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| Status |
Public on Nov 24, 2014 |
| Title |
Transcriptomics and methylomics of human T cells [transcriptome] |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by array
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| 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.
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| 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'.
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| Contributor(s) |
Liu Y |
| Citation(s) |
25404168, 30096133, 29166816, 25898983, 28855511, 35073575 |
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| Submission date |
Apr 07, 2014 |
| Last update date |
Apr 20, 2022 |
| Contact name |
Yongmei Liu |
| E-mail(s) |
[email protected]
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| Organization name |
Wake Forest School of Medicine
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| Street address |
Medical Center Blvd.
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| City |
Winston-Salem |
| State/province |
NC |
| ZIP/Postal code |
27157 |
| Country |
USA |
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| Platforms (1) |
| GPL10558 |
Illumina HumanHT-12 V4.0 expression beadchip |
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| Samples (214)
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| This SubSeries is part of SuperSeries: |
| GSE56047 |
Transcriptomics and methylomics of human monocytes |
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| Relations |
| BioProject |
PRJNA243976 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE56580_RAW.tar |
26.2 Mb |
(http)(custom) |
TAR |
| GSE56580_README.txt |
1.6 Kb |
(ftp)(http) |
TXT |
| GSE56580_non_normalized.txt.gz |
62.3 Mb |
(ftp)(http) |
TXT |
| Processed data included within Sample table |
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