Fig. 4

A high-density matrix induces a transcriptomic program indicative of reduced proliferation and cytotoxic activity. a MA plot illustrating the differentially regulated genes (FDR < 0.01 and fold change > +/− 1.5) between cells cultured in a high-density collagen matrix or a low-density collagen matrix for 2 days. Genes that are upregulated in high-density collagen compared to low-density are shown in red and downregulated genes are shown in blue. b Gene ontology analysis illustrates biological processes most significantly enriched within genes that are upregulated (left panel, red bars) or downregulated (right panel, blue bars) in high density compared to low density. c-e Heatmaps of normalized (Z-score) RNAseq read counts of genes encoding markers of T cell activity (c), Tregs (d), or T cell exhaustion (e). d-e Asterisks indicate significantly regulated genes. f Heatmap of most significantly up- or downregulated TF motifs in high-density vs. low-density collagen