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Series GSE31555 Query DataSets for GSE31555
Status Public on Sep 01, 2014
Title Integrating Genomics, Transcriptomics, and T-Cell Biology: An RNA-seq Atlas of the Murine CD4+ Transcriptome
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary CD4+ cells are key regulators of the adaptive immune system and can be classified into two main groups: T helper cells (naive, Th1, Th2 and Th17 cells), and regulatory T cells, iTreg and nTreg cells). We performed mRNA-sequencing on these major CD4+ cell subtypes, and integrated multiple computational methods for analyzing gene/isoform expression, differential expression, and functional annotation. Our primary analysis not only provides evidence for the very high quality of the sequence data, but also reveals novel patterns of read distributions inside and adjacent to genes. We identify 168 novel transcripts, which are differentially expressed in the various CD4+ cell subtypes. Further, we identify a wealth of novel, uniquely differentially expressed 'signature' transcripts for each cell type. nTreg cells have the largest number of these, with 477 signature genes in total, of which 58 are transcription factors. The data is compiled into an easily accessible online database publically available at
Overall design RNA-seq data of Murine CD4+ cells
Contributor(s) Hebenstreit D, Deonarine A, Gu M, Nissen JK, Betz AG, Teichmann SA
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Submission date Aug 20, 2011
Last update date May 15, 2019
Contact name Daniel Hebenstreit
Organization name University of Warwick
Street address Gibbet Hill Rd
City Coventry
ZIP/Postal code CV47AL
Country United Kingdom
Platforms (1)
GPL11002 Illumina Genome Analyzer IIx (Mus musculus)
Samples (9)
GSM783253 Naive_rep1
GSM783254 Naive_rep2
GSM783255 Th1_rep1
SRA SRP007954
BioProject PRJNA145675

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Supplementary file Size Download File type/resource
GSE31555_RAW.tar 6.6 Gb (http)(custom) TAR (of SAM)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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