Fig. 3
From: Collagen density regulates the activity of tumor-infiltrating T cells
Distinct transcriptomic signatures in 2D culture and in 3D culture in different collagen densities. a Principal component analysis of each RNAseq replicate of T cells cultured on plastic (2D) or in 1 mg/ml (low density) or 4 mg/ml (high density) collagen matrices for 2 days. b MA plot illustrating the differentially regulated genes (FDR < 0.01 and fold change > +/− 1.5) between cells cultured in a low-density collagen matrix or in regular 2D culture. Genes that are upregulated in low-density collagen compared to 2D are shown in red and downregulated genes are shown in blue. c 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 low density collagen compared to 2D. d-f Heatmaps of normalized (Z-score) RNAseq read counts of genes encoding markers of T cell activity (d), Tregs (e), or T cell exhaustion (f). d-f Asterisks indicate significantly regulated genes