Extended Data Fig. 1: Sorting strategy and quality controls for scATAC-seq data.
From: Divergent clonal differentiation trajectories of T cell exhaustion
(a) Sorting strategy to obtain antigen specific gp33+ and gp33− CD8+ T cells from different organs. (b) Sorting strategy to obtain the main Tex subsets (left). UMAPs of scRNA-seq and scATAC-seq results, originating from the indicated Tex subsets. (c) Bar plot of cell counts from the scRNA-seq samples (top). Stacked bar plot of the phenotypic composition of the indicated scRNA-seq samples (bottom). (d) Quality control of scATAC-seq data. Histogram shows normalized read enrichment on the transcription start sites (TSS) of genes from the indicated samples (top). Density plots depict the cells that passed the TSS enrichment and Log10 unique fragment count threshold. Median TSS enrichment (MTE) is also indicated. (e) Density plots of scATAC-seq data from the main Tex populations depicting the same quality controls as panel (c). (f) UMAP of scATAC-seq data colored by integrated scRNA-seq cluster labels. (g) Heat map of TF motif enrichment at the specific open chromatin regions (OCRs) of the annotated T cell populations (p-values determined by hypergeometric enrichment and adjusted using the Bonferroni correction method).
