Extended Data Fig. 2: Related to Fig. 2.
From: Stepwise chromatin and transcriptional acquisition of an intraepithelial lymphocyte program
a–d, Foxp3eGFP-Cre-ERT2xRosa26lsl-tdTomatoxZbtb7bGFP(iFoxp3TomThPOKGFP) mice were treated with tamoxifen for 10 weeks, 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– and Tomato+ cells were pooled in a 2:1 ratio per tissue, resulting in 3 separate libraries. a–c, mLN-derived cells were re-clustered into 8 new clusters (0–7). a, Re-clustered mLN cells with number indicating the new clusters, consistent throughout the figure. b, Expression levels of top differentially expressed genes among re-clustered cells. c, Proportion of original UMAP clusters per re-clustered mLN clusters (X-axis), as indicated. Top 3 original UMAP cluster contained within re-clustered mLN indicated in a box. d, Scatter plot of gene expression ranked based on pseudotime principle component 1 (PC1).
