM4912583/suppl/GSM4912583_204088010047_R04C01_Red.idat.gz + + + + ID_REF + + + VALUE + The signal intensity values were normalized using the dasen method. + + + Detection Pval + + +GSM4912583-tbl-1.txt + + + + + + + 2020-11-17 + 2020-12-11 + 2020-12-11 + + PC_2_EPIC_TA2 + GSM4912584 + genomic + 1 + + Peripheral Whole Blood + Homo sapiens + +No Remssion + + +57 + + +2 + + +2 + + genomic DNA + +Blood (2.7 mL) was taken from each patient into an Ethylenediaminetetraacetic acid (EDTA) monovette (Sarstedt) to decelerate blood coagulation. The monovette was centrifuged for 15 min at 3000 rpm and the buffy coat was frozen in micronic tubes at -80°C. DNA was extracted using the QIAamp DNA Blood Mini Kit (Qiagen) according to manufacturer’s protocol with a QIACube (Qiagen). + + + +Standard Illumina Protocol + + + +Standard Illumina Protocol + + +The Infinium© MethylationEPIC BeadChip was used to measure the DNA methylation levels. The Infinium© MethylationEPIC BeadChip targets the following regions: CpG islands, CpG sites, open chromatin, transcription factor binding sites, enhancer and miRNA promoter regions. The EPIC arrays were processed according to Illumina recommendations. + + +DNA methylation data was analysed using the Bioconductor package RnBeads (version 1.12.1). Sites that overlapped with SNPs and had unreliable measurements were filtered resulting in the removal of 17,371 sites and 19,745 probes. 2,977 Context-specific probes, 18,976 probes on the sex chromosomes, and 4 probes with missing values were also removed. In total 41,702 out of 866,895 probes were filtered. + + + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4912nnn/GSM4912584/suppl/GSM4912584_204088010047_R08C01_Grn.idat.gz + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4912nnn/GSM4912584/suppl/GSM4912584_204088010047_R08C01_Red.idat.gz + + + + ID_REF + + + VALUE + The signal intensity values were normalized using the dasen method. + + + Detection Pval + + +GSM4912584-tbl-1.txt + + + + + + + 2020-11-17 + 2020-12-11 + 2020-12-11 + + PC_3_EPIC_TA + GSM4912585 + genomic + 1 + + Peripheral Whole Blood + Homo sapiens + +No Remssion + + +80 + + +2 + + +3 + + genomic DNA + +Blood (2.7 mL) was taken from each patient into an Ethylenediaminetetraacetic acid (EDTA) monovette (Sarstedt) to decelerate blood coagulation. The monovette was centrifuged for 15 min at 3000 rpm and the buffy coat was frozen in micronic tubes at -80°C. DNA was extracted using the QIAamp DNA Blood Mini Kit (Qiagen) according to manufacturer’s protocol with a QIACube (Qiagen). + + + +Standard Illumina Protocol + + + +Standard Illumina Protocol + + +The Infinium© MethylationEPIC BeadChip was used to measure the DNA methylation levels. The Infinium© MethylationEPIC BeadChip targets the following regions: CpG islands, CpG sites, open chromatin, transcription factor binding sites, enhancer and miRNA promoter regions. The EPIC arrays were processed according to Illumina recommendations. + + +DNA methylation data was analysed using the Bioconductor package RnBeads (version 1.12.1). Sites that overlapped with SNPs and had unreliable measurements were filtered resulting in the removal of 17,371 sites and 19,745 probes. 2,977 Context-specific probes, 18,976 probes on the sex chromosomes, and 4 probes with missing values were also removed. In total 41,702 out of 866,895 probes were filtered. + + + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4912nnn/GSM4912585/suppl/GSM4912585_204088010077_R03C01_Grn.idat.gz + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4912nnn/GSM4912585/suppl/GSM4912585_204088010077_R03C01_Red.idat.gz + + + + ID_REF + + + VALUE + The signal intensity values were normalized using the dasen method. + + + Detection Pval + + +GSM4912585-tbl-1.txt + + + + + + + 2020-11-17 + 2020-12-11 + 2020-12-11 + + PC_4_EPIC_TA + GSM4912586 + genomic + 1 + + Peripheral Whole Blood + Homo sapiens + +Remission + + +60 + + +1 + + +4 + + genomic DNA + +Blood (2.7 mL) was taken from each patient into an Ethylenediaminetetraacetic acid (EDTA) monovette (Sarstedt) to decelerate blood coagulation. The monovette was centrifuged for 15 min at 3000 rpm and the buffy coat was frozen in micronic tubes at -80°C. DNA was extracted using the QIAamp DNA Blood Mini Kit (Qiagen) according to manufacturer’s protocol with a QIACube (Qiagen). + + + +Standard Illumina Protocol + + + +Standard Illumina Protocol + + +The Infinium© MethylationEPIC BeadChip was used to measure the DNA methylation levels. The Infinium© MethylationEPIC BeadChip targets the following regions: CpG islands, CpG sites, open chromatin, transcription factor binding sites, enhancer and miRNA promoter regions. The EPIC arrays were processed according to Illumina recommendations. + + +DNA methylation data was analysed using the Bioconductor package RnBeads (version 1.12.1). Sites that overlapped with SNPs and had unreliable measurements were filtered resulting in the removal of 17,371 sites and 19,745 probes. 2,977 Context-specific probes, 18,976 probes on the sex chromosomes, and 4 probes with missing values were also removed. In total 41,702 out of 866,895 probes were filtered. + + + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4912nnn/GSM4912586/suppl/GSM4912586_204088010047_R05C01_Grn.idat.gz + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4912nnn/GSM4912586/suppl/GSM4912586_204088010047_R05C01_Red.idat.gz + + + + ID_REF + + + VALUE + The signal intensity values were normalized using the dasen method. + + + Detection Pval + + +GSM4912586-tbl-1.txt + + + + + + + 2020-11-17 + 2020-12-11 + 2020-12-11 + + PC_4_EPIC_TA2 + GSM4912587 + genomic + 1 + + Peripheral Whole Blood + Homo sapiens + +Remission + + +60 + + +3 + + +4 + + genomic DNA + +Blood (2.7 mL) was taken from each patient into an Ethylenediaminetetraacetic acid (EDTA) monovette (Sarstedt) to decelerate blood coagulation. The monovette was centrifuged for 15 min at 3000 rpm and the buffy coat was frozen in micronic tubes at -80°C. DNA was extracted using the QIAamp DNA Blood Mini Kit (Qiagen) according to manufacturer’s protocol with a QIACube (Qiagen). + + + +Standard Illumina Protocol + + + +Standard Illumina Protocol + + +The Infinium© MethylationEPIC BeadChip was used to measure the DNA methylation levels. The Infinium© MethylationEPIC BeadChip targets the following regions: CpG islands, CpG sites, open chromatin, transcription factor binding sites, enhancer and miRNA promoter regions. The EPIC arrays were processed according to Illumina recommendations. + + +DNA methylation data was analysed using the Bioconductor package RnBeads (version 1.12.1). Sites that overlapped with SNPs and had unreliable measurements were filtered resulting in the removal of 17,371 sites and 19,745 probes. 2,977 Context-specific probes, 18,976 probes on the sex chromosomes, and 4 probes with missing values were also removed. In total 41,702 out of 866,895 probes were filtered. + + + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4912nnn/GSM4912587/suppl/GSM4912587_204088010047_R07C01_Grn.idat.gz + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4912nnn/GSM4912587/suppl/GSM4912587_204088010047_R07C01_Red.idat.gz + + + + ID_REF + + + VALUE + The signal intensity values were normalized using the dasen method. + + + Detection Pval + + +GSM4912587-tbl-1.txt + + + + + + + 2020-11-17 + 2020-12-11 + 2020-12-11 + + PC_4_EPIC_TB + GSM4912588 + genomic + 1 + + Peripheral Whole Blood + Homo sapiens + +Remission + + +60 + + +5 + + +4 + + genomic DNA + +Blood (2.7 mL) was taken from each patient into an Ethylenediaminetetraacetic acid (EDTA) monovette (Sarstedt) to decelerate blood coagulation. The monovette was centrifuged for 15 min at 3000 rpm and the buffy coat was frozen in micronic tubes at -80°C. DNA was extracted using the QIAamp DNA Blood Mini Kit (Qiagen) according to manufacturer’s protocol with a QIACube (Qiagen). + + + +Standard Illumina Protocol + + + +Standard Illumina Protocol + + +The Infinium© MethylationEPIC BeadChip was used to measure the DNA methylation levels. The Infinium© MethylationEPIC BeadChip targets the following regions: CpG islands, CpG sites, open chromatin, transcription factor binding sites, enhancer and miRNA promoter regions. The EPIC arrays were processed according to Illumina recommendations. + + +DNA methylation data was analysed using the Bioconductor package RnBeads (version 1.12.1). Sites that overlapped with SNPs and had unreliable measurements were filtered resulting in the removal of 17,371 sites and 19,745 probes. 2,977 Context-specific probes, 18,976 probes on the sex chromosomes, and 4 probes with missing values were also removed. In total 41,702 out of 866,895 probes were filtered. + + + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4912nnn/GSM4912588/suppl/GSM4912588_204088010077_R01C01_Grn.idat.gz + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4912nnn/GSM4912588/suppl/GSM4912588_204088010077_R01C01_Red.idat.gz + + + + ID_REF + + + VALUE + The signal intensity values were normalized using the dasen method. + + + Detection Pval + + +GSM4912588-tbl-1.txt + + + + + + + 2020-11-17 + 2020-12-11 + 2020-12-11 + + PC_5_EPIC_TA + GSM4912589 + genomic + 1 + + Peripheral Whole Blood + Homo sapiens + +Remission + + +49 + + +1 + + +5 + + genomic DNA + +Blood (2.7 mL) was taken from each patient into an Ethylenediaminetetraacetic acid (EDTA) monovette (Sarstedt) to decelerate blood coagulation. The monovette was centrifuged for 15 min at 3000 rpm and the buffy coat was frozen in micronic tubes at -80°C. DNA was extracted using the QIAamp DNA Blood Mini Kit (Qiagen) according to manufacturer’s protocol with a QIACube (Qiagen). + + + +Standard Illumina Protocol + + + +Standard Illumina Protocol + + +The Infinium© MethylationEPIC BeadChip was used to measure the DNA methylation levels. The Infinium© MethylationEPIC BeadChip targets the following regions: CpG islands, CpG sites, open chromatin, transcription factor binding sites, enhancer and miRNA promoter regions. The EPIC arrays were processed according to Illumina recommendations. + + +DNA methylation data was analysed using the Bioconductor package RnBeads (version 1.12.1). Sites that overlapped with SNPs and had unreliable measurements were filtered resulting in the removal of 17,371 sites and 19,745 probes. 2,977 Context-specific probes, 18,976 probes on the sex chromosomes, and 4 probes with missing values were also removed. In total 41,702 out of 866,895 probes were filtered. + + + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4912nnn/GSM4912589/suppl/GSM4912589_204088010077_R04C01_Grn.idat.gz + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4912nnn/GSM4912589/suppl/GSM4912589_204088010077_R04C01_Red.idat.gz + + + + ID_REF + + + VALUE + The signal intensity values were normalized using the dasen method. + + + Detection Pval + + +GSM4912589-tbl-1.txt + + + + + + + 2020-11-17 + 2020-12-11 + 2020-12-11 + + PC_5_EPIC_TA2 + GSM4912590 + genomic + 1 + + Peripheral Whole Blood + Homo sapiens + +Remission + + +49 + + +3 + + +5 + + genomic DNA + +Blood (2.7 mL) was taken from each patient into an Ethylenediaminetetraacetic acid (EDTA) monovette (Sarstedt) to decelerate blood coagulation. The monovette was centrifuged for 15 min at 3000 rpm and the buffy coat was frozen in micronic tubes at -80°C. DNA was extracted using the QIAamp DNA Blood Mini Kit (Qiagen) according to manufacturer’s protocol with a QIACube (Qiagen). + + + +Standard Illumina Protocol + + + +Standard Illumina Protocol + + +The Infinium© MethylationEPIC BeadChip was used to measure the DNA methylation levels. The Infinium© MethylationEPIC BeadChip targets the following regions: CpG islands, CpG sites, open chromatin, transcription factor binding sites, enhancer and miRNA promoter regions. The EPIC arrays were processed according to Illumina recommendations. + + +DNA methylation data was analysed using the Bioconductor package RnBeads (version 1.12.1). Sites that overlapped with SNPs and had unreliable measurements were filtered resulting in the removal of 17,371 sites and 19,745 probes. 2,977 Context-specific probes, 18,976 probes on the sex chromosomes, and 4 probes with missing values were also removed. In total 41,702 out of 866,895 probes were filtered. + + + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4912nnn/GSM4912590/suppl/GSM4912590_204088010047_R01C01_Grn.idat.gz + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4912nnn/GSM4912590/suppl/GSM4912590_204088010047_R01C01_Red.idat.gz + + + + ID_REF + + + VALUE + The signal intensity values were normalized using the dasen method. + + + Detection Pval + + +GSM4912590-tbl-1.txt + + + + + + + 2020-11-17 + 2020-12-11 + 2020-12-11 + + PC_5_EPIC_TB + GSM4912591 + genomic + 1 + + Peripheral Whole Blood + Homo sapiens + +Remission + + +49 + + +6 + + +5 + + genomic DNA + +Blood (2.7 mL) was taken from each patient into an Ethylenediaminetetraacetic acid (EDTA) monovette (Sarstedt) to decelerate blood coagulation. The monovette was centrifuged for 15 min at 3000 rpm and the buffy coat was frozen in micronic tubes at -80°C. DNA was extracted using the QIAamp DNA Blood Mini Kit (Qiagen) according to manufacturer’s protocol with a QIACube (Qiagen). + + + +Standard Illumina Protocol + + + +Standard Illumina Protocol + + +The Infinium© MethylationEPIC BeadChip was used to measure the DNA methylation levels. The Infinium© MethylationEPIC BeadChip targets the following regions: CpG islands, CpG sites, open chromatin, transcription factor binding sites, enhancer and miRNA promoter regions. The EPIC arrays were processed according to Illumina recommendations. + + +DNA methylation data was analysed using the Bioconductor package RnBeads (version 1.12.1). Sites that overlapped with SNPs and had unreliable measurements were filtered resulting in the removal of 17,371 sites and 19,745 probes. 2,977 Context-specific probes, 18,976 probes on the sex chromosomes, and 4 probes with missing values were also removed. In total 41,702 out of 866,895 probes were filtered. + + + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4912nnn/GSM4912591/suppl/GSM4912591_203991470114_R08C01_Grn.idat.gz + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4912nnn/GSM4912591/suppl/GSM4912591_203991470114_R08C01_Red.idat.gz + + + + ID_REF + + + VALUE + The signal intensity values were normalized using the dasen method. + + + Detection Pval + + +GSM4912591-tbl-1.txt + + + + + + + 2020-11-17 + 2020-12-11 + 2020-12-11 + + PC_5_EPIC_TB2 + GSM4912592 + genomic + 1 + + Peripheral Whole Blood + Homo sapiens + +Remission + + +49 + + +6 + + +5 + + genomic DNA + +Blood (2.7 mL) was taken from each patient into an Ethylenediaminetetraacetic acid (EDTA) monovette (Sarstedt) to decelerate blood coagulation. The monovette was centrifuged for 15 min at 3000 rpm and the buffy coat was frozen in micronic tubes at -80°C. DNA was extracted using the QIAamp DNA Blood Mini Kit (Qiagen) according to manufacturer’s protocol with a QIACube (Qiagen). + + + +Standard Illumina Protocol + + + +Standard Illumina Protocol + + +The Infinium© MethylationEPIC BeadChip was used to measure the DNA methylation levels. The Infinium© MethylationEPIC BeadChip targets the following regions: CpG islands, CpG sites, open chromatin, transcription factor binding sites, enhancer and miRNA promoter regions. The EPIC arrays were processed according to Illumina recommendations. + + +DNA methylation data was analysed using the Bioconductor package RnBeads (version 1.12.1). Sites that overlapped with SNPs and had unreliable measurements were filtered resulting in the removal of 17,371 sites and 19,745 probes. 2,977 Context-specific probes, 18,976 probes on the sex chromosomes, and 4 probes with missing values were also removed. In total 41,702 out of 866,895 probes were filtered. + + + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4912nnn/GSM4912592/suppl/GSM4912592_204088010077_R06C01_Grn.idat.gz + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4912nnn/GSM4912592/suppl/GSM4912592_204088010077_R06C01_Red.idat.gz + + + + ID_REF + + + VALUE + The signal intensity values were normalized using the dasen method. + + + Detection Pval + + +GSM4912592-tbl-1.txt + + + + + + + 2020-11-17 + 2020-12-11 + 2020-12-11 + + PC_6_EPIC_TA + GSM4912593 + genomic + 1 + + Peripheral Whole Blood + Homo sapiens + +Remission + + +70 + + +5 + + +6 + + genomic DNA + +Blood (2.7 mL) was taken from each patient into an Ethylenediaminetetraacetic acid (EDTA) monovette (Sarstedt) to decelerate blood coagulation. The monovette was centrifuged for 15 min at 3000 rpm and the buffy coat was frozen in micronic tubes at -80°C. DNA was extracted using the QIAamp DNA Blood Mini Kit (Qiagen) according to manufacturer’s protocol with a QIACube (Qiagen). + + + +Standard Illumina Protocol + + + +Standard Illumina Protocol + + +The Infinium© MethylationEPIC BeadChip was used to measure the DNA methylation levels. The Infinium© MethylationEPIC BeadChip targets the following regions: CpG islands, CpG sites, open chromatin, transcription factor binding sites, enhancer and miRNA promoter regions. The EPIC arrays were processed according to Illumina recommendations. + + +DNA methylation data was analysed using the Bioconductor package RnBeads (version 1.12.1). Sites that overlapped with SNPs and had unreliable measurements were filtered resulting in the removal of 17,371 sites and 19,745 probes. 2,977 Context-specific probes, 18,976 probes on the sex chromosomes, and 4 probes with missing values were also removed. In total 41,702 out of 866,895 probes were filtered. + + + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4912nnn/GSM4912593/suppl/GSM4912593_204088010077_R05C01_Grn.idat.gz + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4912nnn/GSM4912593/suppl/GSM4912593_204088010077_R05C01_Red.idat.gz + + + + ID_REF + + + VALUE + The signal intensity values were normalized using the dasen method. + + + Detection Pval + + +GSM4912593-tbl-1.txt + + + + + + + 2020-11-17 + 2020-12-11 + 2020-12-11 + + PC_6_EPIC_TA2 + GSM4912594 + genomic + 1 + + Peripheral Whole Blood + Homo sapiens + +Remission + + +70 + + +5 + + +6 + + genomic DNA + +Blood (2.7 mL) was taken from each patient into an Ethylenediaminetetraacetic acid (EDTA) monovette (Sarstedt) to decelerate blood coagulation. The monovette was centrifuged for 15 min at 3000 rpm and the buffy coat was frozen in micronic tubes at -80°C. DNA was extracted using the QIAamp DNA Blood Mini Kit (Qiagen) according to manufacturer’s protocol with a QIACube (Qiagen). + + + +Standard Illumina Protocol + + + +Standard Illumina Protocol + + +The Infinium© MethylationEPIC BeadChip was used to measure the DNA methylation levels. The Infinium© MethylationEPIC BeadChip targets the following regions: CpG islands, CpG sites, open chromatin, transcription factor binding sites, enhancer and miRNA promoter regions. The EPIC arrays were processed according to Illumina recommendations. + + +DNA methylation data was analysed using the Bioconductor package RnBeads (version 1.12.1). Sites that overlapped with SNPs and had unreliable measurements were filtered resulting in the removal of 17,371 sites and 19,745 probes. 2,977 Context-specific probes, 18,976 probes on the sex chromosomes, and 4 probes with missing values were also removed. In total 41,702 out of 866,895 probes were filtered. + + + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4912nnn/GSM4912594/suppl/GSM4912594_204088010077_R07C01_Grn.idat.gz + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4912nnn/GSM4912594/suppl/GSM4912594_204088010077_R07C01_Red.idat.gz + + + + ID_REF + + + VALUE + The signal intensity values were normalized using the dasen method. + + + Detection Pval + + +GSM4912594-tbl-1.txt + + + + + + + 2020-11-17 + 2020-12-11 + 2020-12-11 + + PC_6_EPIC_TB + GSM4912595 + genomic + 1 + + Peripheral Whole Blood + Homo sapiens + +Remission + + +70 + + +6 + + +6 + + genomic DNA + +Blood (2.7 mL) was taken from each patient into an Ethylenediaminetetraacetic acid (EDTA) monovette (Sarstedt) to decelerate blood coagulation. The monovette was centrifuged for 15 min at 3000 rpm and the buffy coat was frozen in micronic tubes at -80°C. DNA was extracted using the QIAamp DNA Blood Mini Kit (Qiagen) according to manufacturer’s protocol with a QIACube (Qiagen). + + + +Standard Illumina Protocol + + + +Standard Illumina Protocol + + +The Infinium© MethylationEPIC BeadChip was used to measure the DNA methylation levels. The Infinium© MethylationEPIC BeadChip targets the following regions: CpG islands, CpG sites, open chromatin, transcription factor binding sites, enhancer and miRNA promoter regions. The EPIC arrays were processed according to Illumina recommendations. + + +DNA methylation data was analysed using the Bioconductor package RnBeads (version 1.12.1). Sites that overlapped with SNPs and had unreliable measurements were filtered resulting in the removal of 17,371 sites and 19,745 probes. 2,977 Context-specific probes, 18,976 probes on the sex chromosomes, and 4 probes with missing values were also removed. In total 41,702 out of 866,895 probes were filtered. + + + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4912nnn/GSM4912595/suppl/GSM4912595_204088010077_R08C01_Grn.idat.gz + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4912nnn/GSM4912595/suppl/GSM4912595_204088010077_R08C01_Red.idat.gz + + + + ID_REF + + + VALUE + The signal intensity values were normalized using the dasen method. + + + Detection Pval + + +GSM4912595-tbl-1.txt + + + + + + + 2020-11-17 + 2020-12-11 + 2020-12-11 + + HC_1_EPIC + GSM4912596 + genomic + 1 + + Peripheral Whole Blood + Homo sapiens + +Healthy + + +65 + + +0 + + +7 + + genomic DNA + +Blood (2.7 mL) was taken from each patient into an Ethylenediaminetetraacetic acid (EDTA) monovette (Sarstedt) to decelerate blood coagulation. The monovette was centrifuged for 15 min at 3000 rpm and the buffy coat was frozen in micronic tubes at -80°C. DNA was extracted using the QIAamp DNA Blood Mini Kit (Qiagen) according to manufacturer’s protocol with a QIACube (Qiagen). + + + +Standard Illumina Protocol + + + +Standard Illumina Protocol + + +The Infinium© MethylationEPIC BeadChip was used to measure the DNA methylation levels. The Infinium© MethylationEPIC BeadChip targets the following regions: CpG islands, CpG sites, open chromatin, transcription factor binding sites, enhancer and miRNA promoter regions. The EPIC arrays were processed according to Illumina recommendations. + + +DNA methylation data was analysed using the Bioconductor package RnBeads (version 1.12.1). Sites that overlapped with SNPs and had unreliable measurements were filtered resulting in the removal of 17,371 sites and 19,745 probes. 2,977 Context-specific probes, 18,976 probes on the sex chromosomes, and 4 probes with missing values were also removed. In total 41,702 out of 866,895 probes were filtered. + + + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4912nnn/GSM4912596/suppl/GSM4912596_201220980037_R04C01_Grn.idat.gz + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4912nnn/GSM4912596/suppl/GSM4912596_201220980037_R04C01_Red.idat.gz + + + + ID_REF + + + VALUE + The signal intensity values were normalized using the dasen method. + + + Detection Pval + + +GSM4912596-tbl-1.txt + + + + + + + 2020-11-17 + 2020-12-11 + 2020-12-11 + + HC_2_EPIC + GSM4912597 + genomic + 1 + + Peripheral Whole Blood + Homo sapiens + +Healthy + + +52 + + +0 + + +8 + + genomic DNA + +Blood (2.7 mL) was taken from each patient into an Ethylenediaminetetraacetic acid (EDTA) monovette (Sarstedt) to decelerate blood coagulation. The monovette was centrifuged for 15 min at 3000 rpm and the buffy coat was frozen in micronic tubes at -80°C. DNA was extracted using the QIAamp DNA Blood Mini Kit (Qiagen) according to manufacturer’s protocol with a QIACube (Qiagen). + + + +Standard Illumina Protocol + + + +Standard Illumina Protocol + + +The Infinium© MethylationEPIC BeadChip was used to measure the DNA methylation levels. The Infinium© MethylationEPIC BeadChip targets the following regions: CpG islands, CpG sites, open chromatin, transcription factor binding sites, enhancer and miRNA promoter regions. The EPIC arrays were processed according to Illumina recommendations. + + +DNA methylation data was analysed using the Bioconductor package RnBeads (version 1.12.1). Sites that overlapped with SNPs and had unreliable measurements were filtered resulting in the removal of 17,371 sites and 19,745 probes. 2,977 Context-specific probes, 18,976 probes on the sex chromosomes, and 4 probes with missing values were also removed. In total 41,702 out of 866,895 probes were filtered. + + + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4912nnn/GSM4912597/suppl/GSM4912597_201228780134_R01C01_Grn.idat.gz + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4912nnn/GSM4912597/suppl/GSM4912597_201228780134_R01C01_Red.idat.gz + + + + ID_REF + + + VALUE + The signal intensity values were normalized using the dasen method. + + + Detection Pval + + +GSM4912597-tbl-1.txt + + + + + + + 2020-11-17 + 2020-12-11 + 2020-12-11 + + HC_3_EPIC + GSM4912598 + genomic + 1 + + Peripheral Whole Blood + Homo sapiens + +Healthy + + +47 + + +0 + + +9 + + genomic DNA + +Blood (2.7 mL) was taken from each patient into an Ethylenediaminetetraacetic acid (EDTA) monovette (Sarstedt) to decelerate blood coagulation. The monovette was centrifuged for 15 min at 3000 rpm and the buffy coat was frozen in micronic tubes at -80°C. DNA was extracted using the QIAamp DNA Blood Mini Kit (Qiagen) according to manufacturer’s protocol with a QIACube (Qiagen). + + + +Standard Illumina Protocol + + + +Standard Illumina Protocol + + +The Infinium© MethylationEPIC BeadChip was used to measure the DNA methylation levels. The Infinium© MethylationEPIC BeadChip targets the following regions: CpG islands, CpG sites, open chromatin, transcription factor binding sites, enhancer and miRNA promoter regions. The EPIC arrays were processed according to Illumina recommendations. + + +DNA methylation data was analysed using the Bioconductor package RnBeads (version 1.12.1). Sites that overlapped with SNPs and had unreliable measurements were filtered resulting in the removal of 17,371 sites and 19,745 probes. 2,977 Context-specific probes, 18,976 probes on the sex chromosomes, and 4 probes with missing values were also removed. In total 41,702 out of 866,895 probes were filtered. + + + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4912nnn/GSM4912598/suppl/GSM4912598_202119820133_R02C01_Grn.idat.gz + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4912nnn/GSM4912598/suppl/GSM4912598_202119820133_R02C01_Red.idat.gz + + + + ID_REF + + + VALUE + The signal intensity values were normalized using the dasen method. + + + Detection Pval + + +GSM4912598-tbl-1.txt + + + + + + + 2020-11-17 + 2020-12-11 + 2020-12-11 + + HC_4_EPIC + GSM4912599 + genomic + 1 + + Peripheral Whole Blood + Homo sapiens + +Healthy + + +59 + + +0 + + +10 + + genomic DNA + +Blood (2.7 mL) was taken from each patient into an Ethylenediaminetetraacetic acid (EDTA) monovette (Sarstedt) to decelerate blood coagulation. The monovette was centrifuged for 15 min at 3000 rpm and the buffy coat was frozen in micronic tubes at -80°C. DNA was extracted using the QIAamp DNA Blood Mini Kit (Qiagen) according to manufacturer’s protocol with a QIACube (Qiagen). + + + +Standard Illumina Protocol + + + +Standard Illumina Protocol + + +The Infinium© MethylationEPIC BeadChip was used to measure the DNA methylation levels. The Infinium© MethylationEPIC BeadChip targets the following regions: CpG islands, CpG sites, open chromatin, transcription factor binding sites, enhancer and miRNA promoter regions. The EPIC arrays were processed according to Illumina recommendations. + + +DNA methylation data was analysed using the Bioconductor package RnBeads (version 1.12.1). Sites that overlapped with SNPs and had unreliable measurements were filtered resulting in the removal of 17,371 sites and 19,745 probes. 2,977 Context-specific probes, 18,976 probes on the sex chromosomes, and 4 probes with missing values were also removed. In total 41,702 out of 866,895 probes were filtered. + + + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4912nnn/GSM4912599/suppl/GSM4912599_202119820190_R06C01_Grn.idat.gz + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4912nnn/GSM4912599/suppl/GSM4912599_202119820190_R06C01_Red.idat.gz + + + + ID_REF + + + VALUE + The signal intensity values were normalized using the dasen method. + + + Detection Pval + + +GSM4912599-tbl-1.txt + + + + + + + 2020-11-17 + 2020-12-11 + 2020-12-11 + + HC_5_EPIC + GSM4912600 + genomic + 1 + + Peripheral Whole Blood + Homo sapiens + +Healthy + + +57 + + +0 + + +11 + + genomic DNA + +Blood (2.7 mL) was taken from each patient into an Ethylenediaminetetraacetic acid (EDTA) monovette (Sarstedt) to decelerate blood coagulation. The monovette was centrifuged for 15 min at 3000 rpm and the buffy coat was frozen in micronic tubes at -80°C. DNA was extracted using the QIAamp DNA Blood Mini Kit (Qiagen) according to manufacturer’s protocol with a QIACube (Qiagen). + + + +Standard Illumina Protocol + + + +Standard Illumina Protocol + + +The Infinium© MethylationEPIC BeadChip was used to measure the DNA methylation levels. The Infinium© MethylationEPIC BeadChip targets the following regions: CpG islands, CpG sites, open chromatin, transcription factor binding sites, enhancer and miRNA promoter regions. The EPIC arrays were processed according to Illumina recommendations. + + +DNA methylation data was analysed using the Bioconductor package RnBeads (version 1.12.1). Sites that overlapped with SNPs and had unreliable measurements were filtered resulting in the removal of 17,371 sites and 19,745 probes. 2,977 Context-specific probes, 18,976 probes on the sex chromosomes, and 4 probes with missing values were also removed. In total 41,702 out of 866,895 probes were filtered. + + + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4912nnn/GSM4912600/suppl/GSM4912600_202119820125_R07C01_Grn.idat.gz + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4912nnn/GSM4912600/suppl/GSM4912600_202119820125_R07C01_Red.idat.gz + + + + ID_REF + + + VALUE + The signal intensity values were normalized using the dasen method. + + + Detection Pval + + +GSM4912600-tbl-1.txt + + + + + + + 2020-11-17 + 2020-12-11 + 2020-12-11 + + HC_6_EPIC + GSM4912601 + genomic + 1 + + Peripheral Whole Blood + Homo sapiens + +Healthy + + +55 + + +0 + + +12 + + genomic DNA + +Blood (2.7 mL) was taken from each patient into an Ethylenediaminetetraacetic acid (EDTA) monovette (Sarstedt) to decelerate blood coagulation. The monovette was centrifuged for 15 min at 3000 rpm and the buffy coat was frozen in micronic tubes at -80°C. DNA was extracted using the QIAamp DNA Blood Mini Kit (Qiagen) according to manufacturer’s protocol with a QIACube (Qiagen). + + + +Standard Illumina Protocol + + + +Standard Illumina Protocol + + +The Infinium© MethylationEPIC BeadChip was used to measure the DNA methylation levels. The Infinium© MethylationEPIC BeadChip targets the following regions: CpG islands, CpG sites, open chromatin, transcription factor binding sites, enhancer and miRNA promoter regions. The EPIC arrays were processed according to Illumina recommendations. + + +DNA methylation data was analysed using the Bioconductor package RnBeads (version 1.12.1). Sites that overlapped with SNPs and had unreliable measurements were filtered resulting in the removal of 17,371 sites and 19,745 probes. 2,977 Context-specific probes, 18,976 probes on the sex chromosomes, and 4 probes with missing values were also removed. In total 41,702 out of 866,895 probes were filtered. + + + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4912nnn/GSM4912601/suppl/GSM4912601_202119820252_R06C01_Grn.idat.gz + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4912nnn/GSM4912601/suppl/GSM4912601_202119820252_R06C01_Red.idat.gz + + + + ID_REF + + + VALUE + The signal intensity values were normalized using the dasen method. + + + Detection Pval + + +GSM4912601-tbl-1.txt + + + + + + + 2020-11-17 + 2020-12-11 + 2020-12-11 + + Longitudinal multi-omics identifies responses of megakaryocytes, erythroid cells and plasmablasts as hallmarks of severe COVID-19 trajectories [methylation] + GSE161678 + 33296687 + +To help characterise the temporal dynamics of host response during COVID-19, we performed a longitudinal DNA methylation analysis in a cohort of 12 patients. DNA was extracted from peripheral blood sampled at up to 5 time points per patient. At each sample point, a patient’s disease trajectory, “pseudotime”, was categorised according to clinical parameters. DNA methylation profiling by Illumina Bead Arrays was performed on each sample. We found CpG sites hypomethylated during COVID-19 were highly enriched in cis of transcripts related to positive regulation of TNF secretion and innate immune signalling, indicating potential long-term regulation of immunological misfiring by epigenetic processes. + + +6 patients were sampled at days 0, 2, 7, 10, 13 and/or at discharge. 6 healthy donors were sampled at a single time point. + + Methylation profiling by genome tiling array + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE161nnn/GSE161678/suppl/GSE161678_RAW.tar + + + + + + diff --git a/LC/GSE174818/.DS_Store b/LC/GSE174818/.DS_Store new file mode 100644 index 0000000000000000000000000000000000000000..49599abfcd0ba9c32882f8f86e74806b433827e8 Binary files /dev/null and b/LC/GSE174818/.DS_Store differ diff --git a/LC/GSE174818/._.DS_Store b/LC/GSE174818/._.DS_Store new file mode 100644 index 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a/LC/GSE197152/meta/._GSE197152_family.xml b/LC/GSE197152/meta/._GSE197152_family.xml new file mode 100644 index 0000000000000000000000000000000000000000..88b77a77c5f0f848f3a633d10a5fb1d1409742d3 Binary files /dev/null and b/LC/GSE197152/meta/._GSE197152_family.xml differ diff --git a/LC/GSE197152/meta/GSE197152_family.xml/GSE197152_family.xml b/LC/GSE197152/meta/GSE197152_family.xml/GSE197152_family.xml new file mode 100644 index 0000000000000000000000000000000000000000..eaa59933ffa957a9ce80819f5433728fb24ab0b5 --- /dev/null +++ b/LC/GSE197152/meta/GSE197152_family.xml/GSE197152_family.xml @@ -0,0 +1,1048 @@ + + + + + + AndyMadrid + madrid2@wisc.edu + Alisch + Neurological Surgery + University of Wiconsin - Madison +
+ 600 Highland Ave + Madison + Wisconsin + 53792 + USA +
+ + + + Illumina Inc. + expression@illumina.com, techsupport@illumina.com + 1 800 809 4566 + Illumina Inc. +
+ 9885 Towne Centre Drive + San Diego + CA + 92121 + USA +
+ www.illumina.com + + + + Gene Expression Omnibus (GEO) + GEO + NCBI NLM NIH + http://www.ncbi.nlm.nih.gov/geo + geo@ncbi.nlm.nih.gov + + + + + 2015-11-16 + 2015-11-16 + 2019-01-20 + + Infinium MethylationEPIC + GPL21145 + oligonucleotide beads + commercial + Homo sapiens + Illumina, Inc. + +See manufacturer's website + + + +ftp://ftp.ncbi.nlm.nih.gov/geo/platforms/GPL21nnn/GPL21145/suppl/GPL21145_MethylationEPIC_15073387_v-1-0.csv.gz + + + + + ID + IlmnID + + + SPOT_ID + + + AddressA_ID + + + AlleleA_ProbeSeq + + + AddressB_ID + + + AlleleB_ProbeSeq + + + Infinium_Design_Type + + + Next_Base + + + Color_Channel + + + Forward_Sequence + + + Genome_Build + + + CHR + + + MAPINFO + + + SourceSeq + + +GPL21145-tbl-1.txt + + + + + + + 2022-02-22 + 2022-02-23 + 2022-02-23 + + PostCovid_1 + GSM5910329 + genomic + 1 + + PostCovid_1 + Homo sapiens + +C33 + + +post COVID-19 + + +one year after infection + + +whole blood + + genomic DNA + +genomic DNA from whole blood tissue was extracted using tehe GeneJET whole blood kit according to the manufacturer's recommendations + + + +standard illumina protocol + + + +hybridized to Illumina HumanMethylationEPIC arrays using standard Illumina instructions + + +arrays were imaged using BeadArray Readerusing standard recommended settings + + +blood from COVID-19 patient one year after infection +Sample name: PC2002 + + +minfi +matrix processed file: average beta +matrix signal file: Unmethylated and methylated signal intensities + + + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5910nnn/GSM5910329/suppl/GSM5910329_205333460001_R04C01_Grn.idat.gz + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5910nnn/GSM5910329/suppl/GSM5910329_205333460001_R04C01_Red.idat.gz + + + + + + 2022-02-22 + 2022-02-23 + 2022-02-23 + + PostCovid_2 + GSM5910330 + genomic + 1 + + PostCovid_2 + Homo sapiens + +C16 + + +post COVID-19 + + +one year after infection + + +whole blood + + genomic DNA + +genomic DNA from whole blood tissue was extracted using tehe GeneJET whole blood kit according to the manufacturer's recommendations + + + +standard illumina protocol + + + +hybridized to Illumina HumanMethylationEPIC arrays using standard Illumina instructions + + +arrays were imaged using BeadArray Readerusing standard recommended settings + + +blood from COVID-19 patient one year after infection +Sample name: PC2003 + + +minfi +matrix processed file: average beta +matrix signal file: Unmethylated and methylated signal intensities + + + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5910nnn/GSM5910330/suppl/GSM5910330_205333460001_R05C01_Grn.idat.gz + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5910nnn/GSM5910330/suppl/GSM5910330_205333460001_R05C01_Red.idat.gz + + + + + + 2022-02-22 + 2022-02-23 + 2022-02-23 + + PostCovid_3 + GSM5910331 + genomic + 1 + + PostCovid_3 + Homo sapiens + +C51 + + +post COVID-19 + + +one year after infection + + +whole blood + + genomic DNA + +genomic DNA from whole blood tissue was extracted using tehe GeneJET whole blood kit according to the manufacturer's recommendations + + + +standard illumina protocol + + + +hybridized to Illumina HumanMethylationEPIC arrays using standard Illumina instructions + + +arrays were imaged using BeadArray Readerusing standard recommended settings + + +blood from COVID-19 patient one year after infection +Sample name: PC2004 + + +minfi +matrix processed file: average beta +matrix signal file: Unmethylated and methylated signal intensities + + + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5910nnn/GSM5910331/suppl/GSM5910331_205333460001_R06C01_Grn.idat.gz + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5910nnn/GSM5910331/suppl/GSM5910331_205333460001_R06C01_Red.idat.gz + + + + + + 2022-02-22 + 2022-02-23 + 2022-02-23 + + PostCovid_4 + GSM5910332 + genomic + 1 + + PostCovid_4 + Homo sapiens + +C66 + + +post COVID-19 + + +one year after infection + + +whole blood + + genomic DNA + +genomic DNA from whole blood tissue was extracted using tehe GeneJET whole blood kit according to the manufacturer's recommendations + + + +standard illumina protocol + + + +hybridized to Illumina HumanMethylationEPIC arrays using standard Illumina instructions + + +arrays were imaged using BeadArray Readerusing standard recommended settings + + +blood from COVID-19 patient one year after infection +Sample name: PC2005 + + +minfi +matrix processed file: average beta +matrix signal file: Unmethylated and methylated signal intensities + + + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5910nnn/GSM5910332/suppl/GSM5910332_205333460001_R07C01_Grn.idat.gz + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5910nnn/GSM5910332/suppl/GSM5910332_205333460001_R07C01_Red.idat.gz + + + + + + 2022-02-22 + 2022-02-23 + 2022-02-23 + + PostCovid_5 + GSM5910333 + genomic + 1 + + PostCovid_5 + Homo sapiens + +C95 + + +post COVID-19 + + +one year after infection + + +whole blood + + genomic DNA + +genomic DNA from whole blood tissue was extracted using tehe GeneJET whole blood kit according to the manufacturer's recommendations + + + +standard illumina protocol + + + +hybridized to Illumina HumanMethylationEPIC arrays using standard Illumina instructions + + +arrays were imaged using BeadArray Readerusing standard recommended settings + + +blood from COVID-19 patient one year after infection +Sample name: PC2006 + + +minfi +matrix processed file: average beta +matrix signal file: Unmethylated and methylated signal intensities + + + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5910nnn/GSM5910333/suppl/GSM5910333_205333460001_R08C01_Grn.idat.gz + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5910nnn/GSM5910333/suppl/GSM5910333_205333460001_R08C01_Red.idat.gz + + + + + + 2022-02-22 + 2022-02-23 + 2022-02-23 + + PostCovid_6 + GSM5910334 + genomic + 1 + + PostCovid_6 + Homo sapiens + +C57 + + +post COVID-19 + + +one year after infection + + +whole blood + + genomic DNA + +genomic DNA from whole blood tissue was extracted using tehe GeneJET whole blood kit according to the manufacturer's recommendations + + + +standard illumina protocol + + + +hybridized to Illumina HumanMethylationEPIC arrays using standard Illumina instructions + + +arrays were imaged using BeadArray Readerusing standard recommended settings + + +blood from COVID-19 patient one year after infection +Sample name: PC2007 + + +minfi +matrix processed file: average beta +matrix signal file: Unmethylated and methylated signal intensities + + + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5910nnn/GSM5910334/suppl/GSM5910334_205333460001_R03C01_Grn.idat.gz + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5910nnn/GSM5910334/suppl/GSM5910334_205333460001_R03C01_Red.idat.gz + + + + + + 2022-02-22 + 2022-02-23 + 2022-02-23 + + PostCovid_7 + GSM5910335 + genomic + 1 + + PostCovid_7 + Homo sapiens + +C53 + + +post COVID-19 + + +one year after infection + + +whole blood + + genomic DNA + +genomic DNA from whole blood tissue was extracted using tehe GeneJET whole blood kit according to the manufacturer's recommendations + + + +standard illumina protocol + + + +hybridized to Illumina HumanMethylationEPIC arrays using standard Illumina instructions + + +arrays were imaged using BeadArray Readerusing standard recommended settings + + +blood from COVID-19 patient one year after infection +Sample name: PC2008 + + +minfi +matrix processed file: average beta +matrix signal file: Unmethylated and methylated signal intensities + + + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5910nnn/GSM5910335/suppl/GSM5910335_205333460058_R01C01_Grn.idat.gz + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5910nnn/GSM5910335/suppl/GSM5910335_205333460058_R01C01_Red.idat.gz + + + + + + 2022-02-22 + 2022-02-23 + 2022-02-23 + + PostCovid_8 + GSM5910336 + genomic + 1 + + PostCovid_8 + Homo sapiens + +C56 + + +post COVID-19 + + +one year after infection + + +whole blood + + genomic DNA + +genomic DNA from whole blood tissue was extracted using tehe GeneJET whole blood kit according to the manufacturer's recommendations + + + +standard illumina protocol + + + +hybridized to Illumina HumanMethylationEPIC arrays using standard Illumina instructions + + +arrays were imaged using BeadArray Readerusing standard recommended settings + + +blood from COVID-19 patient one year after infection +Sample name: PC2009 + + +minfi +matrix processed file: average beta +matrix signal file: Unmethylated and methylated signal intensities + + + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5910nnn/GSM5910336/suppl/GSM5910336_205333460058_R02C01_Grn.idat.gz + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5910nnn/GSM5910336/suppl/GSM5910336_205333460058_R02C01_Red.idat.gz + + + + + + 2022-02-22 + 2022-02-23 + 2022-02-23 + + PostCovid_9 + GSM5910337 + genomic + 1 + + PostCovid_9 + Homo sapiens + +C11 + + +post COVID-19 + + +one year after infection + + +whole blood + + genomic DNA + +genomic DNA from whole blood tissue was extracted using tehe GeneJET whole blood kit according to the manufacturer's recommendations + + + +standard illumina protocol + + + +hybridized to Illumina HumanMethylationEPIC arrays using standard Illumina instructions + + +arrays were imaged using BeadArray Readerusing standard recommended settings + + +blood from COVID-19 patient one year after infection +Sample name: PC2010 + + +minfi +matrix processed file: average beta +matrix signal file: Unmethylated and methylated signal intensities + + + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5910nnn/GSM5910337/suppl/GSM5910337_205333460058_R03C01_Grn.idat.gz + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5910nnn/GSM5910337/suppl/GSM5910337_205333460058_R03C01_Red.idat.gz + + + + + + 2022-02-22 + 2022-02-23 + 2022-02-23 + + PostCovid_10 + GSM5910338 + genomic + 1 + + PostCovid_10 + Homo sapiens + +C101 + + +post COVID-19 + + +one year after infection + + +whole blood + + genomic DNA + +genomic DNA from whole blood tissue was extracted using tehe GeneJET whole blood kit according to the manufacturer's recommendations + + + +standard illumina protocol + + + +hybridized to Illumina HumanMethylationEPIC arrays using standard Illumina instructions + + +arrays were imaged using BeadArray Readerusing standard recommended settings + + +blood from COVID-19 patient one year after infection +Sample name: PC2011 + + +minfi +matrix processed file: average beta +matrix signal file: Unmethylated and methylated signal intensities + + + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5910nnn/GSM5910338/suppl/GSM5910338_205333460058_R04C01_Grn.idat.gz + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5910nnn/GSM5910338/suppl/GSM5910338_205333460058_R04C01_Red.idat.gz + + + + + + 2022-02-22 + 2022-02-23 + 2022-02-23 + + PostCovid_11 + GSM5910339 + genomic + 1 + + PostCovid_11 + Homo sapiens + +C78 + + +post COVID-19 + + +one year after infection + + +whole blood + + genomic DNA + +genomic DNA from whole blood tissue was extracted using tehe GeneJET whole blood kit according to the manufacturer's recommendations + + + +standard illumina protocol + + + +hybridized to Illumina HumanMethylationEPIC arrays using standard Illumina instructions + + +arrays were imaged using BeadArray Readerusing standard recommended settings + + +blood from COVID-19 patient one year after infection +Sample name: PC2012 + + +minfi +matrix processed file: average beta +matrix signal file: Unmethylated and methylated signal intensities + + + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5910nnn/GSM5910339/suppl/GSM5910339_205333460058_R05C01_Grn.idat.gz + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5910nnn/GSM5910339/suppl/GSM5910339_205333460058_R05C01_Red.idat.gz + + + + + + 2022-02-22 + 2022-02-23 + 2022-02-23 + + PostCovid_12 + GSM5910340 + genomic + 1 + + PostCovid_12 + Homo sapiens + +C24 + + +post COVID-19 + + +one year after infection + + +whole blood + + genomic DNA + +genomic DNA from whole blood tissue was extracted using tehe GeneJET whole blood kit according to the manufacturer's recommendations + + + +standard illumina protocol + + + +hybridized to Illumina HumanMethylationEPIC arrays using standard Illumina instructions + + +arrays were imaged using BeadArray Readerusing standard recommended settings + + +blood from COVID-19 patient one year after infection +Sample name: PC2013 + + +minfi +matrix processed file: average beta +matrix signal file: Unmethylated and methylated signal intensities + + + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5910nnn/GSM5910340/suppl/GSM5910340_205333460058_R06C01_Grn.idat.gz + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5910nnn/GSM5910340/suppl/GSM5910340_205333460058_R06C01_Red.idat.gz + + + + + + 2022-02-22 + 2022-02-23 + 2022-02-23 + + PostCovid_13 + GSM5910341 + genomic + 1 + + PostCovid_13 + Homo sapiens + +C77 + + +post COVID-19 + + +one year after infection + + +whole blood + + genomic DNA + +genomic DNA from whole blood tissue was extracted using tehe GeneJET whole blood kit according to the manufacturer's recommendations + + + +standard illumina protocol + + + +hybridized to Illumina HumanMethylationEPIC arrays using standard Illumina instructions + + +arrays were imaged using BeadArray Readerusing standard recommended settings + + +blood from COVID-19 patient one year after infection +Sample name: PC2015 + + +minfi +matrix processed file: average beta +matrix signal file: Unmethylated and methylated signal intensities + + + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5910nnn/GSM5910341/suppl/GSM5910341_205333460058_R07C01_Grn.idat.gz + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5910nnn/GSM5910341/suppl/GSM5910341_205333460058_R07C01_Red.idat.gz + + + + + + 2022-02-22 + 2022-02-23 + 2022-02-23 + + PostCovid_14 + GSM5910342 + genomic + 1 + + PostCovid_14 + Homo sapiens + +C67 + + +post COVID-19 + + +one year after infection + + +whole blood + + genomic DNA + +genomic DNA from whole blood tissue was extracted using tehe GeneJET whole blood kit according to the manufacturer's recommendations + + + +standard illumina protocol + + + +hybridized to Illumina HumanMethylationEPIC arrays using standard Illumina instructions + + +arrays were imaged using BeadArray Readerusing standard recommended settings + + +blood from COVID-19 patient one year after infection +Sample name: PC2018 + + +minfi +matrix processed file: average beta +matrix signal file: Unmethylated and methylated signal intensities + + + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5910nnn/GSM5910342/suppl/GSM5910342_205333460058_R08C01_Grn.idat.gz + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5910nnn/GSM5910342/suppl/GSM5910342_205333460058_R08C01_Red.idat.gz + + + + + + 2022-02-22 + 2022-02-23 + 2022-02-23 + + PostCovid_15 + GSM5910343 + genomic + 1 + + PostCovid_15 + Homo sapiens + +C61 + + +post COVID-19 + + +one year after infection + + +whole blood + + genomic DNA + +genomic DNA from whole blood tissue was extracted using tehe GeneJET whole blood kit according to the manufacturer's recommendations + + + +standard illumina protocol + + + +hybridized to Illumina HumanMethylationEPIC arrays using standard Illumina instructions + + +arrays were imaged using BeadArray Readerusing standard recommended settings + + +blood from COVID-19 patient one year after infection +Sample name: PC2019 + + +minfi +matrix processed file: average beta +matrix signal file: Unmethylated and methylated signal intensities + + + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5910nnn/GSM5910343/suppl/GSM5910343_205333460084_R01C01_Grn.idat.gz + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5910nnn/GSM5910343/suppl/GSM5910343_205333460084_R01C01_Red.idat.gz + + + + + + 2022-02-22 + 2022-02-23 + 2022-02-26 + + Genome-wide DNA methylation analysis one year post-COVID-19 infection + GSE197152 + +Genome-wide DNA methylation analysis of COVID-19 severity using the Illumina HumanMethylationEPIC microarray platform to analyze over 850,000 methylation sites, comparing COVID-19 patients during and one year after infection, using whole blood tissue. + + +Bisulfite converted DNA from whole blood tissue from 15 COVID-19 patients during infection and one year post-infection were run on the Illumina HumanMethylationEPIC platform. +This dataset: blood from COVID-19 patients one year after infection +GSE174818: blood from COVID-19 patients during infection + + Methylation profiling by array + + + + + + + + + + + + + + + + + + +ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE197nnn/GSE197152/suppl/GSE197152_RAW.tar + + +ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE197nnn/GSE197152/suppl/GSE197152_matrixSignal.csv.gz + + +ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE197nnn/GSE197152/suppl/GSE197152_matrix_processed.csv.gz + + + + + diff --git a/LC/GSE197152/meta/GSE197152_series_matrix.txt b/LC/GSE197152/meta/GSE197152_series_matrix.txt new file mode 100644 index 0000000000000000000000000000000000000000..f828dab77fdde658f25703fa66378c20d0e475ba --- /dev/null +++ b/LC/GSE197152/meta/GSE197152_series_matrix.txt @@ -0,0 +1,72 @@ +!Series_title "Genome-wide DNA methylation analysis one year post-COVID-19 infection" +!Series_geo_accession "GSE197152" +!Series_status "Public on Feb 23 2022" +!Series_submission_date "Feb 22 2022" +!Series_last_update_date "Feb 26 2022" +!Series_summary "Genome-wide DNA methylation analysis of COVID-19 severity using the Illumina HumanMethylationEPIC microarray platform to analyze over 850,000 methylation sites, comparing COVID-19 patients during and one year after infection, using whole blood tissue." +!Series_overall_design "Bisulfite converted DNA from whole blood tissue from 15 COVID-19 patients during infection and one year post-infection were run on the Illumina HumanMethylationEPIC platform." +!Series_overall_design "This dataset: blood from COVID-19 patients one year after infection" +!Series_overall_design "GSE174818: blood from COVID-19 patients during infection" +!Series_type "Methylation profiling by array" +!Series_contributor "Andy,,Madrid" +!Series_sample_id "GSM5910329 GSM5910330 GSM5910331 GSM5910332 GSM5910333 GSM5910334 GSM5910335 GSM5910336 GSM5910337 GSM5910338 GSM5910339 GSM5910340 GSM5910341 GSM5910342 GSM5910343 " +!Series_contact_name "Andy,,Madrid" +!Series_contact_email "madrid2@wisc.edu" +!Series_contact_laboratory "Alisch" +!Series_contact_department "Neurological Surgery" +!Series_contact_institute "University of Wiconsin - Madison" +!Series_contact_address "600 Highland Ave" +!Series_contact_city "Madison" +!Series_contact_state "Wisconsin" +!Series_contact_zip/postal_code "53792" +!Series_contact_country "USA" +!Series_supplementary_file "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE197nnn/GSE197152/suppl/GSE197152_RAW.tar" +!Series_supplementary_file "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE197nnn/GSE197152/suppl/GSE197152_matrixSignal.csv.gz" +!Series_supplementary_file "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE197nnn/GSE197152/suppl/GSE197152_matrix_processed.csv.gz" +!Series_platform_id "GPL21145" +!Series_platform_taxid "9606" +!Series_sample_taxid "9606" +!Series_relation "BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA809228" + +!Sample_title "PostCovid_1" "PostCovid_2" "PostCovid_3" "PostCovid_4" "PostCovid_5" "PostCovid_6" "PostCovid_7" "PostCovid_8" "PostCovid_9" "PostCovid_10" "PostCovid_11" "PostCovid_12" "PostCovid_13" "PostCovid_14" "PostCovid_15" +!Sample_geo_accession "GSM5910329" "GSM5910330" "GSM5910331" "GSM5910332" "GSM5910333" "GSM5910334" "GSM5910335" "GSM5910336" "GSM5910337" "GSM5910338" "GSM5910339" "GSM5910340" "GSM5910341" "GSM5910342" "GSM5910343" +!Sample_status "Public on Feb 23 2022" "Public on Feb 23 2022" "Public on Feb 23 2022" "Public on Feb 23 2022" "Public on Feb 23 2022" "Public on Feb 23 2022" "Public on Feb 23 2022" "Public on Feb 23 2022" "Public on Feb 23 2022" "Public on Feb 23 2022" "Public on Feb 23 2022" "Public on Feb 23 2022" "Public on Feb 23 2022" "Public on Feb 23 2022" "Public on Feb 23 2022" +!Sample_submission_date "Feb 22 2022" "Feb 22 2022" "Feb 22 2022" "Feb 22 2022" "Feb 22 2022" "Feb 22 2022" "Feb 22 2022" "Feb 22 2022" "Feb 22 2022" "Feb 22 2022" "Feb 22 2022" "Feb 22 2022" "Feb 22 2022" "Feb 22 2022" "Feb 22 2022" +!Sample_last_update_date "Feb 23 2022" "Feb 23 2022" "Feb 23 2022" "Feb 23 2022" "Feb 23 2022" "Feb 23 2022" "Feb 23 2022" "Feb 23 2022" "Feb 23 2022" "Feb 23 2022" "Feb 23 2022" "Feb 23 2022" "Feb 23 2022" "Feb 23 2022" "Feb 23 2022" +!Sample_type "genomic" "genomic" "genomic" "genomic" "genomic" "genomic" "genomic" "genomic" "genomic" "genomic" "genomic" "genomic" "genomic" "genomic" "genomic" +!Sample_channel_count "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" +!Sample_source_name_ch1 "PostCovid_1" "PostCovid_2" "PostCovid_3" "PostCovid_4" "PostCovid_5" "PostCovid_6" "PostCovid_7" "PostCovid_8" "PostCovid_9" "PostCovid_10" "PostCovid_11" "PostCovid_12" "PostCovid_13" "PostCovid_14" "PostCovid_15" +!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" +!Sample_characteristics_ch1 "individual: C33" "individual: C16" "individual: C51" "individual: C66" "individual: C95" "individual: C57" "individual: C53" "individual: C56" "individual: C11" "individual: C101" "individual: C78" "individual: C24" "individual: C77" "individual: C67" "individual: C61" +!Sample_characteristics_ch1 "disease state: post COVID-19" "disease state: post COVID-19" "disease state: post COVID-19" "disease state: post COVID-19" "disease state: post COVID-19" "disease state: post COVID-19" "disease state: post COVID-19" "disease state: post COVID-19" "disease state: post COVID-19" "disease state: post COVID-19" "disease state: post COVID-19" "disease state: post COVID-19" "disease state: post COVID-19" "disease state: post COVID-19" "disease state: post COVID-19" +!Sample_characteristics_ch1 "time: one year after infection" "time: one year after infection" "time: one year after infection" "time: one year after infection" "time: one year after infection" "time: one year after infection" "time: one year after infection" "time: one year after infection" "time: one year after infection" "time: one year after infection" "time: one year after infection" "time: one year after infection" "time: one year after infection" "time: one year after infection" "time: one year after infection" +!Sample_characteristics_ch1 "tissue: whole blood" "tissue: whole blood" "tissue: whole blood" "tissue: whole blood" "tissue: whole blood" "tissue: whole blood" "tissue: whole blood" "tissue: whole blood" "tissue: whole blood" "tissue: whole blood" "tissue: whole blood" "tissue: whole blood" "tissue: whole blood" "tissue: whole blood" "tissue: whole blood" +!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" +!Sample_extract_protocol_ch1 "genomic DNA from whole blood tissue was extracted using tehe GeneJET whole blood kit according to the manufacturer's recommendations" "genomic DNA from whole blood tissue was extracted using tehe GeneJET whole blood kit according to the manufacturer's recommendations" "genomic DNA from whole blood tissue was extracted using tehe GeneJET whole blood kit according to the manufacturer's recommendations" "genomic DNA from whole blood tissue was extracted using tehe GeneJET whole blood kit according to the manufacturer's recommendations" "genomic DNA from whole blood tissue was extracted using tehe GeneJET whole blood kit according to the manufacturer's recommendations" "genomic DNA from whole blood tissue was extracted using tehe GeneJET whole blood kit according to the manufacturer's recommendations" "genomic DNA from whole blood tissue was extracted using tehe GeneJET whole blood kit according to the manufacturer's recommendations" "genomic DNA from whole blood tissue was extracted using tehe GeneJET whole blood kit according to the manufacturer's recommendations" "genomic DNA from whole blood tissue was extracted using tehe GeneJET whole blood kit according to the manufacturer's recommendations" "genomic DNA from whole blood tissue was extracted using tehe GeneJET whole blood kit according to the manufacturer's recommendations" "genomic DNA from whole blood tissue was extracted using tehe GeneJET whole blood kit according to the manufacturer's recommendations" "genomic DNA from whole blood tissue was extracted using tehe GeneJET whole blood kit according to the manufacturer's recommendations" "genomic DNA from whole blood tissue was extracted using tehe GeneJET whole blood kit according to the manufacturer's recommendations" "genomic DNA from whole blood tissue was extracted using tehe GeneJET whole blood kit according to the manufacturer's recommendations" "genomic DNA from whole blood tissue was extracted using tehe GeneJET whole blood kit according to the manufacturer's recommendations" +!Sample_label_ch1 "Cy5 and Cy3" "Cy5 and Cy3" "Cy5 and Cy3" "Cy5 and Cy3" "Cy5 and Cy3" "Cy5 and Cy3" "Cy5 and Cy3" "Cy5 and Cy3" "Cy5 and Cy3" "Cy5 and Cy3" "Cy5 and Cy3" "Cy5 and Cy3" "Cy5 and Cy3" "Cy5 and Cy3" "Cy5 and Cy3" +!Sample_label_protocol_ch1 "standard illumina protocol" "standard illumina protocol" "standard illumina protocol" "standard illumina protocol" "standard illumina protocol" "standard illumina protocol" "standard illumina protocol" "standard illumina protocol" "standard illumina protocol" "standard illumina protocol" "standard illumina protocol" "standard illumina protocol" "standard illumina protocol" "standard illumina protocol" "standard illumina protocol" +!Sample_taxid_ch1 "9606" "9606" "9606" "9606" "9606" "9606" "9606" "9606" "9606" "9606" "9606" "9606" "9606" "9606" "9606" +!Sample_hyb_protocol "hybridized to Illumina HumanMethylationEPIC arrays using standard Illumina instructions" "hybridized to Illumina HumanMethylationEPIC arrays using standard Illumina instructions" "hybridized to Illumina HumanMethylationEPIC arrays using standard Illumina instructions" "hybridized to Illumina HumanMethylationEPIC arrays using standard Illumina instructions" "hybridized to Illumina HumanMethylationEPIC arrays using standard Illumina instructions" "hybridized to Illumina HumanMethylationEPIC arrays using standard Illumina instructions" "hybridized to Illumina HumanMethylationEPIC arrays using standard Illumina instructions" "hybridized to Illumina HumanMethylationEPIC arrays using standard Illumina instructions" "hybridized to Illumina HumanMethylationEPIC arrays using standard Illumina instructions" "hybridized to Illumina HumanMethylationEPIC arrays using standard Illumina instructions" "hybridized to Illumina HumanMethylationEPIC arrays using standard Illumina instructions" "hybridized to Illumina HumanMethylationEPIC arrays using standard Illumina instructions" "hybridized to Illumina HumanMethylationEPIC arrays using standard Illumina instructions" "hybridized to Illumina HumanMethylationEPIC arrays using standard Illumina instructions" "hybridized to Illumina HumanMethylationEPIC arrays using standard Illumina instructions" +!Sample_scan_protocol "arrays were imaged using BeadArray Readerusing standard recommended settings" "arrays were imaged using BeadArray Readerusing standard recommended settings" "arrays were imaged using BeadArray Readerusing standard recommended settings" "arrays were imaged using BeadArray Readerusing standard recommended settings" "arrays were imaged using BeadArray Readerusing standard recommended settings" "arrays were imaged using BeadArray Readerusing standard recommended settings" "arrays were imaged using BeadArray Readerusing standard recommended settings" "arrays were imaged using BeadArray Readerusing standard recommended settings" "arrays were imaged using BeadArray Readerusing standard recommended settings" "arrays were imaged using BeadArray Readerusing standard recommended settings" "arrays were imaged using BeadArray Readerusing standard recommended settings" "arrays were imaged using BeadArray Readerusing standard recommended settings" "arrays were imaged using BeadArray Readerusing standard recommended settings" "arrays were imaged using BeadArray Readerusing standard recommended settings" "arrays were imaged using BeadArray Readerusing standard recommended settings" +!Sample_description "blood from COVID-19 patient one year after infection" "blood from COVID-19 patient one year after infection" "blood from COVID-19 patient one year after infection" "blood from COVID-19 patient one year after infection" "blood from COVID-19 patient one year after infection" "blood from COVID-19 patient one year after infection" "blood from COVID-19 patient one year after infection" "blood from COVID-19 patient one year after infection" "blood from COVID-19 patient one year after infection" "blood from COVID-19 patient one year after infection" "blood from COVID-19 patient one year after infection" "blood from COVID-19 patient one year after infection" "blood from COVID-19 patient one year after infection" "blood from COVID-19 patient one year after infection" "blood from COVID-19 patient one year after infection" +!Sample_description "Sample name: PC2002" "Sample name: PC2003" "Sample name: PC2004" "Sample name: PC2005" "Sample name: PC2006" "Sample name: PC2007" "Sample name: PC2008" "Sample name: PC2009" "Sample name: PC2010" "Sample name: PC2011" "Sample name: PC2012" "Sample name: PC2013" "Sample name: PC2015" "Sample name: PC2018" "Sample name: PC2019" +!Sample_data_processing "minfi" "minfi" "minfi" "minfi" "minfi" "minfi" "minfi" "minfi" "minfi" "minfi" "minfi" "minfi" "minfi" "minfi" "minfi" +!Sample_data_processing "matrix processed file: average beta" "matrix processed file: average beta" "matrix processed file: average beta" "matrix processed file: average beta" "matrix processed file: average beta" "matrix processed file: average beta" "matrix processed file: average beta" "matrix processed file: average beta" "matrix processed file: average beta" "matrix processed file: average beta" "matrix processed file: average beta" "matrix processed file: average beta" "matrix processed file: average beta" "matrix processed file: average beta" "matrix processed file: average beta" +!Sample_data_processing "matrix signal file: Unmethylated and methylated signal intensities" "matrix signal file: Unmethylated and methylated signal intensities" "matrix signal file: Unmethylated and methylated signal intensities" "matrix signal file: Unmethylated and methylated signal intensities" "matrix signal file: Unmethylated and methylated signal intensities" "matrix signal file: Unmethylated and methylated signal intensities" "matrix signal file: Unmethylated and methylated signal intensities" "matrix signal file: Unmethylated and methylated signal intensities" "matrix signal file: Unmethylated and methylated signal intensities" "matrix signal file: Unmethylated and methylated signal intensities" "matrix signal file: Unmethylated and methylated signal intensities" "matrix signal file: Unmethylated and methylated signal intensities" "matrix signal file: Unmethylated and methylated signal intensities" "matrix signal file: Unmethylated and methylated signal intensities" "matrix signal file: Unmethylated and methylated signal intensities" +!Sample_platform_id "GPL21145" "GPL21145" "GPL21145" "GPL21145" "GPL21145" "GPL21145" "GPL21145" "GPL21145" "GPL21145" "GPL21145" "GPL21145" "GPL21145" "GPL21145" "GPL21145" "GPL21145" +!Sample_contact_name "Andy,,Madrid" "Andy,,Madrid" "Andy,,Madrid" "Andy,,Madrid" "Andy,,Madrid" "Andy,,Madrid" "Andy,,Madrid" "Andy,,Madrid" "Andy,,Madrid" "Andy,,Madrid" "Andy,,Madrid" "Andy,,Madrid" "Andy,,Madrid" "Andy,,Madrid" "Andy,,Madrid" +!Sample_contact_email "madrid2@wisc.edu" "madrid2@wisc.edu" "madrid2@wisc.edu" "madrid2@wisc.edu" "madrid2@wisc.edu" "madrid2@wisc.edu" "madrid2@wisc.edu" "madrid2@wisc.edu" "madrid2@wisc.edu" "madrid2@wisc.edu" "madrid2@wisc.edu" "madrid2@wisc.edu" "madrid2@wisc.edu" "madrid2@wisc.edu" "madrid2@wisc.edu" +!Sample_contact_laboratory "Alisch" "Alisch" "Alisch" "Alisch" "Alisch" "Alisch" "Alisch" "Alisch" "Alisch" "Alisch" "Alisch" "Alisch" "Alisch" "Alisch" "Alisch" +!Sample_contact_department "Neurological Surgery" "Neurological Surgery" "Neurological Surgery" "Neurological Surgery" "Neurological Surgery" "Neurological Surgery" "Neurological Surgery" "Neurological Surgery" "Neurological Surgery" "Neurological Surgery" "Neurological Surgery" "Neurological Surgery" "Neurological Surgery" "Neurological Surgery" "Neurological Surgery" +!Sample_contact_institute "University of Wiconsin - Madison" "University of Wiconsin - Madison" "University of Wiconsin - Madison" "University of Wiconsin - Madison" "University of Wiconsin - Madison" "University of Wiconsin - Madison" "University of Wiconsin - Madison" "University of Wiconsin - Madison" "University of Wiconsin - Madison" "University of Wiconsin - Madison" "University of Wiconsin - Madison" "University of Wiconsin - Madison" "University of Wiconsin - Madison" "University of Wiconsin - Madison" "University of Wiconsin - Madison" +!Sample_contact_address "600 Highland Ave" "600 Highland Ave" "600 Highland Ave" "600 Highland Ave" "600 Highland Ave" "600 Highland Ave" "600 Highland Ave" "600 Highland Ave" "600 Highland Ave" "600 Highland Ave" "600 Highland Ave" "600 Highland Ave" "600 Highland Ave" "600 Highland Ave" "600 Highland Ave" +!Sample_contact_city "Madison" "Madison" "Madison" "Madison" "Madison" "Madison" "Madison" "Madison" "Madison" "Madison" "Madison" "Madison" "Madison" "Madison" "Madison" +!Sample_contact_state "Wisconsin" "Wisconsin" "Wisconsin" "Wisconsin" "Wisconsin" "Wisconsin" "Wisconsin" "Wisconsin" "Wisconsin" "Wisconsin" "Wisconsin" "Wisconsin" "Wisconsin" "Wisconsin" "Wisconsin" +!Sample_contact_zip/postal_code "53792" "53792" "53792" "53792" "53792" "53792" "53792" "53792" "53792" "53792" "53792" "53792" "53792" "53792" "53792" +!Sample_contact_country "USA" "USA" "USA" "USA" "USA" "USA" "USA" "USA" "USA" "USA" "USA" "USA" "USA" "USA" "USA" +!Sample_supplementary_file "ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5910nnn/GSM5910329/suppl/GSM5910329_205333460001_R04C01_Grn.idat.gz" "ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5910nnn/GSM5910330/suppl/GSM5910330_205333460001_R05C01_Grn.idat.gz" "ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5910nnn/GSM5910331/suppl/GSM5910331_205333460001_R06C01_Grn.idat.gz" "ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5910nnn/GSM5910332/suppl/GSM5910332_205333460001_R07C01_Grn.idat.gz" "ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5910nnn/GSM5910333/suppl/GSM5910333_205333460001_R08C01_Grn.idat.gz" "ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5910nnn/GSM5910334/suppl/GSM5910334_205333460001_R03C01_Grn.idat.gz" "ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5910nnn/GSM5910335/suppl/GSM5910335_205333460058_R01C01_Grn.idat.gz" "ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5910nnn/GSM5910336/suppl/GSM5910336_205333460058_R02C01_Grn.idat.gz" "ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5910nnn/GSM5910337/suppl/GSM5910337_205333460058_R03C01_Grn.idat.gz" "ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5910nnn/GSM5910338/suppl/GSM5910338_205333460058_R04C01_Grn.idat.gz" "ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5910nnn/GSM5910339/suppl/GSM5910339_205333460058_R05C01_Grn.idat.gz" "ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5910nnn/GSM5910340/suppl/GSM5910340_205333460058_R06C01_Grn.idat.gz" "ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5910nnn/GSM5910341/suppl/GSM5910341_205333460058_R07C01_Grn.idat.gz" "ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5910nnn/GSM5910342/suppl/GSM5910342_205333460058_R08C01_Grn.idat.gz" "ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5910nnn/GSM5910343/suppl/GSM5910343_205333460084_R01C01_Grn.idat.gz" +!Sample_supplementary_file "ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5910nnn/GSM5910329/suppl/GSM5910329_205333460001_R04C01_Red.idat.gz" "ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5910nnn/GSM5910330/suppl/GSM5910330_205333460001_R05C01_Red.idat.gz" "ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5910nnn/GSM5910331/suppl/GSM5910331_205333460001_R06C01_Red.idat.gz" "ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5910nnn/GSM5910332/suppl/GSM5910332_205333460001_R07C01_Red.idat.gz" "ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5910nnn/GSM5910333/suppl/GSM5910333_205333460001_R08C01_Red.idat.gz" "ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5910nnn/GSM5910334/suppl/GSM5910334_205333460001_R03C01_Red.idat.gz" "ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5910nnn/GSM5910335/suppl/GSM5910335_205333460058_R01C01_Red.idat.gz" "ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5910nnn/GSM5910336/suppl/GSM5910336_205333460058_R02C01_Red.idat.gz" "ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5910nnn/GSM5910337/suppl/GSM5910337_205333460058_R03C01_Red.idat.gz" "ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5910nnn/GSM5910338/suppl/GSM5910338_205333460058_R04C01_Red.idat.gz" "ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5910nnn/GSM5910339/suppl/GSM5910339_205333460058_R05C01_Red.idat.gz" "ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5910nnn/GSM5910340/suppl/GSM5910340_205333460058_R06C01_Red.idat.gz" "ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5910nnn/GSM5910341/suppl/GSM5910341_205333460058_R07C01_Red.idat.gz" "ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5910nnn/GSM5910342/suppl/GSM5910342_205333460058_R08C01_Red.idat.gz" "ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5910nnn/GSM5910343/suppl/GSM5910343_205333460084_R01C01_Red.idat.gz" +!Sample_data_row_count "0" "0" "0" "0" "0" "0" "0" "0" "0" "0" "0" "0" "0" "0" "0" +!series_matrix_table_begin +"ID_REF" "GSM5910329" "GSM5910330" "GSM5910331" "GSM5910332" "GSM5910333" "GSM5910334" "GSM5910335" "GSM5910336" "GSM5910337" "GSM5910338" "GSM5910339" "GSM5910340" "GSM5910341" "GSM5910342" "GSM5910343" +!series_matrix_table_end diff --git a/LC/GSE210430/.DS_Store b/LC/GSE210430/.DS_Store new file mode 100644 index 0000000000000000000000000000000000000000..11f1ac29fe3093f33c0aabef5a888f0aefd20027 Binary files /dev/null and b/LC/GSE210430/.DS_Store differ diff --git a/LC/GSE210430/._.DS_Store b/LC/GSE210430/._.DS_Store new file mode 100644 index 0000000000000000000000000000000000000000..28c42fb20a1f27e695fb64323501fc6476578b13 Binary files /dev/null and b/LC/GSE210430/._.DS_Store differ diff --git a/LC/GSE210430/._GSE210430_RAW b/LC/GSE210430/._GSE210430_RAW new file mode 100644 index 0000000000000000000000000000000000000000..3786ce2d017a768492015aa4c8a83edb7257c042 Binary files /dev/null and b/LC/GSE210430/._GSE210430_RAW differ diff --git a/LC/GSE210430/meta/._GSE210430_family.xml b/LC/GSE210430/meta/._GSE210430_family.xml new file mode 100644 index 0000000000000000000000000000000000000000..88b77a77c5f0f848f3a633d10a5fb1d1409742d3 Binary files /dev/null and b/LC/GSE210430/meta/._GSE210430_family.xml differ diff --git a/LC/GSE210430/meta/GSE210430_family.xml/GSE210430_family.xml b/LC/GSE210430/meta/GSE210430_family.xml/GSE210430_family.xml new file mode 100644 index 0000000000000000000000000000000000000000..896399aa8a98c2673b7a093423f9f39678006b71 --- /dev/null +++ b/LC/GSE210430/meta/GSE210430_family.xml/GSE210430_family.xml @@ -0,0 +1,1273 @@ + + + + + + AlexandreGaspar-Maia + Mayo Clinic +
+ 200 First street SW + Rochester + MN + 55905 + USA +
+ + + + Illumina Inc. + expression@illumina.com, techsupport@illumina.com + 1 800 809 4566 + Illumina Inc. +
+ 9885 Towne Centre Drive + San Diego + CA + 92121 + USA +
+ www.illumina.com + + + + JennaFernandez + + + + TerraLasho + + + + WazimMIsmail + + + + MrinalPatnaik + + + + AlexandreGMaia + + + + Gene Expression Omnibus (GEO) + GEO + NCBI NLM NIH + http://www.ncbi.nlm.nih.gov/geo + geo@ncbi.nlm.nih.gov + + + + + 2015-11-16 + 2015-11-16 + 2019-01-20 + + Infinium MethylationEPIC + GPL21145 + oligonucleotide beads + commercial + Homo sapiens + Illumina, Inc. + +See manufacturer's website + + + +ftp://ftp.ncbi.nlm.nih.gov/geo/platforms/GPL21nnn/GPL21145/suppl/GPL21145_MethylationEPIC_15073387_v-1-0.csv.gz + + + + + ID + IlmnID + + + SPOT_ID + + + AddressA_ID + + + AlleleA_ProbeSeq + + + AddressB_ID + + + AlleleB_ProbeSeq + + + Infinium_Design_Type + + + Next_Base + + + Color_Channel + + + Forward_Sequence + + + Genome_Build + + + CHR + + + MAPINFO + + + SourceSeq + + +GPL21145-tbl-1.txt + + + + + + + 2022-08-03 + 2024-08-13 + 2024-08-13 + + Methylation - Patient 1 + GSM6430109 + genomic + 1 + + Peripheral blood mononuclear cells + Homo sapiens + +Clonal hematopoiesis + + genomic DNA + +Genomic DNA was isolated and checked for quality by standard protocols. 1 µg genomic DNA then underwent bisulfite treatment using the TrueMethyl oxBS Module (Tecan Genomics, Männedorf, Switzerland) according to the manufacturer’s specifications. Briefly, DNA was purified using magnetic beads, denatured, and underwent bisulfite conversion followed by desulfonation and purification. The TrueMethyl converted DNA samples were then eluted in 10 µL and then processed through the Illumina Infinium MethylationEPIC BeadChip array (Illumina, San Diego, CA) protocol. In brief, 7 µl of converted DNA was denatured with 1 µL of 0.4N sodium hydroxide prior to whole genome amplification on the MSA4 plate. All other steps were followed as per manufacturer’s guidelines. + + + +standard protocol + + + +standard protocol + + +standard protocol + + +Quality control of Infinium MethylationEPIC BeadChips was performed via the Genome Studio Methylation Module (Illumina). Subset-quantile Within Array Normalization (SWAN) was performed on the Infinium MethylationEPIC BeadChip IDAT files via the R package “minfi”. + + + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM6430nnn/GSM6430109/suppl/GSM6430109_204295600039_R04C01_Grn.idat.gz + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM6430nnn/GSM6430109/suppl/GSM6430109_204295600039_R04C01_Red.idat.gz + + + + ID_REF + + + VALUE + SWAN normalized Average Beta + + + DetectionP + + +GSM6430109-tbl-1.txt + + + + + + + 2022-08-03 + 2024-08-13 + 2024-08-13 + + Methylation - Patient 5 + GSM6430110 + genomic + 1 + + Peripheral blood mononuclear cells + Homo sapiens + +Clonal hematopoiesis + + genomic DNA + +Genomic DNA was isolated and checked for quality by standard protocols. 1 µg genomic DNA then underwent bisulfite treatment using the TrueMethyl oxBS Module (Tecan Genomics, Männedorf, Switzerland) according to the manufacturer’s specifications. Briefly, DNA was purified using magnetic beads, denatured, and underwent bisulfite conversion followed by desulfonation and purification. The TrueMethyl converted DNA samples were then eluted in 10 µL and then processed through the Illumina Infinium MethylationEPIC BeadChip array (Illumina, San Diego, CA) protocol. In brief, 7 µl of converted DNA was denatured with 1 µL of 0.4N sodium hydroxide prior to whole genome amplification on the MSA4 plate. All other steps were followed as per manufacturer’s guidelines. + + + +standard protocol + + + +standard protocol + + +standard protocol + + +Quality control of Infinium MethylationEPIC BeadChips was performed via the Genome Studio Methylation Module (Illumina). Subset-quantile Within Array Normalization (SWAN) was performed on the Infinium MethylationEPIC BeadChip IDAT files via the R package “minfi”. + + + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM6430nnn/GSM6430110/suppl/GSM6430110_204295600039_R03C01_Grn.idat.gz + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM6430nnn/GSM6430110/suppl/GSM6430110_204295600039_R03C01_Red.idat.gz + + + + ID_REF + + + VALUE + SWAN normalized Average Beta + + + DetectionP + + +GSM6430110-tbl-1.txt + + + + + + + 2022-08-03 + 2024-08-13 + 2024-08-13 + + Methylation - Patient 6 + GSM6430111 + genomic + 1 + + Peripheral blood mononuclear cells + Homo sapiens + +Clonal hematopoiesis + + genomic DNA + +Genomic DNA was isolated and checked for quality by standard protocols. 1 µg genomic DNA then underwent bisulfite treatment using the TrueMethyl oxBS Module (Tecan Genomics, Männedorf, Switzerland) according to the manufacturer’s specifications. Briefly, DNA was purified using magnetic beads, denatured, and underwent bisulfite conversion followed by desulfonation and purification. The TrueMethyl converted DNA samples were then eluted in 10 µL and then processed through the Illumina Infinium MethylationEPIC BeadChip array (Illumina, San Diego, CA) protocol. In brief, 7 µl of converted DNA was denatured with 1 µL of 0.4N sodium hydroxide prior to whole genome amplification on the MSA4 plate. All other steps were followed as per manufacturer’s guidelines. + + + +standard protocol + + + +standard protocol + + +standard protocol + + +Quality control of Infinium MethylationEPIC BeadChips was performed via the Genome Studio Methylation Module (Illumina). Subset-quantile Within Array Normalization (SWAN) was performed on the Infinium MethylationEPIC BeadChip IDAT files via the R package “minfi”. + + + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM6430nnn/GSM6430111/suppl/GSM6430111_204305180051_R05C01_Grn.idat.gz + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM6430nnn/GSM6430111/suppl/GSM6430111_204305180051_R05C01_Red.idat.gz + + + + ID_REF + + + VALUE + SWAN normalized Average Beta + + + DetectionP + + +GSM6430111-tbl-1.txt + + + + + + + 2022-08-03 + 2024-08-13 + 2024-08-13 + + Methylation - Patient 8 + GSM6430112 + genomic + 1 + + Peripheral blood mononuclear cells + Homo sapiens + +Clonal hematopoiesis + + genomic DNA + +Genomic DNA was isolated and checked for quality by standard protocols. 1 µg genomic DNA then underwent bisulfite treatment using the TrueMethyl oxBS Module (Tecan Genomics, Männedorf, Switzerland) according to the manufacturer’s specifications. Briefly, DNA was purified using magnetic beads, denatured, and underwent bisulfite conversion followed by desulfonation and purification. The TrueMethyl converted DNA samples were then eluted in 10 µL and then processed through the Illumina Infinium MethylationEPIC BeadChip array (Illumina, San Diego, CA) protocol. In brief, 7 µl of converted DNA was denatured with 1 µL of 0.4N sodium hydroxide prior to whole genome amplification on the MSA4 plate. All other steps were followed as per manufacturer’s guidelines. + + + +standard protocol + + + +standard protocol + + +standard protocol + + +Quality control of Infinium MethylationEPIC BeadChips was performed via the Genome Studio Methylation Module (Illumina). Subset-quantile Within Array Normalization (SWAN) was performed on the Infinium MethylationEPIC BeadChip IDAT files via the R package “minfi”. + + + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM6430nnn/GSM6430112/suppl/GSM6430112_204295600089_R04C01_Grn.idat.gz + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM6430nnn/GSM6430112/suppl/GSM6430112_204295600089_R04C01_Red.idat.gz + + + + ID_REF + + + VALUE + SWAN normalized Average Beta + + + DetectionP + + +GSM6430112-tbl-1.txt + + + + + + + 2022-08-03 + 2024-08-13 + 2024-08-13 + + Methylation - Patient 12 + GSM6430113 + genomic + 1 + + Peripheral blood mononuclear cells + Homo sapiens + +Clonal hematopoiesis + + genomic DNA + +Genomic DNA was isolated and checked for quality by standard protocols. 1 µg genomic DNA then underwent bisulfite treatment using the TrueMethyl oxBS Module (Tecan Genomics, Männedorf, Switzerland) according to the manufacturer’s specifications. Briefly, DNA was purified using magnetic beads, denatured, and underwent bisulfite conversion followed by desulfonation and purification. The TrueMethyl converted DNA samples were then eluted in 10 µL and then processed through the Illumina Infinium MethylationEPIC BeadChip array (Illumina, San Diego, CA) protocol. In brief, 7 µl of converted DNA was denatured with 1 µL of 0.4N sodium hydroxide prior to whole genome amplification on the MSA4 plate. All other steps were followed as per manufacturer’s guidelines. + + + +standard protocol + + + +standard protocol + + +standard protocol + + +Quality control of Infinium MethylationEPIC BeadChips was performed via the Genome Studio Methylation Module (Illumina). Subset-quantile Within Array Normalization (SWAN) was performed on the Infinium MethylationEPIC BeadChip IDAT files via the R package “minfi”. + + + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM6430nnn/GSM6430113/suppl/GSM6430113_204295600039_R05C01_Grn.idat.gz + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM6430nnn/GSM6430113/suppl/GSM6430113_204295600039_R05C01_Red.idat.gz + + + + ID_REF + + + VALUE + SWAN normalized Average Beta + + + DetectionP + + +GSM6430113-tbl-1.txt + + + + + + + 2022-08-03 + 2024-08-13 + 2024-08-13 + + Methylation - Patient 16 + GSM6430114 + genomic + 1 + + Peripheral blood mononuclear cells + Homo sapiens + +COVID-19 + + genomic DNA + +Genomic DNA was isolated and checked for quality by standard protocols. 1 µg genomic DNA then underwent bisulfite treatment using the TrueMethyl oxBS Module (Tecan Genomics, Männedorf, Switzerland) according to the manufacturer’s specifications. Briefly, DNA was purified using magnetic beads, denatured, and underwent bisulfite conversion followed by desulfonation and purification. The TrueMethyl converted DNA samples were then eluted in 10 µL and then processed through the Illumina Infinium MethylationEPIC BeadChip array (Illumina, San Diego, CA) protocol. In brief, 7 µl of converted DNA was denatured with 1 µL of 0.4N sodium hydroxide prior to whole genome amplification on the MSA4 plate. All other steps were followed as per manufacturer’s guidelines. + + + +standard protocol + + + +standard protocol + + +standard protocol + + +Quality control of Infinium MethylationEPIC BeadChips was performed via the Genome Studio Methylation Module (Illumina). Subset-quantile Within Array Normalization (SWAN) was performed on the Infinium MethylationEPIC BeadChip IDAT files via the R package “minfi”. + + + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM6430nnn/GSM6430114/suppl/GSM6430114_204305180051_R03C01_Grn.idat.gz + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM6430nnn/GSM6430114/suppl/GSM6430114_204305180051_R03C01_Red.idat.gz + + + + ID_REF + + + VALUE + SWAN normalized Average Beta + + + DetectionP + + +GSM6430114-tbl-1.txt + + + + + + + 2022-08-03 + 2024-08-13 + 2024-08-13 + + Methylation - Patient 17 + GSM6430115 + genomic + 1 + + Peripheral blood mononuclear cells + Homo sapiens + +COVID-19 + + genomic DNA + +Genomic DNA was isolated and checked for quality by standard protocols. 1 µg genomic DNA then underwent bisulfite treatment using the TrueMethyl oxBS Module (Tecan Genomics, Männedorf, Switzerland) according to the manufacturer’s specifications. Briefly, DNA was purified using magnetic beads, denatured, and underwent bisulfite conversion followed by desulfonation and purification. The TrueMethyl converted DNA samples were then eluted in 10 µL and then processed through the Illumina Infinium MethylationEPIC BeadChip array (Illumina, San Diego, CA) protocol. In brief, 7 µl of converted DNA was denatured with 1 µL of 0.4N sodium hydroxide prior to whole genome amplification on the MSA4 plate. All other steps were followed as per manufacturer’s guidelines. + + + +standard protocol + + + +standard protocol + + +standard protocol + + +Quality control of Infinium MethylationEPIC BeadChips was performed via the Genome Studio Methylation Module (Illumina). Subset-quantile Within Array Normalization (SWAN) was performed on the Infinium MethylationEPIC BeadChip IDAT files via the R package “minfi”. + + + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM6430nnn/GSM6430115/suppl/GSM6430115_204305180051_R04C01_Grn.idat.gz + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM6430nnn/GSM6430115/suppl/GSM6430115_204305180051_R04C01_Red.idat.gz + + + + ID_REF + + + VALUE + SWAN normalized Average Beta + + + DetectionP + + +GSM6430115-tbl-1.txt + + + + + + + 2022-08-03 + 2024-08-13 + 2024-08-13 + + Methylation - Patient 26 + GSM6430116 + genomic + 1 + + Peripheral blood mononuclear cells + Homo sapiens + +COVID-19 + + genomic DNA + +Genomic DNA was isolated and checked for quality by standard protocols. 1 µg genomic DNA then underwent bisulfite treatment using the TrueMethyl oxBS Module (Tecan Genomics, Männedorf, Switzerland) according to the manufacturer’s specifications. Briefly, DNA was purified using magnetic beads, denatured, and underwent bisulfite conversion followed by desulfonation and purification. The TrueMethyl converted DNA samples were then eluted in 10 µL and then processed through the Illumina Infinium MethylationEPIC BeadChip array (Illumina, San Diego, CA) protocol. In brief, 7 µl of converted DNA was denatured with 1 µL of 0.4N sodium hydroxide prior to whole genome amplification on the MSA4 plate. All other steps were followed as per manufacturer’s guidelines. + + + +standard protocol + + + +standard protocol + + +standard protocol + + +Quality control of Infinium MethylationEPIC BeadChips was performed via the Genome Studio Methylation Module (Illumina). Subset-quantile Within Array Normalization (SWAN) was performed on the Infinium MethylationEPIC BeadChip IDAT files via the R package “minfi”. + + + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM6430nnn/GSM6430116/suppl/GSM6430116_204295600066_R02C01_Grn.idat.gz + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM6430nnn/GSM6430116/suppl/GSM6430116_204295600066_R02C01_Red.idat.gz + + + + ID_REF + + + VALUE + SWAN normalized Average Beta + + + DetectionP + + +GSM6430116-tbl-1.txt + + + + + + + 2022-08-03 + 2024-08-13 + 2024-08-13 + + Methylation - Patient 33 + GSM6430117 + genomic + 1 + + Peripheral blood mononuclear cells + Homo sapiens + +COVID-19 + + genomic DNA + +Genomic DNA was isolated and checked for quality by standard protocols. 1 µg genomic DNA then underwent bisulfite treatment using the TrueMethyl oxBS Module (Tecan Genomics, Männedorf, Switzerland) according to the manufacturer’s specifications. Briefly, DNA was purified using magnetic beads, denatured, and underwent bisulfite conversion followed by desulfonation and purification. The TrueMethyl converted DNA samples were then eluted in 10 µL and then processed through the Illumina Infinium MethylationEPIC BeadChip array (Illumina, San Diego, CA) protocol. In brief, 7 µl of converted DNA was denatured with 1 µL of 0.4N sodium hydroxide prior to whole genome amplification on the MSA4 plate. All other steps were followed as per manufacturer’s guidelines. + + + +standard protocol + + + +standard protocol + + +standard protocol + + +Quality control of Infinium MethylationEPIC BeadChips was performed via the Genome Studio Methylation Module (Illumina). Subset-quantile Within Array Normalization (SWAN) was performed on the Infinium MethylationEPIC BeadChip IDAT files via the R package “minfi”. + + + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM6430nnn/GSM6430117/suppl/GSM6430117_204297500090_R05C01_Grn.idat.gz + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM6430nnn/GSM6430117/suppl/GSM6430117_204297500090_R05C01_Red.idat.gz + + + + ID_REF + + + VALUE + SWAN normalized Average Beta + + + DetectionP + + +GSM6430117-tbl-1.txt + + + + + + + 2022-08-03 + 2024-08-13 + 2024-08-13 + + Methylation - Patient 35 + GSM6430118 + genomic + 1 + + Peripheral blood mononuclear cells + Homo sapiens + +Clonal hematopoiesis + + +COVID-19 + + genomic DNA + +Genomic DNA was isolated and checked for quality by standard protocols. 1 µg genomic DNA then underwent bisulfite treatment using the TrueMethyl oxBS Module (Tecan Genomics, Männedorf, Switzerland) according to the manufacturer’s specifications. Briefly, DNA was purified using magnetic beads, denatured, and underwent bisulfite conversion followed by desulfonation and purification. The TrueMethyl converted DNA samples were then eluted in 10 µL and then processed through the Illumina Infinium MethylationEPIC BeadChip array (Illumina, San Diego, CA) protocol. In brief, 7 µl of converted DNA was denatured with 1 µL of 0.4N sodium hydroxide prior to whole genome amplification on the MSA4 plate. All other steps were followed as per manufacturer’s guidelines. + + + +standard protocol + + + +standard protocol + + +standard protocol + + +Quality control of Infinium MethylationEPIC BeadChips was performed via the Genome Studio Methylation Module (Illumina). Subset-quantile Within Array Normalization (SWAN) was performed on the Infinium MethylationEPIC BeadChip IDAT files via the R package “minfi”. + + + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM6430nnn/GSM6430118/suppl/GSM6430118_204297500090_R07C01_Grn.idat.gz + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM6430nnn/GSM6430118/suppl/GSM6430118_204297500090_R07C01_Red.idat.gz + + + + ID_REF + + + VALUE + SWAN normalized Average Beta + + + DetectionP + + +GSM6430118-tbl-1.txt + + + + + + + 2022-08-03 + 2024-08-13 + 2024-08-13 + + Methylation - Patient 36 + GSM6430119 + genomic + 1 + + Peripheral blood mononuclear cells + Homo sapiens + +Clonal hematopoiesis + + +COVID-19 + + genomic DNA + +Genomic DNA was isolated and checked for quality by standard protocols. 1 µg genomic DNA then underwent bisulfite treatment using the TrueMethyl oxBS Module (Tecan Genomics, Männedorf, Switzerland) according to the manufacturer’s specifications. Briefly, DNA was purified using magnetic beads, denatured, and underwent bisulfite conversion followed by desulfonation and purification. The TrueMethyl converted DNA samples were then eluted in 10 µL and then processed through the Illumina Infinium MethylationEPIC BeadChip array (Illumina, San Diego, CA) protocol. In brief, 7 µl of converted DNA was denatured with 1 µL of 0.4N sodium hydroxide prior to whole genome amplification on the MSA4 plate. All other steps were followed as per manufacturer’s guidelines. + + + +standard protocol + + + +standard protocol + + +standard protocol + + +Quality control of Infinium MethylationEPIC BeadChips was performed via the Genome Studio Methylation Module (Illumina). Subset-quantile Within Array Normalization (SWAN) was performed on the Infinium MethylationEPIC BeadChip IDAT files via the R package “minfi”. + + + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM6430nnn/GSM6430119/suppl/GSM6430119_204295600039_R01C01_Grn.idat.gz + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM6430nnn/GSM6430119/suppl/GSM6430119_204295600039_R01C01_Red.idat.gz + + + + ID_REF + + + VALUE + SWAN normalized Average Beta + + + DetectionP + + +GSM6430119-tbl-1.txt + + + + + + + 2022-08-03 + 2024-08-13 + 2024-08-13 + + Methylation - Patient 38 + GSM6430120 + genomic + 1 + + Peripheral blood mononuclear cells + Homo sapiens + +Clonal hematopoiesis + + +COVID-19 + + genomic DNA + +Genomic DNA was isolated and checked for quality by standard protocols. 1 µg genomic DNA then underwent bisulfite treatment using the TrueMethyl oxBS Module (Tecan Genomics, Männedorf, Switzerland) according to the manufacturer’s specifications. Briefly, DNA was purified using magnetic beads, denatured, and underwent bisulfite conversion followed by desulfonation and purification. The TrueMethyl converted DNA samples were then eluted in 10 µL and then processed through the Illumina Infinium MethylationEPIC BeadChip array (Illumina, San Diego, CA) protocol. In brief, 7 µl of converted DNA was denatured with 1 µL of 0.4N sodium hydroxide prior to whole genome amplification on the MSA4 plate. All other steps were followed as per manufacturer’s guidelines. + + + +standard protocol + + + +standard protocol + + +standard protocol + + +Quality control of Infinium MethylationEPIC BeadChips was performed via the Genome Studio Methylation Module (Illumina). Subset-quantile Within Array Normalization (SWAN) was performed on the Infinium MethylationEPIC BeadChip IDAT files via the R package “minfi”. + + + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM6430nnn/GSM6430120/suppl/GSM6430120_204305180051_R06C01_Grn.idat.gz + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM6430nnn/GSM6430120/suppl/GSM6430120_204305180051_R06C01_Red.idat.gz + + + + ID_REF + + + VALUE + SWAN normalized Average Beta + + + DetectionP + + +GSM6430120-tbl-1.txt + + + + + + + 2022-08-03 + 2024-08-13 + 2024-08-13 + + Methylation - Patient 41 + GSM6430121 + genomic + 1 + + Peripheral blood mononuclear cells + Homo sapiens + +Clonal hematopoiesis + + +COVID-19 + + genomic DNA + +Genomic DNA was isolated and checked for quality by standard protocols. 1 µg genomic DNA then underwent bisulfite treatment using the TrueMethyl oxBS Module (Tecan Genomics, Männedorf, Switzerland) according to the manufacturer’s specifications. Briefly, DNA was purified using magnetic beads, denatured, and underwent bisulfite conversion followed by desulfonation and purification. The TrueMethyl converted DNA samples were then eluted in 10 µL and then processed through the Illumina Infinium MethylationEPIC BeadChip array (Illumina, San Diego, CA) protocol. In brief, 7 µl of converted DNA was denatured with 1 µL of 0.4N sodium hydroxide prior to whole genome amplification on the MSA4 plate. All other steps were followed as per manufacturer’s guidelines. + + + +standard protocol + + + +standard protocol + + +standard protocol + + +Quality control of Infinium MethylationEPIC BeadChips was performed via the Genome Studio Methylation Module (Illumina). Subset-quantile Within Array Normalization (SWAN) was performed on the Infinium MethylationEPIC BeadChip IDAT files via the R package “minfi”. + + + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM6430nnn/GSM6430121/suppl/GSM6430121_204295600089_R06C01_Grn.idat.gz + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM6430nnn/GSM6430121/suppl/GSM6430121_204295600089_R06C01_Red.idat.gz + + + + ID_REF + + + VALUE + SWAN normalized Average Beta + + + DetectionP + + +GSM6430121-tbl-1.txt + + + + + + + 2022-08-03 + 2024-08-13 + 2024-08-13 + + Methylation - Patient 42 + GSM6430122 + genomic + 1 + + Peripheral blood mononuclear cells + Homo sapiens + +Clonal hematopoiesis + + +COVID-19 + + genomic DNA + +Genomic DNA was isolated and checked for quality by standard protocols. 1 µg genomic DNA then underwent bisulfite treatment using the TrueMethyl oxBS Module (Tecan Genomics, Männedorf, Switzerland) according to the manufacturer’s specifications. Briefly, DNA was purified using magnetic beads, denatured, and underwent bisulfite conversion followed by desulfonation and purification. The TrueMethyl converted DNA samples were then eluted in 10 µL and then processed through the Illumina Infinium MethylationEPIC BeadChip array (Illumina, San Diego, CA) protocol. In brief, 7 µl of converted DNA was denatured with 1 µL of 0.4N sodium hydroxide prior to whole genome amplification on the MSA4 plate. All other steps were followed as per manufacturer’s guidelines. + + + +standard protocol + + + +standard protocol + + +standard protocol + + +Quality control of Infinium MethylationEPIC BeadChips was performed via the Genome Studio Methylation Module (Illumina). Subset-quantile Within Array Normalization (SWAN) was performed on the Infinium MethylationEPIC BeadChip IDAT files via the R package “minfi”. + + + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM6430nnn/GSM6430122/suppl/GSM6430122_204297500090_R06C01_Grn.idat.gz + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM6430nnn/GSM6430122/suppl/GSM6430122_204297500090_R06C01_Red.idat.gz + + + + ID_REF + + + VALUE + SWAN normalized Average Beta + + + DetectionP + + +GSM6430122-tbl-1.txt + + + + + + + 2022-08-03 + 2024-08-13 + 2024-08-13 + + Methylation - Patient 44 + GSM6430123 + genomic + 1 + + Peripheral blood mononuclear cells + Homo sapiens + +Clonal hematopoiesis + + +COVID-19 + + genomic DNA + +Genomic DNA was isolated and checked for quality by standard protocols. 1 µg genomic DNA then underwent bisulfite treatment using the TrueMethyl oxBS Module (Tecan Genomics, Männedorf, Switzerland) according to the manufacturer’s specifications. Briefly, DNA was purified using magnetic beads, denatured, and underwent bisulfite conversion followed by desulfonation and purification. The TrueMethyl converted DNA samples were then eluted in 10 µL and then processed through the Illumina Infinium MethylationEPIC BeadChip array (Illumina, San Diego, CA) protocol. In brief, 7 µl of converted DNA was denatured with 1 µL of 0.4N sodium hydroxide prior to whole genome amplification on the MSA4 plate. All other steps were followed as per manufacturer’s guidelines. + + + +standard protocol + + + +standard protocol + + +standard protocol + + +Quality control of Infinium MethylationEPIC BeadChips was performed via the Genome Studio Methylation Module (Illumina). Subset-quantile Within Array Normalization (SWAN) was performed on the Infinium MethylationEPIC BeadChip IDAT files via the R package “minfi”. + + + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM6430nnn/GSM6430123/suppl/GSM6430123_204295600039_R06C01_Grn.idat.gz + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM6430nnn/GSM6430123/suppl/GSM6430123_204295600039_R06C01_Red.idat.gz + + + + ID_REF + + + VALUE + SWAN normalized Average Beta + + + DetectionP + + +GSM6430123-tbl-1.txt + + + + + + + 2022-08-03 + 2024-08-13 + 2024-08-13 + + Methylation - Patient 45 + GSM6430124 + genomic + 1 + + Peripheral blood mononuclear cells + Homo sapiens + +Clonal hematopoiesis + + +COVID-19 + + genomic DNA + +Genomic DNA was isolated and checked for quality by standard protocols. 1 µg genomic DNA then underwent bisulfite treatment using the TrueMethyl oxBS Module (Tecan Genomics, Männedorf, Switzerland) according to the manufacturer’s specifications. Briefly, DNA was purified using magnetic beads, denatured, and underwent bisulfite conversion followed by desulfonation and purification. The TrueMethyl converted DNA samples were then eluted in 10 µL and then processed through the Illumina Infinium MethylationEPIC BeadChip array (Illumina, San Diego, CA) protocol. In brief, 7 µl of converted DNA was denatured with 1 µL of 0.4N sodium hydroxide prior to whole genome amplification on the MSA4 plate. All other steps were followed as per manufacturer’s guidelines. + + + +standard protocol + + + +standard protocol + + +standard protocol + + +Quality control of Infinium MethylationEPIC BeadChips was performed via the Genome Studio Methylation Module (Illumina). Subset-quantile Within Array Normalization (SWAN) was performed on the Infinium MethylationEPIC BeadChip IDAT files via the R package “minfi”. + + + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM6430nnn/GSM6430124/suppl/GSM6430124_204295600039_R07C01_Grn.idat.gz + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM6430nnn/GSM6430124/suppl/GSM6430124_204295600039_R07C01_Red.idat.gz + + + + ID_REF + + + VALUE + SWAN normalized Average Beta + + + DetectionP + + +GSM6430124-tbl-1.txt + + + + + + + 2022-08-03 + 2024-08-13 + 2024-08-13 + + Methylation - Patient 46 + GSM6430125 + genomic + 1 + + Peripheral blood mononuclear cells + Homo sapiens + +Clonal hematopoiesis + + +COVID-19 + + genomic DNA + +Genomic DNA was isolated and checked for quality by standard protocols. 1 µg genomic DNA then underwent bisulfite treatment using the TrueMethyl oxBS Module (Tecan Genomics, Männedorf, Switzerland) according to the manufacturer’s specifications. Briefly, DNA was purified using magnetic beads, denatured, and underwent bisulfite conversion followed by desulfonation and purification. The TrueMethyl converted DNA samples were then eluted in 10 µL and then processed through the Illumina Infinium MethylationEPIC BeadChip array (Illumina, San Diego, CA) protocol. In brief, 7 µl of converted DNA was denatured with 1 µL of 0.4N sodium hydroxide prior to whole genome amplification on the MSA4 plate. All other steps were followed as per manufacturer’s guidelines. + + + +standard protocol + + + +standard protocol + + +standard protocol + + +Quality control of Infinium MethylationEPIC BeadChips was performed via the Genome Studio Methylation Module (Illumina). Subset-quantile Within Array Normalization (SWAN) was performed on the Infinium MethylationEPIC BeadChip IDAT files via the R package “minfi”. + + + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM6430nnn/GSM6430125/suppl/GSM6430125_204295600089_R03C01_Grn.idat.gz + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM6430nnn/GSM6430125/suppl/GSM6430125_204295600089_R03C01_Red.idat.gz + + + + ID_REF + + + VALUE + SWAN normalized Average Beta + + + DetectionP + + +GSM6430125-tbl-1.txt + + + + + + + 2022-08-03 + 2024-08-13 + 2024-08-13 + + Methylation - Patient 48 + GSM6430126 + genomic + 1 + + Peripheral blood mononuclear cells + Homo sapiens + +Clonal hematopoiesis + + +COVID-19 + + genomic DNA + +Genomic DNA was isolated and checked for quality by standard protocols. 1 µg genomic DNA then underwent bisulfite treatment using the TrueMethyl oxBS Module (Tecan Genomics, Männedorf, Switzerland) according to the manufacturer’s specifications. Briefly, DNA was purified using magnetic beads, denatured, and underwent bisulfite conversion followed by desulfonation and purification. The TrueMethyl converted DNA samples were then eluted in 10 µL and then processed through the Illumina Infinium MethylationEPIC BeadChip array (Illumina, San Diego, CA) protocol. In brief, 7 µl of converted DNA was denatured with 1 µL of 0.4N sodium hydroxide prior to whole genome amplification on the MSA4 plate. All other steps were followed as per manufacturer’s guidelines. + + + +standard protocol + + + +standard protocol + + +standard protocol + + +Quality control of Infinium MethylationEPIC BeadChips was performed via the Genome Studio Methylation Module (Illumina). Subset-quantile Within Array Normalization (SWAN) was performed on the Infinium MethylationEPIC BeadChip IDAT files via the R package “minfi”. + + + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM6430nnn/GSM6430126/suppl/GSM6430126_204297500090_R08C01_Grn.idat.gz + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM6430nnn/GSM6430126/suppl/GSM6430126_204297500090_R08C01_Red.idat.gz + + + + ID_REF + + + VALUE + SWAN normalized Average Beta + + + DetectionP + + +GSM6430126-tbl-1.txt + + + + + + + 2022-08-03 + 2024-08-14 + 2024-11-13 + + Methylation analysis of patients with COVID-19 and Clonal Hematopoiesis + GSE210430 + 39189614 + +Coronavirus disease 2019 (COVID-19) is associated with significant morbidity and mortality, albeit with considerable heterogeneity among affected individuals. Emerging evidence points towards an important role of preexisting host factors, such as a deregulated inflammatory response at the time of infection. Here, we demonstrate the negative impact of clonal hematopoiesis, a prevalent clonal disorder of ageing individuals, on COVID-19-related cytokine release severity and mortality. In this study we perform use the Illumina MethylationEPIC array to quantify methylation levels in PBMCs from COVID19 patients and patients with clonal hematopoiesis. + + +DNA was isolated from purified PBMCs from 18 patients. There are three sample groups: 5 individuals with clonal hematopoiesis, 4 individuals with COVID-19, and 9 individuals with both clonal hematopoiesis and COVID-19. Samples were processed for DNA methylation using Tecan TrueMethyl oxBS module. + + Methylation profiling by genome tiling array + + + + + + + + + + + + + + + + + + + + + + + + + +ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE210nnn/GSE210430/suppl/GSE210430_GEO_metadata_Methylation_Matrix_signal_intensities.csv.gz + + +ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE210nnn/GSE210430/suppl/GSE210430_RAW.tar + + + + + + diff --git a/controls/GSE112905/meta/GSE112905_family 2.xml/._GPL21145-tbl-1.txt b/controls/GSE112905/meta/GSE112905_family 2.xml/._GPL21145-tbl-1.txt new file mode 100644 index 0000000000000000000000000000000000000000..ded6dc1b7e15a04059d5995d5b76a87e5b66dab0 Binary files /dev/null and b/controls/GSE112905/meta/GSE112905_family 2.xml/._GPL21145-tbl-1.txt differ diff --git a/controls/GSE112905/meta/GSE112905_family 2.xml/._GSE112905_family.xml b/controls/GSE112905/meta/GSE112905_family 2.xml/._GSE112905_family.xml new file mode 100644 index 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0000000000000000000000000000000000000000..0e1cdf97cb3e7a522d413456de6d94db3e9aafbf --- /dev/null +++ b/controls/GSE112905/meta/GSE112905_family 2.xml/GSE112905_family.xml @@ -0,0 +1,1638 @@ + + + + + + LubovNathanson + lnathanson@nova.edu + INIM + Nova Southeastern University +
+ 3321 College Ave. + Fort Lauderdale + Florida + 33314 + USA +
+ + + + Illumina Inc. + expression@illumina.com, techsupport@illumina.com + 1 800 809 4566 + Illumina Inc. +
+ 9885 Towne Centre Drive + San Diego + CA + 92121 + USA +
+ www.illumina.com + + + + MalavSTrivedi + + + + MariaAbreu + + + + LeonorSarria + + + + NatashaRose + + + + VladimirBeljanski + + + + MaryAFletcher + + + + NancyGKlimas + + + + Gene Expression Omnibus (GEO) + GEO + NCBI NLM NIH + http://www.ncbi.nlm.nih.gov/geo + geo@ncbi.nlm.nih.gov + + + + + 2015-11-16 + 2015-11-16 + 2019-01-20 + + Infinium MethylationEPIC + GPL21145 + oligonucleotide beads + commercial + Homo sapiens + Illumina, Inc. + +See manufacturer's website + + + +ftp://ftp.ncbi.nlm.nih.gov/geo/platforms/GPL21nnn/GPL21145/suppl/GPL21145_MethylationEPIC_15073387_v-1-0.csv.gz + + + + + ID + IlmnID + + + SPOT_ID + + + AddressA_ID + + + AlleleA_ProbeSeq + + + AddressB_ID + + + AlleleB_ProbeSeq + + + Infinium_Design_Type + + + Next_Base + + + Color_Channel + + + Forward_Sequence + + + Genome_Build + + + CHR + + + MAPINFO + + + SourceSeq + + +GPL21145-tbl-1.txt + + + + + + + 2018-04-10 + 2019-03-15 + 2019-03-15 + + PBMC genomic DNA Healthy Control [HC] 1 + GSM3090983 + genomic + 1 + + HC PBMC + Homo sapiens + +male + + +HC subject 1 + + +Healthy Control [HC] + + +peripheral blood mononuclear cells (PBMC) + + genomic DNA + +genomic DNA was extracted and purified from PBMC samples using Qiagen DNeasy Blood & Tissue Kit according to manufacturer instructions + + + +Standard Illumina Protocol + + + +bisulphite converted DNA was hybridised to Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol + + +Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting + + +PBMC genomic DNA from HC subject 1 +10H + + +Illumina Genome Studio; Matrix signal intensities contains unmethylated and methylated signal intensities; Matrix processed contains non-normalized average beta values. + + + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM3090nnn/GSM3090983/suppl/GSM3090983_200526590034_R02C01_Grn.idat.gz + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM3090nnn/GSM3090983/suppl/GSM3090983_200526590034_R02C01_Red.idat.gz + + + + ID_REF + + + VALUE + Average Beta + + + Detection Pval + + +GSM3090983-tbl-1.txt + + + + + + + 2018-04-10 + 2019-03-15 + 2019-03-15 + + PBMC genomic DNA Healthy Control [HC] 2 + GSM3090984 + genomic + 1 + + HC PBMC + Homo sapiens + +male + + +HC subject 2 + + +Healthy Control [HC] + + +peripheral blood mononuclear cells (PBMC) + + genomic DNA + +genomic DNA was extracted and purified from PBMC samples using Qiagen DNeasy Blood & Tissue Kit according to manufacturer instructions + + + +Standard Illumina Protocol + + + +bisulphite converted DNA was hybridised to Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol + + +Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting + + +PBMC genomic DNA from HC subject 2 +34H + + +Illumina Genome Studio; Matrix signal intensities contains unmethylated and methylated signal intensities; Matrix processed contains non-normalized average beta values. + + + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM3090nnn/GSM3090984/suppl/GSM3090984_200526580039_R02C01_Grn.idat.gz + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM3090nnn/GSM3090984/suppl/GSM3090984_200526580039_R02C01_Red.idat.gz + + + + ID_REF + + + VALUE + Average Beta + + + Detection Pval + + +GSM3090984-tbl-1.txt + + + + + + + 2018-04-10 + 2019-03-15 + 2019-03-15 + + PBMC genomic DNA Healthy Control [HC] 3 + GSM3090985 + genomic + 1 + + HC PBMC + Homo sapiens + +male + + +HC subject 3 + + +Healthy Control [HC] + + +peripheral blood mononuclear cells (PBMC) + + genomic DNA + +genomic DNA was extracted and purified from PBMC samples using Qiagen DNeasy Blood & Tissue Kit according to manufacturer instructions + + + +Standard Illumina Protocol + + + +bisulphite converted DNA was hybridised to Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol + + +Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting + + +PBMC genomic DNA from HC subject 3 +46H + + +Illumina Genome Studio; Matrix signal intensities contains unmethylated and methylated signal intensities; Matrix processed contains non-normalized average beta values. + + + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM3090nnn/GSM3090985/suppl/GSM3090985_200526580053_R06C01_Grn.idat.gz + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM3090nnn/GSM3090985/suppl/GSM3090985_200526580053_R06C01_Red.idat.gz + + + + ID_REF + + + VALUE + Average Beta + + + Detection Pval + + +GSM3090985-tbl-1.txt + + + + + + + 2018-04-10 + 2019-03-15 + 2019-03-15 + + PBMC genomic DNA Healthy Control [HC] 4 + GSM3090986 + genomic + 1 + + HC PBMC + Homo sapiens + +male + + +HC subject 4 + + +Disease state:Healthy Control [HC] + + +peripheral blood mononuclear cells (PBMC) + + genomic DNA + +genomic DNA was extracted and purified from PBMC samples using Qiagen DNeasy Blood & Tissue Kit according to manufacturer instructions + + + +Standard Illumina Protocol + + + +bisulphite converted DNA was hybridised to Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol + + +Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting + + +PBMC genomic DNA from HC subject 4 +58H + + +Illumina Genome Studio; Matrix signal intensities contains unmethylated and methylated signal intensities; Matrix processed contains non-normalized average beta values. + + + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM3090nnn/GSM3090986/suppl/GSM3090986_200526580069_R02C01_Grn.idat.gz + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM3090nnn/GSM3090986/suppl/GSM3090986_200526580069_R02C01_Red.idat.gz + + + + ID_REF + + + VALUE + Average Beta + + + Detection Pval + + +GSM3090986-tbl-1.txt + + + + + + + 2018-04-10 + 2019-03-15 + 2019-03-15 + + PBMC genomic DNA GWI 1 + GSM3090987 + genomic + 1 + + GWI PBMC + Homo sapiens + +male + + +GWI subject 1 + + +Gulf War Illness (GWI) + + +peripheral blood mononuclear cells (PBMC) + + genomic DNA + +genomic DNA was extracted and purified from PBMC samples using Qiagen DNeasy Blood & Tissue Kit according to manufacturer instructions + + + +Standard Illumina Protocol + + + +bisulphite converted DNA was hybridised to Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol + + +Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting + + +PBMC genomic DNA from GWI subject 1 +67G + + +Illumina Genome Studio; Matrix signal intensities contains unmethylated and methylated signal intensities; Matrix processed contains non-normalized average beta values. + + + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM3090nnn/GSM3090987/suppl/GSM3090987_200526580034_R03C01_Grn.idat.gz + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM3090nnn/GSM3090987/suppl/GSM3090987_200526580034_R03C01_Red.idat.gz + + + + ID_REF + + + VALUE + Average Beta + + + Detection Pval + + +GSM3090987-tbl-1.txt + + + + + + + 2018-04-10 + 2019-03-15 + 2019-03-15 + + PBMC genomic DNA Healthy Control [HC] 5 + GSM3090988 + genomic + 1 + + HC PBMC + Homo sapiens + +male + + +HC subject 5 + + +Healthy Control [HC] + + +peripheral blood mononuclear cells (PBMC) + + genomic DNA + +genomic DNA was extracted and purified from PBMC samples using Qiagen DNeasy Blood & Tissue Kit according to manufacturer instructions + + + +Standard Illumina Protocol + + + +bisulphite converted DNA was hybridised to Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol + + +Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting + + +PBMC genomic DNA from HC subject 5 +82H + + +Illumina Genome Studio; Matrix signal intensities contains unmethylated and methylated signal intensities; Matrix processed contains non-normalized average beta values. + + + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM3090nnn/GSM3090988/suppl/GSM3090988_200526580035_R02C01_Grn.idat.gz + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM3090nnn/GSM3090988/suppl/GSM3090988_200526580035_R02C01_Red.idat.gz + + + + ID_REF + + + VALUE + Average Beta + + + Detection Pval + + +GSM3090988-tbl-1.txt + + + + + + + 2018-04-10 + 2019-03-15 + 2019-03-15 + + PBMC genomic DNA GWI 2 + GSM3090989 + genomic + 1 + + GWI PBMC + Homo sapiens + +male + + +GWI subject 2 + + +Gulf War Illness (GWI) + + +peripheral blood mononuclear cells (PBMC) + + genomic DNA + +genomic DNA was extracted and purified from PBMC samples using Qiagen DNeasy Blood & Tissue Kit according to manufacturer instructions + + + +Standard Illumina Protocol + + + +bisulphite converted DNA was hybridised to Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol + + +Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting + + +PBMC genomic DNA from GWI subject 2 +91G + + +Illumina Genome Studio; Matrix signal intensities contains unmethylated and methylated signal intensities; Matrix processed contains non-normalized average beta values. + + + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM3090nnn/GSM3090989/suppl/GSM3090989_200526580088_R03C01_Grn.idat.gz + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM3090nnn/GSM3090989/suppl/GSM3090989_200526580088_R03C01_Red.idat.gz + + + + ID_REF + + + VALUE + Average Beta + + + Detection Pval + + +GSM3090989-tbl-1.txt + + + + + + + 2018-04-10 + 2019-03-15 + 2019-03-15 + + PBMC genomic DNA Healthy Control [HC] 6 + GSM3090990 + genomic + 1 + + HC PBMC + Homo sapiens + +male + + +HC subject 6 + + +Healthy Control [HC] + + +peripheral blood mononuclear cells (PBMC) + + genomic DNA + +genomic DNA was extracted and purified from PBMC samples using Qiagen DNeasy Blood & Tissue Kit according to manufacturer instructions + + + +Standard Illumina Protocol + + + +bisulphite converted DNA was hybridised to Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol + + +Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting + + +PBMC genomic DNA from HC subject 6 +94H + + +Illumina Genome Studio; Matrix signal intensities contains unmethylated and methylated signal intensities; Matrix processed contains non-normalized average beta values. + + + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM3090nnn/GSM3090990/suppl/GSM3090990_200526580088_R06C01_Grn.idat.gz + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM3090nnn/GSM3090990/suppl/GSM3090990_200526580088_R06C01_Red.idat.gz + + + + ID_REF + + + VALUE + Average Beta + + + Detection Pval + + +GSM3090990-tbl-1.txt + + + + + + + 2018-04-10 + 2019-03-15 + 2019-03-15 + + PBMC genomic DNA GWI 3 + GSM3090991 + genomic + 1 + + GWI PBMC + Homo sapiens + +male + + +GWI subject 3 + + +Gulf War Illness (GWI) + + +peripheral blood mononuclear cells (PBMC) + + genomic DNA + +genomic DNA was extracted and purified from PBMC samples using Qiagen DNeasy Blood & Tissue Kit according to manufacturer instructions + + + +Standard Illumina Protocol + + + +bisulphite converted DNA was hybridised to Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol + + +Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting + + +PBMC genomic DNA from GWI subject 3 +103G + + +Illumina Genome Studio; Matrix signal intensities contains unmethylated and methylated signal intensities; Matrix processed contains non-normalized average beta values. + + + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM3090nnn/GSM3090991/suppl/GSM3090991_200134080024_R07C01_Grn.idat.gz + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM3090nnn/GSM3090991/suppl/GSM3090991_200134080024_R07C01_Red.idat.gz + + + + ID_REF + + + VALUE + Average Beta + + + Detection Pval + + +GSM3090991-tbl-1.txt + + + + + + + 2018-04-10 + 2019-03-15 + 2019-03-15 + + PBMC genomic DNA Healthy Control [HC] 7 + GSM3090992 + genomic + 1 + + HC PBMC + Homo sapiens + +male + + +HC subject 7 + + +Healthy Control [HC] + + +peripheral blood mononuclear cells (PBMC) + + genomic DNA + +genomic DNA was extracted and purified from PBMC samples using Qiagen DNeasy Blood & Tissue Kit according to manufacturer instructions + + + +Standard Illumina Protocol + + + +bisulphite converted DNA was hybridised to Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol + + +Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting + + +PBMC genomic DNA from HC subject 7 +106H + + +Illumina Genome Studio; Matrix signal intensities contains unmethylated and methylated signal intensities; Matrix processed contains non-normalized average beta values. + + + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM3090nnn/GSM3090992/suppl/GSM3090992_200526580062_R02C01_Grn.idat.gz + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM3090nnn/GSM3090992/suppl/GSM3090992_200526580062_R02C01_Red.idat.gz + + + + ID_REF + + + VALUE + Average Beta + + + Detection Pval + + +GSM3090992-tbl-1.txt + + + + + + + 2018-04-10 + 2019-03-15 + 2019-03-15 + + PBMC genomic DNA GWI 4 + GSM3090993 + genomic + 1 + + GWI PBMC + Homo sapiens + +male + + +GWI subject 4 + + +Gulf War Illness (GWI) + + +peripheral blood mononuclear cells (PBMC) + + genomic DNA + +genomic DNA was extracted and purified from PBMC samples using Qiagen DNeasy Blood & Tissue Kit according to manufacturer instructions + + + +Standard Illumina Protocol + + + +bisulphite converted DNA was hybridised to Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol + + +Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting + + +PBMC genomic DNA from GWI subject 4 +127G + + +Illumina Genome Studio; Matrix signal intensities contains unmethylated and methylated signal intensities; Matrix processed contains non-normalized average beta values. + + + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM3090nnn/GSM3090993/suppl/GSM3090993_200526580071_R07C01_Grn.idat.gz + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM3090nnn/GSM3090993/suppl/GSM3090993_200526580071_R07C01_Red.idat.gz + + + + ID_REF + + + VALUE + Average Beta + + + Detection Pval + + +GSM3090993-tbl-1.txt + + + + + + + 2018-04-10 + 2019-03-15 + 2019-03-15 + + PBMC genomic DNA Healthy Control [HC] 8 + GSM3090994 + genomic + 1 + + HC PBMC + Homo sapiens + +male + + +HC subject 8 + + +Healthy Control [HC] + + +peripheral blood mononuclear cells (PBMC) + + genomic DNA + +genomic DNA was extracted and purified from PBMC samples using Qiagen DNeasy Blood & Tissue Kit according to manufacturer instructions + + + +Standard Illumina Protocol + + + +bisulphite converted DNA was hybridised to Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol + + +Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting + + +PBMC genomic DNA from HC subject 8 +142H + + +Illumina Genome Studio; Matrix signal intensities contains unmethylated and methylated signal intensities; Matrix processed contains non-normalized average beta values. + + + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM3090nnn/GSM3090994/suppl/GSM3090994_200526580078_R06C01_Grn.idat.gz + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM3090nnn/GSM3090994/suppl/GSM3090994_200526580078_R06C01_Red.idat.gz + + + + ID_REF + + + VALUE + Average Beta + + + Detection Pval + + +GSM3090994-tbl-1.txt + + + + + + + 2018-04-10 + 2019-03-15 + 2019-03-15 + + PBMC genomic DNA GWI 5 + GSM3090995 + genomic + 1 + + GWI PBMC + Homo sapiens + +male + + +GWI subject 5 + + +Gulf War Illness (GWI) + + +peripheral blood mononuclear cells (PBMC) + + genomic DNA + +genomic DNA was extracted and purified from PBMC samples using Qiagen DNeasy Blood & Tissue Kit according to manufacturer instructions + + + +Standard Illumina Protocol + + + +bisulphite converted DNA was hybridised to Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol + + +Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting + + +PBMC genomic DNA from GWI subject 5 +151G + + +Illumina Genome Studio; Matrix signal intensities contains unmethylated and methylated signal intensities; Matrix processed contains non-normalized average beta values. + + + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM3090nnn/GSM3090995/suppl/GSM3090995_200526580083_R07C01_Grn.idat.gz + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM3090nnn/GSM3090995/suppl/GSM3090995_200526580083_R07C01_Red.idat.gz + + + + ID_REF + + + VALUE + Average Beta + + + Detection Pval + + +GSM3090995-tbl-1.txt + + + + + + + 2018-04-10 + 2019-03-15 + 2019-03-15 + + PBMC genomic DNA GWI 6 + GSM3090996 + genomic + 1 + + GWI PBMC + Homo sapiens + +male + + +GWI subject 6 + + +Gulf War Illness (GWI) + + +peripheral blood mononuclear cells (PBMC) + + genomic DNA + +genomic DNA was extracted and purified from PBMC samples using Qiagen DNeasy Blood & Tissue Kit according to manufacturer instructions + + + +Standard Illumina Protocol + + + +bisulphite converted DNA was hybridised to Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol + + +Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting + + +PBMC genomic DNA from GWI subject 6 +163G + + +Illumina Genome Studio; Matrix signal intensities contains unmethylated and methylated signal intensities; Matrix processed contains non-normalized average beta values. + + + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM3090nnn/GSM3090996/suppl/GSM3090996_200134080026_R03C01_Grn.idat.gz + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM3090nnn/GSM3090996/suppl/GSM3090996_200134080026_R03C01_Red.idat.gz + + + + ID_REF + + + VALUE + Average Beta + + + Detection Pval + + +GSM3090996-tbl-1.txt + + + + + + + 2018-04-10 + 2019-03-15 + 2019-03-15 + + PBMC genomic DNA GWI 7 + GSM3090997 + genomic + 1 + + GWI PBMC + Homo sapiens + +male + + +GWI subject 7 + + +Gulf War Illness (GWI) + + +peripheral blood mononuclear cells (PBMC) + + genomic DNA + +genomic DNA was extracted and purified from PBMC samples using Qiagen DNeasy Blood & Tissue Kit according to manufacturer instructions + + + +Standard Illumina Protocol + + + +bisulphite converted DNA was hybridised to Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol + + +Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting + + +PBMC genomic DNA from GWI subject 7 +181G + + +Illumina Genome Studio; Matrix signal intensities contains unmethylated and methylated signal intensities; Matrix processed contains non-normalized average beta values. + + + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM3090nnn/GSM3090997/suppl/GSM3090997_200526580044_R05C01_Grn.idat.gz + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM3090nnn/GSM3090997/suppl/GSM3090997_200526580044_R05C01_Red.idat.gz + + + + ID_REF + + + VALUE + Average Beta + + + Detection Pval + + +GSM3090997-tbl-1.txt + + + + + + + 2018-04-10 + 2019-03-15 + 2019-03-15 + + PBMC genomic DNA Healthy Control [HC] 9 + GSM3090998 + genomic + 1 + + HC PBMC + Homo sapiens + +male + + +HC subject 9 + + +Healthy Control [HC] + + +peripheral blood mononuclear cells (PBMC) + + genomic DNA + +genomic DNA was extracted and purified from PBMC samples using Qiagen DNeasy Blood & Tissue Kit according to manufacturer instructions + + + +Standard Illumina Protocol + + + +bisulphite converted DNA was hybridised to Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol + + +Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting + + +PBMC genomic DNA from HC subject 9 +196H + + +Illumina Genome Studio; Matrix signal intensities contains unmethylated and methylated signal intensities; Matrix processed contains non-normalized average beta values. + + + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM3090nnn/GSM3090998/suppl/GSM3090998_200526580051_R04C01_Grn.idat.gz + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM3090nnn/GSM3090998/suppl/GSM3090998_200526580051_R04C01_Red.idat.gz + + + + ID_REF + + + VALUE + Average Beta + + + Detection Pval + + +GSM3090998-tbl-1.txt + + + + + + + 2018-04-10 + 2019-03-15 + 2019-03-15 + + PBMC genomic DNA GWI 8 + GSM3090999 + genomic + 1 + + GWI PBMC + Homo sapiens + +male + + +GWI subject 8 + + +Gulf War Illness (GWI) + + +peripheral blood mononuclear cells (PBMC) + + genomic DNA + +genomic DNA was extracted and purified from PBMC samples using Qiagen DNeasy Blood & Tissue Kit according to manufacturer instructions + + + +Standard Illumina Protocol + + + +bisulphite converted DNA was hybridised to Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol + + +Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting + + +PBMC genomic DNA from GWI subject 8 +205G + + +Illumina Genome Studio; Matrix signal intensities contains unmethylated and methylated signal intensities; Matrix processed contains non-normalized average beta values. + + + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM3090nnn/GSM3090999/suppl/GSM3090999_200526580080_R05C01_Grn.idat.gz + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM3090nnn/GSM3090999/suppl/GSM3090999_200526580080_R05C01_Red.idat.gz + + + + ID_REF + + + VALUE + Average Beta + + + Detection Pval + + +GSM3090999-tbl-1.txt + + + + + + + 2018-04-10 + 2019-03-15 + 2019-03-15 + + PBMC genomic DNA GWI 9 + GSM3091000 + genomic + 1 + + GWI PBMC + Homo sapiens + +male + + +GWI subject 9 + + +Gulf War Illness (GWI) + + +peripheral blood mononuclear cells (PBMC) + + genomic DNA + +genomic DNA was extracted and purified from PBMC samples using Qiagen DNeasy Blood & Tissue Kit according to manufacturer instructions + + + +Standard Illumina Protocol + + + +bisulphite converted DNA was hybridised to Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol + + +Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting + + +PBMC genomic DNA from GWI subject 9 +214G + + +Illumina Genome Studio; Matrix signal intensities contains unmethylated and methylated signal intensities; Matrix processed contains non-normalized average beta values. + + + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM3091nnn/GSM3091000/suppl/GSM3091000_200526580037_R06C01_Grn.idat.gz + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM3091nnn/GSM3091000/suppl/GSM3091000_200526580037_R06C01_Red.idat.gz + + + + ID_REF + + + VALUE + Average Beta + + + Detection Pval + + +GSM3091000-tbl-1.txt + + + + + + + 2018-04-10 + 2019-03-15 + 2019-03-15 + + PBMC genomic DNA Healthy Control [HC] 10 + GSM3091001 + genomic + 1 + + HC PBMC + Homo sapiens + +male + + +HC subject 10 + + +Healthy Control [HC] + + +peripheral blood mononuclear cells (PBMC) + + genomic DNA + +genomic DNA was extracted and purified from PBMC samples using Qiagen DNeasy Blood & Tissue Kit according to manufacturer instructions + + + +Standard Illumina Protocol + + + +bisulphite converted DNA was hybridised to Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol + + +Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting + + +PBMC genomic DNA from HC subject 10 +217H + + +Illumina Genome Studio; Matrix signal intensities contains unmethylated and methylated signal intensities; Matrix processed contains non-normalized average beta values. + + + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM3091nnn/GSM3091001/suppl/GSM3091001_200526580007_R01C01_Grn.idat.gz + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM3091nnn/GSM3091001/suppl/GSM3091001_200526580007_R01C01_Red.idat.gz + + + + ID_REF + + + VALUE + Average Beta + + + Detection Pval + + +GSM3091001-tbl-1.txt + + + + + + + 2018-04-10 + 2019-03-15 + 2019-03-15 + + PBMC genomic DNA GWI 10 + GSM3091002 + genomic + 1 + + GWI PBMC + Homo sapiens + +male + + +GWI subject 10 + + +Gulf War Illness (GWI) + + +peripheral blood mononuclear cells (PBMC) + + genomic DNA + +genomic DNA was extracted and purified from PBMC samples using Qiagen DNeasy Blood & Tissue Kit according to manufacturer instructions + + + +Standard Illumina Protocol + + + +bisulphite converted DNA was hybridised to Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol + + +Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting + + +PBMC genomic DNA from GWI subject 10 +223G + + +Illumina Genome Studio; Matrix signal intensities contains unmethylated and methylated signal intensities; Matrix processed contains non-normalized average beta values. + + + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM3091nnn/GSM3091002/suppl/GSM3091002_200526580007_R07C01_Grn.idat.gz + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM3091nnn/GSM3091002/suppl/GSM3091002_200526580007_R07C01_Red.idat.gz + + + + ID_REF + + + VALUE + Average Beta + + + Detection Pval + + +GSM3091002-tbl-1.txt + + + + + + + 2018-04-10 + 2019-03-15 + 2019-06-14 + + Changes in DNA methylation patterns associated with Gulf War Illness + GSE112905 + 30920300 + +Gulf War Illness (GWI) is a complex condition that involves multiple organ systems and is characterized by an abrupt or delayed onset of persistent/relapsing symptomatology such as memory and other neurological problems, muscle and joint pain, gastrointestinal issues, hormonal imbalance, immune dysfunction and debilitating fatigue. Currently, treatment of the condition relies solely on management of symptomatology and improvement in quality of life due to a lack of knowledgeof the underlying mechanisms of disease onset and progression. An improved understanding of the key mechanisms of GWI and dysfunction within regulatory systems will lead to more objective diagnosis methods and adequate management of patients by providing targeted approaches to treatment. Disruption of DNA methylation patterns has been tied to various immune, neurological and endocrine disease states; however, the status of this epigenetic mark in GWI remains uncertain. This study aimed at identifying biomarkers of GWI by gaining knowledge on DNA methylation patterns of GWI in an effort to determine therapeutic targets of disease activity and provide insight into disease onset and progression. Methods: Genomic DNA from 10 GWI patients and 10 healthy controls [HC] (“experimental cohort”) prepared from PBMCs was analyzed with ELISA-based DNA methylation assays and Illumina MethylationEPIC microarrays. These arrays allow measuring the methylation status at 850,000 CpG sites. Methylation changes in promoter regions were separately analyzed and used as input data in ingenuity pathway analysis software to identify altered functional pathways. Relevant differentially methylated CpG sites (DMS) were validated by pyrosequencing. Results: Global DNA methylation levels using the ELISA-based assay on the DNA isolated from PBMCs of GWI patients were similar to those of HC. However, deeper evaluation using microarray-based genome-wide technology allowed detection of DMS in GWI patients with respect to HC. As an overall 10,767 CpG sites presented with differential DNA methylation levels across promoters, gene regulatory elements and within coding regions of genes. Majority of these DMS were hypermethylated in GWI patients as compared to the HC, and more than half of these sites localized to promoters and gene regulatory elements, relative to distribution of DMSin the network as a whole, indicating gene regulatory potential. Functional pathway analysis of the 776 genes with differentially methylated promoters (DMPs) fulfilling FDR≤0.2 criteriafollowing a genomic region-based approachlinks GWI to defects in at least 15 different pathways mostly related to cell signaling with a strong immune component. Conclusions: This is the first study that has explored genome-wide epigenetic changes associated with GWI using the new MethylationEPIC microarrays covering about 850,000 CpG sites; which builds on previous methylation preliminary reports. The data obtained are consistent with previous evidence for dysregulation of the immune system in GWI and suggests a role of this epigenetic modification on the DNA pathobiology of GWI. They are also consistent with previous reports showing a Th1- to Th2-mediated immune response shift in GWI in addition to altered immune system function. Future validation studies in larger cohorts of GWI patients and evaluation of the effects of these methylation patterns on gene expression regulation are granted. + + +Genomic DNA from 20 peripheral blood mononuclear cells (PBMC) samples (10 GWI, 10 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. + + Methylation profiling by array + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE112nnn/GSE112905/suppl/GSE112905_RAW.tar + + +ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE112nnn/GSE112905/suppl/GSE112905_non-normalized.txt.gz + + + + + diff --git a/controls/GSE40279/GSE40279_average_beta_GSM989827-GSM989990.txt b/controls/GSE40279/GSE40279_average_beta_GSM989827-GSM989990.txt new file mode 100644 index 0000000000000000000000000000000000000000..759eb8c2344582ad0b080bb68befcc97b75a08e9 --- /dev/null +++ b/controls/GSE40279/GSE40279_average_beta_GSM989827-GSM989990.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:c49ccdcbbdfdf7fdf9bdecb7c7c117687f772a46c34d7bbd794f9e7819f92f7a +size 791053312 diff --git a/controls/GSE40279/GSE40279_average_beta_GSM989991-GSM990299.txt b/controls/GSE40279/GSE40279_average_beta_GSM989991-GSM990299.txt new file mode 100644 index 0000000000000000000000000000000000000000..7ea0069437689a160d7619066d4bce6e649d4c7f --- /dev/null +++ b/controls/GSE40279/GSE40279_average_beta_GSM989991-GSM990299.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:d71b71d52d9dcb746cba2f2bcb941b90a1df2bd7e9f922bcd4ac2b1cfa1d1c8c +size 788307015 diff --git a/controls/GSE42861/GSE42861_methylation_signal_matrix_SUBSETS/GSE42861_methylation_signal_matrix_12of13.txt b/controls/GSE42861/GSE42861_methylation_signal_matrix_SUBSETS/GSE42861_methylation_signal_matrix_12of13.txt new file mode 100644 index 0000000000000000000000000000000000000000..aef2ebbee37d8697ea59da27b85d3d433f1a876a --- /dev/null +++ b/controls/GSE42861/GSE42861_methylation_signal_matrix_SUBSETS/GSE42861_methylation_signal_matrix_12of13.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:c2fd20042ef28734279b8664ca61a37011751aa99ef296f58c7a726603659e1e +size 456389748