Extended Data Fig. 3: PDAC compressed screen scRNA-seq quality metrics and cNMF modules.
From: Scalable, compressed phenotypic screening using pooled perturbations
a. Scatter plot of the number of cells per perturbation across all pools in each replicate plate. b. Violin plots of the number of UMIs, the number of unique genes, and the percent of genes that are mitochondrial in the compressed screen scRNA-seq datasets. c. Heatmaps visualizing the Pearson correlation across cells for their usage of cNMF gene expression programs. Bolded GEPs are selected as highly variable and annotated as response GEPs. d. Heatmaps visualizing the Pearson correlation across cells for their module scores of cNMF gene expression programs and their module scores for existing gene signatures. e. Top three genes by gene spectra score for the highly variable cNMF modules. f. Violin plot of IL4I1 expression in macrophage subtypes in the Raghavan et al. dataset. Two-sided Mann-Whitney U test without correction was performed to test score differences (Methods). All the box plots indicate 25th percentile at the bottom, median in the middle and 75th percentile at the top. Whiskers are drawn to the farthest datapoints within 1.5* interquartile range from the nearest hinge. Sample sizes: C1Q1+ TAM n = 2063, FCN1+ TAM n = 1963, SPP1+ TAM n = 567. g. UMAP visualizations of all cells from both compressed screens, colored by cNMF module usage. h. UMAP visualizations of all cells from both compressed screens, colored by density of cells from pools containing specific ligands. i. Top: Scatter plot of mean cognate receptor(s) expression (log-normalized) for each screened ligand over control PDAC organoid cells in the compressed scRNA-seq dataset. Bottom: Scatter plot of mean cognate receptor(s) expression (log-normalized) for each screened ligand over primary tumor cells from the matched patient in the Raghavan et al. study. Ligands are ordered by mean expression of receptor(s) in each dataset and ligands with significant (p value< 0.01, one-sided permutation test without correction) effects on identified cNMF GEPs are colored in orange.
