Next Generation Sequencing Facilitates analysis of IL17 EGFP positive and negative cells from small intestine (SI) lamina propia (lp) genes expression

We performed the bulk RNA seq on IL17 EGFP positive and negative cells from small intestine (SI) lamina propia (lp) of antibiotic treated XBP1?IEC mice and found the different genes expression in the setting of IEC ER stress induced Th17 positive and negative cells Overall design: Two hundred Il17a-egfp positive (CD45+TCRß+CD4+ Il17a-egfp+) or negative T cells (CD45+TCRß+CD4+ Il17a-egfp-) of antibiotic treated Xbp1Two hundred Il17a-egfp positive (CD45+TCRß+CD4+ Il17a-egfp+) or negative T cells (CD45+TCRß+CD4+ Il17a-egfp-) of antibiotic treated Xbp1?IEC mice were sorted by flow cytometry and used as input material. The RNA extraction and cDNA was generated following the smart-seq2 protocol as previous described(Picelli, Faridani et al; Nat Protoc ;2014). The library preparation and sequencing were performed at the Biopolymers Facility at the Harvard Medical School on Illumina NextSeq 500 sequencer to generate 75-bp paired-end reads.