Extended Data Fig. 3: High quality scRNA-seq and ATAC-seq permits interrogation of transcription factor binding within exhaustion-specific enhancer.
From: Epigenetic tuning of PD-1 expression improves exhausted T cell function and viral control
(a) Violin plots of quality control metrics after filtering, by sample (genotype and replicate, n = 6 samples total). Left: number of reads per cell, center: number of unique reads per cell, right: percent mitochondrial reads per cell. (b) UMAP projection of cells separated by sample identity. Top: replicate 1, bottom: replicate 2; left: EnhDel, center: Pdcd1-KO, right: WT. (c) Top 25 differential genes (rows), organized by cluster, with color denoting scaled normalized expression in each cell (columns). (d) Exhausted subset signatures (left: progenitor-exhausted signature, middle: transitory-exhausted signature, right: terminally-exhausted signature) scored across all cells in each cluster (top row: Prog., second from top: Eff.-like, middle: Trans., second from bottom: Term., bottom: Div.). (e) TSS enrichment curves showing chromatin accessibility averaged across all TSS sites genome wide, by sorted genotype (left: EnhDel; center: Pdcd1-KO; right: WT) and exhausted subset (top: Prog., bottom: Term.). (f) Replicate concordance for ATAC-seq samples by sorted genotype (left: EnhDel, center: Pdcd1-KO, right: WT) and exhausted subset (top: Prog., bottom: Term.). (g) Venn diagram of the transcription factor motif sites within the exhaustion-associated Pdcd1 enhancer bound by the transcription factor as predicted by TOBIAS analysis of WT ATAC-seq tracks. Percentage and number for progenitor exhausted (left), terminally-exhausted (right), and both (center) displayed. Subset of predicted transcription factors bound in both Prog. and Term. listed. (h) Significance (p-value by Wilcoxon rank sum) of differential expression between WT Prog. and Term. cells by scRNA-seq for progenitor-specific predicted bound transcription factors (top), transcription factors predicted to be bound in both subsets (middle), and transcription factors without motifs in the exhaustion-associated Pdcd1 enhancer. Positive values denote higher expression in progenitor-exhausted cluster, negative values denote higher expression in terminal-exhausted cluster. Center line denotes mean and error bars denote standard deviation.
