Additional file 4: of Harnessing single-cell genomics to improve the physiological fidelity of organoid-derived cell types

Figure S2. Proteomic pipeline, sample-to-sample comparison, and insights from the in vitro PC proteome. A Schematic of proteomic analysis for samples: culture, collection, lysis, reduction and alkylation, proteolytic digestion, labeling of peptides with isobaric mass tag reagents (Tandem Mass Tags, TMT10-plex; Thermo), off-line fractionation by basic reverse phase chromatography, analysis of fractions by LC-MS/MS, identification of peptides and proteins using Spectrum Mill software (Agilent), and statistical analysis of the resulting data (moderated t test) to identify confidently differential proteins. B Proteome sample correlation between all biological (n = 2) and technical (n = 2/biological) replicates. C ENR + CD-enriched proteins are well-annotated in the gene ontology (GO) database and show robust enrichment for functions and compartments of secretory cells determined by fold enrichment vs. FDR using DAVID. D ENR-enriched proteins are well annotated in the GO database and show enrichment for functions and compartments of transcriptionally and translationally active cells determined by fold enrichment vs. FDR using DAVID. e GSEA enrichment map of transcription factors linked to ENR + CD- and ENR-enriched proteins following a moderately conservative cutoff of p < 0.005, FDR < 0.075, and overlap coefficient of 0.2. (PDF 483 kb