Quantitative Analysis of Follicular Helper T cell Transcriptomes from Wild Type and Apoe-/-

Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goal of this study is to characterize the pathogenic features of follicular helper T cells (TFH cells) generated in atherogenic conditions by NGS-derived transcriptome profiling (RNA-seq). Methods: TFH cell mRNA profiles of 13-week-old wild type (WT) and Apoe knockout (Apoe-/-) mice were generated by deep sequencing, in duplicate, using Invitrogen mirVana miRNA Isolation Kit (Cat#AM1561). The sequence reads that passed quality filters were analyzed by TopHat (version 2.0.13) followed by Cufflinks (version 2.2.0). Results: Using an optimized data analysis workflow, we mapped about 50 million sequence reads per sample to the mouse genome (build mm10) and identified 23997 transcripts in the retinas of WT and Apoe–/– mice with approximately 88% mapping rates. At a setting of greater than two-fold expression changes, p value < 0.05, and false discovery rate (FDR) < 0.1, 211 genes were upregulated and 142 genes were downregulated in TFH cells from Apoe–/–mice compared with those from WT mice. Conclusions: Our study demonstrates detailed transcriptome analysis of TFH cells from WT and Apoe–/–, with biologic replicates, generated by RNA-seq technology. mRNA profiles of follicular T helper cells from wild type and atherogenic mice were generated by deep sequencing, in duplicate, using Illumina Truseq.