Extended Data Fig. 1: Related to Fig. 1.
From: Stepwise chromatin and transcriptional acquisition of an intraepithelial lymphocyte program
a–k, iFoxp3TomThPOKGFP mice were treated with tamoxifen for 10 weeks, and Tomato– and Tomato+ CD4+ T cells from mesenteric lymph nodes (mLN), lamina propria (LP) and intestinal epithelium (IE) were sorted for scRNA-Seq using 10X Genomics platform. Sorted Tomato– (blue gates) and Tomato+ (red gates) cells were pooled in a 2:1 ratio per tissue, resulting in 3 separate libraries. a, b, CD4+ T cells from mLN, LP and IE before (a) and after sorting (b). c, Number of sequenced genes (left) and RNA molecules (middle) per cluster and percent of mitochondrial DNA (right) per library. d, Top expressed genes per UMAP cluster. Circle size represents proportion of cells per cluster expressing the indicated gene and color represents expression level. e, Expression levels of the motility signature among all sequenced cells. f, Expression levels of Sell (top), Klf2 (middle), and Ccr7 (bottom) of cells from indicated tissues. g, tdTomato gene expression in 6,668 sequenced cells. h,i, Expression levels of Th1 signature (h) and Cd8a (i) among all sequenced cells. j, Expression levels of indicated genes among IE clusters. k, Expression heatmap of selected genes in pre-IEL clusters.
