RNAseq identifies distinct gene expression profiles in gBT-I isolated from SPF and GF animals.

Purpose: The aim of this study is to disentangle if microbiota influences the transcriptome of antigen-activated CD8+ T cells. Methods: gBT-I mRNA profiles from SPF and GF mice were generated by deep sequencing, in duplicates, using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. Results: The analysis of RNAseq data of gBT-I from SPF and GF mice lead to 371 differentially expressed genes (FDR < 0.05; fold change >2). GSEA enrichment analysis revealed depletion of memory T cells signatures in gBT-I from GF mice (Sarkar et al., 2008), and underrepresentation of OXPHOS-related genes. Conclusions: Our data shows that microbiota has an impact on the transcriptome of effector CD8+ T cells, in particular their memory and metabolism signature. Overall design: in vitro activated and transferred gBT-I mRNA profiles of SPF and GF mice on d7 were generated by deep sequencing, in duplicate, using Illumina GAIIx.