RNA-seq of Tgfbr2-deficient thymic iNKT1 cells

The goal of this study was to identify genes that are regulated by TGF-b-signaling in thymic iNKT1 cells. To specifically target Tgfbr2 deletion to iNKT1 cells we created Tbx21Cre bacterial artifical chromosome transgenic mice with a Rosa26-floxed-stop-YFP reporter and floxed alleles of Tgfbr2 . We examined gene expression by RNA-sequencing in sorted iNKT1 cells (CD1d-Tet-PBS57+ YFP+) from Ctrl (Tbx21Cre; Rosa26-YFP+) and cKO (Tbx21Cre; Rosa26-YFP+; Tgfbr2F/F) mice. Reads were aligned to the mm10 reference genome using STAR v2.5.2. Reads were assigned to genes using the htseq-count tool from HTSeq v 0.6.1 and gene annotations from Ensembl release 78. Differential expression was calculated across 3 independent replicates by EdgeR. We found that TGF-b was required for normal numbers of iNKT1 cells and induced a classic TGF-b gene program in thymic iNKT1 cells but did not regulate expression of Tbx21 (T-bet). Overall design: Expression profiling analysis of RNA from iNKT1 cells isolated from Ctrl (Tbx21Cre; Rosa26-YFP+) and cKO (Tbx21Cre; Rosa26-YFP+; Tgfbr2F/F) mice by RNA-sequencing. 3 independent replicates for each sample.