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+ 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/.DS_Store b/controls/GSE40279/.DS_Store new file mode 100644 index 0000000000000000000000000000000000000000..b627bdfc61094eb141d7336b6af7dc388872ac85 Binary files /dev/null and b/controls/GSE40279/.DS_Store differ diff --git a/controls/GSE40279/._.DS_Store b/controls/GSE40279/._.DS_Store new file mode 100644 index 0000000000000000000000000000000000000000..28c42fb20a1f27e695fb64323501fc6476578b13 Binary files /dev/null and b/controls/GSE40279/._.DS_Store differ diff --git a/controls/GSE40279/._GSE40279_RAW b/controls/GSE40279/._GSE40279_RAW new file mode 100644 index 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kb from CpG island; Shelves - 2-4 kb from CpG island.IndexTargetIDProbeID_AProbeID_BIdentifies the probe name. 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index 0000000000000000000000000000000000000000..2e1d82de013d7cff6b0748c191ccfead6012b48f --- /dev/null +++ b/controls/GSE42861/meta/GSE42861_family.xml.part4/GSE42861_family.xml @@ -0,0 +1,49863 @@ + + + + + + YunLiu + yliu39@fudan.edu.cn + Fudan University +
+ 130 Dong An Road + Shanghai + 200032 + China +
+ + + + 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 + + + + AndrewPFeinberg + + + + Gene Expression Omnibus (GEO) + GEO + NCBI NLM NIH + http://www.ncbi.nlm.nih.gov/geo + geo@ncbi.nlm.nih.gov + + + + + 2011-05-13 + 2011-05-13 + 2019-03-22 + + Illumina HumanMethylation450 BeadChip (HumanMethylation450_15017482) + GPL13534 + oligonucleotide beads + commercial + Homo sapiens + Illumina, Inc. + +See manufacturer's website + + +1 difference between HumanMethylation450_15017482_v.1.1.bpm and HumanMethylation450_15017482_v.1.2.bpm: + +1.1: + +41636384,NEGATIVE,-99,Negative 604 + +1.2: + +41636384,RESTORATION,Green,Restore + + + +ftp://ftp.ncbi.nlm.nih.gov/geo/platforms/GPL13nnn/GPL13534/suppl/GPL13534_450K_Manifest_header_Descriptions.xlsx.gz + + +ftp://ftp.ncbi.nlm.nih.gov/geo/platforms/GPL13nnn/GPL13534/suppl/GPL13534_HumanMethylation450_15017482_v.1.1.bpm.txt.gz + + +ftp://ftp.ncbi.nlm.nih.gov/geo/platforms/GPL13nnn/GPL13534/suppl/GPL13534_HumanMethylation450_15017482_v.1.1.csv.gz + + +ftp://ftp.ncbi.nlm.nih.gov/geo/platforms/GPL13nnn/GPL13534/suppl/GPL13534_HumanMethylation450_15017482_v.1.2.bpm.gz + + + + + ID + + + Name + + + AddressA_ID + + + AlleleA_ProbeSeq + + + AddressB_ID + + + AlleleB_ProbeSeq + + + Infinium_Design_Type + + + Next_Base + + + Color_Channel + + + Forward_Sequence + + + Genome_Build + + + CHR + + + MAPINFO + + + SourceSeq + + + Chromosome_36 + + + Coordinate_36 + + + Strand + + + Probe_SNPs + + + Probe_SNPs_10 + + + Random_Loci + + + Methyl27_Loci + + + UCSC_RefGene_Name + + + UCSC_RefGene_Accession + + + UCSC_RefGene_Group + + + UCSC_CpG_Islands_Name + + + Relation_to_UCSC_CpG_Island + + + Phantom + + + DMR + + + Enhancer + + + HMM_Island + + + Regulatory_Feature_Name + + + Regulatory_Feature_Group + + + DHS + + + RANGE_START + + + RANGE_END + + + RANGE_GB + + + SPOT_ID + + +GPL13534-tbl-1.txt + + + + + + + 2012-12-12 + 2013-01-21 + 2015-03-17 + + Patient genomic DNA from sample 1 + GSM1051525 + genomic + 1 + + PBL + Homo sapiens + +PBL + + +rheumatoid arthritis + + +Patient + + +67 + + +f + + +current + + genomic DNA + +genomic DNA was extracted and purified from PBLs using Qiagen DNeasy Kit according to standard instructions + + + +Standard Illumina Protocol + + + +Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina HumanMethylation450 Beadchip using standard Illumina protocol + + +Arrays were imaged using Illumina iScan using standard recommended Illumina scanner setting + + +minfi, R + + + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1051nnn/GSM1051525/suppl/GSM1051525_7800246024_R01C01_Grn.idat.gz + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1051nnn/GSM1051525/suppl/GSM1051525_7800246024_R01C01_Red.idat.gz + + + + ID_REF + + + VALUE + Average Beta + + +GSM1051525-tbl-1.txt + + + + + + + 2012-12-12 + 2013-01-21 + 2015-03-17 + + Patient genomic DNA from sample 2 + GSM1051526 + genomic + 1 + + PBL + Homo sapiens + +PBL + + +rheumatoid arthritis + + +Patient + + +49 + + +f + + +current + + genomic DNA + +genomic DNA was extracted and purified from PBLs using Qiagen DNeasy Kit according to standard instructions + + + +Standard Illumina Protocol + + + +Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina HumanMethylation450 Beadchip using standard Illumina protocol + + +Arrays were imaged using Illumina iScan using standard recommended Illumina scanner setting + + +minfi, R + + + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1051nnn/GSM1051526/suppl/GSM1051526_7800246024_R02C01_Grn.idat.gz + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1051nnn/GSM1051526/suppl/GSM1051526_7800246024_R02C01_Red.idat.gz + + + + ID_REF + + + VALUE + Average Beta + + +GSM1051526-tbl-1.txt + + + + + + + 2012-12-12 + 2013-01-21 + 2015-03-17 + + Patient genomic DNA from sample 3 + GSM1051527 + genomic + 1 + + PBL + Homo sapiens + +PBL + + +rheumatoid arthritis + + +Patient + + +53 + + +f + + +ex + + genomic DNA + +genomic DNA was extracted and purified from PBLs using Qiagen DNeasy Kit according to standard instructions + + + +Standard Illumina Protocol + + + +Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina HumanMethylation450 Beadchip using standard Illumina protocol + + +Arrays were imaged using Illumina iScan using standard recommended Illumina scanner setting + + +minfi, R + + + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1051nnn/GSM1051527/suppl/GSM1051527_7800246024_R03C01_Grn.idat.gz + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1051nnn/GSM1051527/suppl/GSM1051527_7800246024_R03C01_Red.idat.gz + + + + ID_REF + + + VALUE + Average Beta + + +GSM1051527-tbl-1.txt + + + + + + + 2012-12-12 + 2013-01-21 + 2015-03-17 + + Patient genomic DNA from sample 4 + GSM1051528 + genomic + 1 + + PBL + Homo sapiens + +PBL + + +rheumatoid arthritis + + +Patient + + +62 + + +f + + +current + + genomic DNA + +genomic DNA was extracted and purified from PBLs using Qiagen DNeasy Kit according to standard instructions + + + +Standard Illumina Protocol + + + +Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina HumanMethylation450 Beadchip using standard Illumina protocol + + +Arrays were imaged using Illumina iScan using standard recommended Illumina scanner setting + + +minfi, R + + + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1051nnn/GSM1051528/suppl/GSM1051528_7800246024_R04C01_Grn.idat.gz + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1051nnn/GSM1051528/suppl/GSM1051528_7800246024_R04C01_Red.idat.gz + + + + ID_REF + + + VALUE + Average Beta + + +GSM1051528-tbl-1.txt + + + + + + + 2012-12-12 + 2013-01-21 + 2015-03-17 + + Patient genomic DNA from sample 5 + GSM1051529 + genomic + 1 + + PBL + Homo sapiens + +PBL + + +rheumatoid arthritis + + +Patient + + +33 + + +f + + +never + + genomic DNA + +genomic DNA was extracted and purified from PBLs using Qiagen DNeasy Kit according to standard instructions + + + +Standard Illumina Protocol + + + +Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina HumanMethylation450 Beadchip using standard Illumina protocol + + +Arrays were imaged using Illumina iScan using standard recommended Illumina scanner setting + + +minfi, R + + + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1051nnn/GSM1051529/suppl/GSM1051529_7800246024_R05C01_Grn.idat.gz + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1051nnn/GSM1051529/suppl/GSM1051529_7800246024_R05C01_Red.idat.gz + + + + ID_REF + + + VALUE + Average Beta + + +GSM1051529-tbl-1.txt + + + + + + + 2012-12-12 + 2013-01-21 + 2015-03-17 + + Patient genomic DNA from sample 6 + GSM1051530 + genomic + 1 + + PBL + Homo sapiens + +PBL + + +rheumatoid arthritis + + +Patient + + +59 + + +f + + +current + + genomic DNA + +genomic DNA was extracted and purified from PBLs using Qiagen DNeasy Kit according to standard instructions + + + +Standard Illumina Protocol + + + +Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina HumanMethylation450 Beadchip using standard Illumina protocol + + +Arrays were imaged using Illumina iScan using standard recommended Illumina scanner setting + + +minfi, R + + + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1051nnn/GSM1051530/suppl/GSM1051530_7800246024_R06C01_Grn.idat.gz + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1051nnn/GSM1051530/suppl/GSM1051530_7800246024_R06C01_Red.idat.gz + + + + ID_REF + + + VALUE + Average Beta + + +GSM1051530-tbl-1.txt + + + + + + + 2012-12-12 + 2013-01-21 + 2015-03-17 + + Patient genomic DNA from sample 7 + GSM1051531 + genomic + 1 + + PBL + Homo sapiens + +PBL + + +rheumatoid arthritis + + +Patient + + +66 + + +f + + +never + + genomic DNA + +genomic DNA was extracted and purified from PBLs using Qiagen DNeasy Kit according to standard instructions + + + +Standard Illumina Protocol + + + +Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina HumanMethylation450 Beadchip using standard Illumina protocol + + +Arrays were imaged using Illumina iScan using standard recommended Illumina scanner setting + + +minfi, R + + + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1051nnn/GSM1051531/suppl/GSM1051531_7800246024_R01C02_Grn.idat.gz + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1051nnn/GSM1051531/suppl/GSM1051531_7800246024_R01C02_Red.idat.gz + + + + ID_REF + + + VALUE + Average Beta + + +GSM1051531-tbl-1.txt + + + + + + + 2012-12-12 + 2013-01-21 + 2015-03-17 + + Patient genomic DNA from sample 8 + GSM1051532 + genomic + 1 + + PBL + Homo sapiens + +PBL + + +rheumatoid arthritis + + +Patient + + +51 + + +f + + +ex + + genomic DNA + +genomic DNA was extracted and purified from PBLs using Qiagen DNeasy Kit according to standard instructions + + + +Standard Illumina Protocol + + + +Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina HumanMethylation450 Beadchip using standard Illumina protocol + + +Arrays were imaged using Illumina iScan using standard recommended Illumina scanner setting + + +minfi, R + + + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1051nnn/GSM1051532/suppl/GSM1051532_7800246024_R02C02_Grn.idat.gz + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1051nnn/GSM1051532/suppl/GSM1051532_7800246024_R02C02_Red.idat.gz + + + + ID_REF + + + VALUE + Average Beta + + +GSM1051532-tbl-1.txt + + + + + + + 2012-12-12 + 2013-01-21 + 2015-03-17 + + Normal genomic DNA from sample 9 + GSM1051533 + genomic + 1 + + PBL + Homo sapiens + +PBL + + +Normal + + +Normal + + +55 + + +m + + +current + + genomic DNA + +genomic DNA was extracted and purified from PBLs using Qiagen DNeasy Kit according to standard instructions + + + +Standard Illumina Protocol + + + +Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina HumanMethylation450 Beadchip using standard Illumina protocol + + +Arrays were imaged using Illumina iScan using standard recommended Illumina scanner setting + + +minfi, R + + + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1051nnn/GSM1051533/suppl/GSM1051533_7800246024_R03C02_Grn.idat.gz + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1051nnn/GSM1051533/suppl/GSM1051533_7800246024_R03C02_Red.idat.gz + + + + ID_REF + + + VALUE + Average Beta + + +GSM1051533-tbl-1.txt + + + + + + + 2012-12-12 + 2013-01-21 + 2015-03-17 + + Normal genomic DNA from sample 10 + GSM1051534 + genomic + 1 + + PBL + Homo sapiens + +PBL + + +Normal + + +Normal + + +37 + + +m + + +never + + genomic DNA + +genomic DNA was extracted and purified from PBLs using Qiagen DNeasy Kit according to standard instructions + + + +Standard Illumina Protocol + + + +Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina HumanMethylation450 Beadchip using standard Illumina protocol + + +Arrays were imaged using Illumina iScan using standard recommended Illumina scanner setting + + +minfi, R + + + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1051nnn/GSM1051534/suppl/GSM1051534_7800246024_R04C02_Grn.idat.gz + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1051nnn/GSM1051534/suppl/GSM1051534_7800246024_R04C02_Red.idat.gz + + + + ID_REF + + + VALUE + Average Beta + + +GSM1051534-tbl-1.txt + + + + + + + 2012-12-12 + 2013-01-21 + 2015-03-17 + + Normal genomic DNA from sample 11 + GSM1051535 + genomic + 1 + + PBL + Homo sapiens + +PBL + + +Normal + + +Normal + + +31 + + +m + + +na + + genomic DNA + +genomic DNA was extracted and purified from PBLs using Qiagen DNeasy Kit according to standard instructions + + + +Standard Illumina Protocol + + + +Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina HumanMethylation450 Beadchip using standard Illumina protocol + + +Arrays were imaged using Illumina iScan using standard recommended Illumina scanner setting + + +minfi, R + + + + 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+ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1052nnn/GSM1052213/suppl/GSM1052213_5730053048_R06C02_Grn.idat.gz + + +ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1052nnn/GSM1052213/suppl/GSM1052213_5730053048_R06C02_Red.idat.gz + + + + ID_REF + + + VALUE + Average Beta + + +GSM1052213-tbl-1.txt + + + + + + + 2012-12-12 + 2013-01-21 + 2022-07-06 + + Differential DNA methylation in Rheumatoid arthritis + GSE42861 + 23334450 + 29921915 + +Genome-wide DNA methylation level was studied to determine whether Rheumatoid arthritis patients (cases) has methylation differences comparing to normal controls in peripheral blood leukocytes (PBLs). +We used Illumina HumanMethylation450 BeadChip array to determine the genome-wide DNA methylation difference in PBLs from Rheumatoid arthritis patients (cases) and normal controls + + +Bisulphite converted DNA from the Rheumatoid arthritis patients (cases) and normal controls were hybridized to the Illumina Illumina HumanMethylation450 BeadChip arrays + + Methylation profiling by array + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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+ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE42nnn/GSE42861/suppl/GSE42861_non-methylated_signal_matrix_SUBSETS.tar.gz + + +ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE42nnn/GSE42861/suppl/GSE42861_processed_methylation_matrix.txt.gz + + +ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE42nnn/GSE42861/suppl/GSE42861_processed_methylation_matrix_SUBSETS.tar.gz + + + + + +