Extended Data Fig. 3: Cell type composition across untreated and treated pancreatic cancer samples.

a, UMAP showing subsets of vascular, lymphoid, and myeloid cells. b, Proportions of major cell types (from Fig. 2c-d) across untreated and treated tumors with (left) or without (right) malignant cells included. U, untreated; T, treated; b, base 960-plex panel; a, augmented 990-plex panel. c, Comparison of malignant/non-malignant cell numbers in treated and untreated FOVs (untreated: n = 164; treated: n = 136); two-sided Mann-Whitney U test. d, Proportions of major non-malignant cell types in treated and untreated FOVs (untreated: n = 164; treated: n = 136); Benjamini-Hochberg corrected two-sided Mann-Whitney U tests. e, Comparison of silhouette scores between subsetting malignant cells (n = 27,463) into two (CLS and BSL) or three (CLS, BSL, and NRP) subtypes. Two-sided Mann-Whitney U tests. f, Expression of chemokines with a role in neutrophil recruitment (CXCL1/2/3/5/6/8) from CAFs and malignant cells in treated and untreated FOVs (untreated: n = 164; treated: n = 136); Benjamini-Hochberg corrected two-sided Mann-Whitney U tests. For boxplots in panel c-f, the box limits denote the first and third quartiles, with the median shown in the center and whiskers covering data within 1.5× the interquartile range from the box, with diamonds representing outliers.