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Series GSE48138 Query DataSets for GSE48138
Status Public on Sep 23, 2013
Title Expression and regulation of lincRNAs during T cell development and differentiation
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Although lincRNAs are implicated in regulating gene expression in various tissues, little is known about lincRNA transcriptomes in the T cell lineages. Here we identify 1,524 lincRNAs in 42 T cell samples from early T cell progenitors to terminally differentiated T helper subsets. Our analysis revealed highly dynamic and cell-specific expression patterns of lincRNAs during T cell differentiation. Importantly, these lincRNAs are located in genomic regions enriched for protein-coding genes with immune-regulatory functions. Many of these transcripts are bound and regulated by the key T cell transcription factors, T-bet, GATA3, STAT4 and STAT6. We demonstrate that the lincRNA LincR-Ccr2-5'AS, together with GATA3, is an essential component of a regulatory circuit in Th2-specific gene expression.
Overall design To obtain comprehensive profiles of lincRNA expression during the development and differentiation of T cell lineages, we purified CD4-CD8 double negative (DN) cells (DN1, DN2, DN3 and DN4), double positive (DP) cells (CD4+CD8+CD3low and CD4+CD8intCD69+), single positive (SP) CD4 and CD8 cells, and thymic-derived regulatory T cells (tTreg) from thymi of C57BL/6 mice. Additionally, we obtained Th1, Th2, Th17 and iTreg cells by in vitro differentiation of naïve CD4 T cells for a various length of time in culture (4 hrs, 8 hrs, 12 hrs, 24 hrs, 48 hrs, 72 hrs, 1 week, 2weeks). Total and/or polyadenylated RNAs from these cells was analyzed using RNA-Seq. To understand the regulation of lincRNAs by T cell master regulator T-bet, we compared the transcriptiomes between T-bet deficient Th1 cells and control Th1 cells. We did similar experiments and data analysis for STAT4 (Th1), GATA3 (Th2) and STAT6 (Th2). Finally, to address the funcation of a Th2-specifically expressed lincRNA, lincR-Ccr2-5'AS, we compared the transcriptomes between lincR-Ccr2-5'AS knockdown Th2 cells and control Th2 cells.
Contributor(s) Gangqing H, Qingsong T, Suveena S, Fang Y, Thelma E, Stefan M, Jinfang Z, Keji Z
Citation(s) 24056746
Submission date Jun 20, 2013
Last update date May 15, 2019
Contact name Gangqing Hu
Organization name West Virginia University
Department MicroBiology, Immunology, and Cell Biology
Lab 2072A, HSC North, Floor 2
Street address 64 Medical Center Drive
City Morgantown
State/province West Virginia
ZIP/Postal code 26506-9177
Country USA
Platforms (2)
GPL11002 Illumina Genome Analyzer IIx (Mus musculus)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (122)
GSM1169395 paTh1_4h_r1
GSM1169396 paTh2_4h_r1
GSM1169397 paTh17_4h_r1
BioProject PRJNA208992
SRA SRP026197

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
GSE48138_LincRNA-cluster-coordinates.gtf.gz 27.4 Kb (ftp)(http) GTF
GSE48138_Pooled-cufflinks-spliced-transcripts-from-non-strand-sp-RNASeq.gtf.gz 11.5 Mb (ftp)(http) GTF
GSE48138_Pooled-cufflinks-transcripts-from-non-strand-sp-RNASeq.gtf.gz 14.8 Mb (ftp)(http) GTF
GSE48138_Pooled-sicer-islands-from-polyA-RNASeq.txt.gz 385.1 Kb (ftp)(http) TXT
GSE48138_Pooled-sicer-islands-from-total-RNASeq.txt.gz 556.1 Kb (ftp)(http) TXT
GSE48138_RAW.tar 2.7 Gb (http)(custom) TAR (of BEDGRAPH, GTF, TXT)
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Processed data provided as supplementary file
Raw data are available in SRA
Processed data are available on Series record

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