RNA-seq of in vitro-generated murine T helper 17 cells

T helper (Th) 17 cells form a T cell subset which is crucial to maintain immunity against extracellular bacteria and fungi at epithelial barriers, but Th17 cells are also enriched at sites of inflammation in autoimmune disease. These sites are commonly characterised by adverse environmental conditions which are prone to trigger an ER (endoplasmic reticulum)-stress response. Our lab recently observed that the ER-stress response can be a strong driving force for Th17 cell differentiation. The aim of this RNA-seq project was to characterise the novel Th17 cell population generated by IL-6 and cyclopiazonic acid (CPA)-induced ER stress by transcriptional profiling of ER-stress generated and conventional Th17 cells. For this purpose naïve IL17A-Cre Rosa-RFP CD4 T cells were cultured with a combination of Interleukin 6 with Transforming growth factor (TGF) ß or CPA for three days. Then, RFP-positive Th17 cells from four different experiments were enriched for by FACS sorting. Following RNA isolation using QIAGEN's RNA Mini Plus Kit and rRNA depletion accomplished with the NEBNext® rRNA Depletion Kit, RNA-seq libraries were generated using the undirectional NEBNext® Ultra™ RNA Library Prep Kit for Illumina. The libraries were sequenced as 75bp paired-end reads on a NextSeq 500 sequencer and analysed using QIAGEN's Biomedical Workbench.