Population ATAC-seq of in vitro polarized ATAC CD4 T cells

To understand the molecular programs driving Th17 heterogeneity and ATAC CD4 T cell fate, we profiled in vitro polarized non-pathogenic Th17, pathogenic Th17, Th1, and Treg cells using ATAC-seq. We profiled in vitro polarized and in vivo mouse primary ATAC CD4 T cells in the following independent experiments: 1) non-pathogenic and pathogenic Th17 cells harvested polarized from naive ATAC CD4 T cells isolated from Il17-eGFP reporter mice, sorted for GFP+ and all cells (ATAC Il17eGFP); 2) non-pathogenic Th17, pathogenic Th17, Th1, and Treg cells harvested after 72h polarization from naive mouse ATAC CD4 T cells (ATAC CD4_diff); 3) non-pathogenic Th17, pathogenic Th17, and Th1 harvested at ATAC Time points ranging from 0 to 48 hr after polarization from naive mouse ATAC CD4 T cells (ATAC 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 (ATAC EAE); 5) non-pathogenic Th17, pathogenic Th17, and Th1 cells with ATAC Bach2 CRISPR KO vs controls; 6) Th17 cells with ATAC Bach2 overexpression vs controls