Whole transcriptome analysis for T cell receptor-affinity and IRF4-regulated clonal expansion of T cells
- Author(s)
- Shi, Wei; Man, Kevin; Smyth, Gordon K; Nutt, Stephen L; Kallies, Axel;
- Journal Title
- Genomics Data
- Publication Type
- Journal Article
- 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).
- Publisher
- Elsevier
- Keywords
- IRF4; RNA-sequencing analysis; TCR-affinity; T cells; Clonal expansion
- Research Division(s)
- Bioinformatics; Molecular Immunology
- Publisher's Version
- https://doi.org/http://dx.doi.org/10.1016/j.gdata.2014.10.019
- Open Access at Publisher's Site
http://www.sciencedirect.com/science/article/pii/S2213596014001081- NHMRC Grants
- NHMRC/1023454, NHMRC/1032850, NHMRC/1054618,
- Terms of Use/Rights Notice
- Refer to copyright notice on published article.
Creation Date: 2015-03-12 03:59:02
Last Modified: 2015-03-16 09:19:40