Display options
Cite
Shi W, Man K, Smyth GK, et al. Whole transcriptome analysis for T cell receptor-affinity and IRF4-regulated clonal expansion of T cells. Genom Data. 2014;2:396-8doi: 10.1016/j.gdata.2014.10.019.
Shi, W., Man, K., Smyth, G. K., Nutt, S. L., & Kallies, A. (2014). Whole transcriptome analysis for T cell receptor-affinity and IRF4-regulated clonal expansion of T cells. Genomics data, 2396-8. https://doi.org/10.1016/j.gdata.2014.10.019
Shi, Wei, et al. "Whole transcriptome analysis for T cell receptor-affinity and IRF4-regulated clonal expansion of T cells." Genomics data vol. 2 (2014): 396-8. doi: https://doi.org/10.1016/j.gdata.2014.10.019
Shi W, Man K, Smyth GK, Nutt SL, Kallies A. Whole transcriptome analysis for T cell receptor-affinity and IRF4-regulated clonal expansion of T cells. Genom Data. 2014 Nov 01;2:396-8. doi: 10.1016/j.gdata.2014.10.019. eCollection 2014 Dec. PMID: 26484137; PMCID: PMC4536053.
Copy Download .nbib Format: NLM
Share it on

Genom Data. 2014 Nov 01;2:396-8. doi: 10.1016/j.gdata.2014.10.019. eCollection 2014 Dec.

Whole transcriptome analysis for T cell receptor-affinity and IRF4-regulated clonal expansion of T cells.

Genomics data

Wei Shi, Kevin Man, Gordon K Smyth, Stephen L Nutt, Axel Kallies

Affiliations

  1. The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia ; The Department of Computing and Information Systems, University of Melbourne, Parkville, Australia.
  2. The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia ; The Department of Medical Biology, University of Melbourne, Parkville, Australia.
  3. The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia ; The Department of Mathematics and Statistics, University of Melbourne, Parkville, Australia.

PMID: 26484137 PMCID: PMC4536053 DOI: 10.1016/j.gdata.2014.10.019

Abstract

Clonal population expansion of T cells during an immune response is dependent on the affinity of the T cell receptor (TCR) for its antigen [1]. However, there is little understanding of how this process is controlled transcriptionally. We found that the transcription factor IRF4 was induced in a manner dependent on TCR-affinity and was critical for the clonal expansion and maintenance of effector function of antigen-specific CD8(+) T cells. We performed a genome-wide expression profiling experiment using RNA sequencing technology (RNA-seq) to interrogate global expression changes when IRF4 was deleted in CD8(+) T cells activated with either a low or high affinity peptide ligand. This allowed us not only to determine IRF4-dependent transcriptional changes but also to identify transcripts dependent on TCR-affinity [2]. Here we describe in detail the analyses of the RNA-seq data, including quality control, read mapping, quantification, normalization and assessment of differential gene expression. The RNA-seq data can be accessed from Gene Expression Omnibus database (accession number GSE49929).

Keywords: Clonal expansion; IRF4; RNA-sequencing analysis; T cells; TCR-affinity

References

  1. Nucleic Acids Res. 2013 May 1;41(10):e108 - PubMed
  2. Science. 1997 Jan 24;275(5299):540-3 - PubMed
  3. Nature. 2009 Mar 12;458(7235):211-4 - PubMed
  4. Nat Biotechnol. 2014 Sep;32(9):903-14 - PubMed
  5. Genome Biol. 2014 Feb 03;15(2):R29 - PubMed
  6. Genome Biol. 2004;5(10):R80 - PubMed
  7. Stat Appl Genet Mol Biol. 2004;3:Article3 - PubMed
  8. Bioinformatics. 2014 Apr 1;30(7):923-30 - PubMed
  9. Cell. 1994 Jan 14;76(1):17-27 - PubMed
  10. Nat Immunol. 2013 Nov;14(11):1155-65 - PubMed

Publication Types