Genomics Data (Dec 2014)

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

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

DOI
https://doi.org/10.1016/j.gdata.2014.10.019
Journal volume & issue
Vol. 2, no. C
pp. 396 – 398

Abstract

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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