Genome structure and organization in mouse CD8 T cells [RNA-seq]
Transcriptomics Dataset
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General Information
AccessionGSE85513
TitleGenome structure and organization in mouse CD8 T cells [RNA-seq]
DescriptionOur experiments aimed to investigate the landscape of enhancers and super-enhancers in nave, effector and memory CD8+ T cells. Here we mapped four histone modification marks and gene expression in naive, effector, and memory cells after viral infection. Our results suggest that the chromatin environment at regulatory DNA sequences in TCM is more permissive than in TN and TE. We further predicted the enhancers and their targets, and constructed transcriptional regulatory networks (TRNs) in three T cell stages. We have identified a highly dynamic repertoire of the enhancers and their targets during CD8 T cell responses, as 77%% of the enhancers and 82%% of the enhancer-promoter interactions are stage-specific. Our results suggest the dynamic change of enhancer activity during cell stage transition leads to TRN rewiring, which explains the expression change of the key factors of T cell function.
Landing Pagehttps://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE85513
RepositoryGene Expression Omnibus
Tools used to analyze the dataset
Dataset Accession
Clustergrammer
Published October 2017
Web-based tool for visualizing and analyzing high-dimensional data as interactive and shareable heatmaps
4645
ARCHS4
Published September 2017
ARCHS4 provides access to gene counts from HiSeq 2000 and HiSeq 2500 platforms for human and mouse experiments from GEO ...
4645
Canned Analyses generated with the dataset
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Tool Name
Interactive heatmap visualization of RNA-seq dataset GSE85513
ARCHS4, Clustergrammer
Highly interactive web-based heatmap visualization of the top 500 most variable genes in t...
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