Fig. 3

Dissociation with collagenase at 37 °C induces a distinct stress response in 23,731 cells from PDX samples that is minimized by dissociation at 6 °C. a The top 40 genes (by log fold change) from the 11,975 identified as significantly differentially expressed between cells digested at 6 °C and 37 °C. b UMAP plots of 23,731 cells colored by digestion temperature (top) then by normalized expression of three key stress response genes (FOS, JUNB, NR4A1) demonstrate a distinct concordance between temperature and induction of the stress gene signature. Expression values are log normalized counts winsorized to [0, 2) then scaled to [0, 1). c Pathway analysis of differentially expressed genes with the MSigDB hallmark gene sets highlights induction of genes involved in NF-κB signaling at 37 °C digestion with 46.5% of 200 genes annotated in the pathway being found in the 512 core gene set