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Series GSE56581 Query DataSets for GSE56581
Status Public on Nov 24, 2014
Title Transcriptomics and methylomics of human T cells [methylome]
Organism Homo sapiens
Experiment type Methylation profiling by genome tiling array
Summary The MESA Epigenomics and Transcriptomics Study has been launched to investigate potential gene expression regulatory methylation sites in humans by examining the association between CpG methylation and gene expression in purified human monocytes and T cells from a large study population (community-dwelling participants in the Multi-Ethnic Study of Atherosclerosis (MESA)).
The MESA Epigenomics and Transcriptomics Study was funded by a National Heart, Lung and Blood Institute grant (R01HL101250) through the NIH Roadmap Epigenomics Program in 2009.
Overall design Data includes transcriptomic and methylomic data from CD4+ samples, collected from 214 individuals. Peripheral T cells were isolated from blood (Exam 5) with anti-CD4 coated magnetic beads, and the Illumina HumanHT-12 v4 Expression BeadChip and the Illumina HumanMethylation450 BeadChip were used to provide genome-wide coverage of mRNA expression and DNA methylation, respectively. This data enabled us to identifyCpG loci whose degree of methylation was associated with age (age-DMR),and identify age- and expression-associated methylation sites (age-eMS), whose degree of methylation was associated with age and cis-gene expression (+/- 1Mb), after adjusting for other covariates such as race, gender, study site, and sample contaimination with B-cells, monocytes, natural killer cells, and neutrophils.

To estimate residual sample contamination for monocyte data analysis, separate enrichment scores for neutrophils, B cells, T cells, and natural killer cells were calculated and provided as sample characteristics.
The participant race, gender, and study site were provided as 'raceGenderSite variable' which represents a combination of those factors.

A detailed description of each sample characteristics is included in the 'README.txt'.
Contributor(s) Liu Y
Citation(s) 25404168, 30096133, 29166816, 25898983, 28855511, 35073575
Submission date Apr 07, 2014
Last update date Apr 20, 2022
Contact name Yongmei Liu
Organization name Wake Forest School of Medicine
Street address Medical Center Blvd.
City Winston-Salem
State/province NC
ZIP/Postal code 27157
Country USA
Platforms (1)
GPL13534 Illumina HumanMethylation450 BeadChip (HumanMethylation450_15017482)
Samples (214)
GSM1364437 100001_peripheral_CD4 [methylation]
GSM1364438 100004_peripheral_CD4 [methylation]
GSM1364439 100007_peripheral_CD4 [methylation]
This SubSeries is part of SuperSeries:
GSE56047 Transcriptomics and methylomics of human monocytes
BioProject PRJNA243975

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE56581_RAW.tar 183.1 Mb (http)(custom) TAR
GSE56581_README.txt 1.6 Kb (ftp)(http) TXT
GSE56581_methylome_normalized.txt.gz 829.9 Mb (ftp)(http) TXT
GSE56581_methylome_signal_intensities.txt.gz 1.7 Gb (ftp)(http) TXT
Processed data are available on Series record

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