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| 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
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| 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.
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| 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.
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| Contributor(s) |
Gangqing H, Qingsong T, Suveena S, Fang Y, Thelma E, Stefan M, Jinfang Z, Keji Z |
| Citation(s) |
24056746 |
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| Submission date |
Jun 20, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Gangqing Hu |
| E-mail(s) |
michael.hu@hsc.wvu.edu
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| Organization name |
West Virginia University
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| Department |
MicroBiology, Immunology, and Cell Biology
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| Lab |
2072A, HSC North, Floor 2
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| Street address |
64 Medical Center Drive
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| City |
Morgantown |
| State/province |
West Virginia |
| ZIP/Postal code |
26506-9177 |
| Country |
USA |
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| Platforms (2) |
| GPL11002 |
Illumina Genome Analyzer IIx (Mus musculus) |
| GPL13112 |
Illumina HiSeq 2000 (Mus musculus) |
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| Samples (122)
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| Relations |
| BioProject |
PRJNA208992 |
| SRA |
SRP026197 |
| 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) |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
| Processed data are available on Series record |
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