Population RNA-seq of in vitro polarized CD4 T cells

To understand the molecular programs driving Th17 heterogeneity and CD4 T cell fate, we profiled in vitro polarized non-pathogenic Th17, pathogenic Th17, Th1, and Treg cells using RNA-seq. Overall design: We profiled in vitro polarized and in vivo mouse primary CD4 T cells in the following independent experiments: 1) non-pathogenic and pathogenic Th17 cells harvested polarized from naïve CD4 T cells isolated from Il17-eGFP reporter mice, sorted for GFP+ and all cells (Il17eGFP); 2) non-pathogenic Th17, pathogenic Th17, Th1, and Treg cells harvested after 72h polarization from naive mouse CD4 T cells (CD4_diff); 3) non-pathogenic Th17, pathogenic Th17, and Th1 harvested at time points ranging from 0 to 48 hr after polarization from naive mouse CD4 T cells (Time_course); 4) Il17-expressing Th17 cells from the draining lymph node and central nervous system of mice at the peak of experimental autoimmune encephalomyelitis response (EAE)