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Series GSE58684 Query DataSets for GSE58684
Status Public on Jan 20, 2015
Title Defining CD4 T Cell Memory by the Epigenetic Landscape of CpG DNA Methylation [Affymetrix]
Organism Homo sapiens
Experiment type Expression profiling by array
Summary Memory T cells are primed for rapid responses to antigen; however, the molecular mechanisms responsible for priming remain incompletely defined. CpG methylation in promoters is an epigenetic modification, which regulates gene transcription. Using targeted bisulfite sequencing, we examined methylation of 2100 genes (56,000 CpG) mapped by deep sequencing to T cell activation in human naïve and memory CD4 T cells. 466 CpGs (132 genes) displayed differential methylation between naïve and memory cells. 21 genes exhibited both differential methylation and gene expression before activation, linking promoter DNA methylation states to gene regulation; 6 genes encode proteins closely studied in T cells while 15 genes represent novel targets for further study. 39 genes exhibited reduced methylation in memory cells coupled with increased gene expression with activation compared to naïve cells, revealing specific genes more rapidly expressed in memory compared to naïve cells and potentially regulated by DNA methylation. These findings define a DNA methylation signature unique to memory CD4 T cells and correlated with activation-induced gene expression.
Overall design transcriptome of primary human naïve and memory CD4 T cells at rest and 48 hours post-activation.
Contributor(s) Komori HK, Hart GT, LaMere SA, Chew PV, Salomon DR
Citation(s) 25576597
Submission date Jun 19, 2014
Last update date Nov 08, 2016
Contact name Daniel Salomon
Organization name The Scripps Research Institute
Department Molecular & Experimental Medicine
Lab Salomon
Street address 10550 N Torrey Pines Rd, MEM-241
City La Jolla
State/province CA
ZIP/Postal code 92037
Country USA
Platforms (1)
GPL11532 [HuGene-1_1-st] Affymetrix Human Gene 1.1 ST Array [transcript (gene) version]
Samples (22)
GSM1416908 4922_CD4_Naive_0 [Affymetrix]
GSM1416909 5211_CD4_Naive_0 [Affymetrix]
GSM1416910 5220_CD4_Naive_0 [Affymetrix]
This SubSeries is part of SuperSeries:
GSE59860 Defining CD4 T Cell Memory by the Epigenetic Landscape of CpG DNA Methylation
BioProject PRJNA256917

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
GSE58684_RAW.tar 100.5 Mb (http)(custom) TAR (of CEL)
Processed data included within Sample table

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