Extended Data Fig. 1: Subtype and transcriptomic analysis of PDAC-HD samples.
From: Persister cell phenotypes contribute to poor patient outcomes after neoadjuvant chemotherapy in PDAC
a) Bar stat plots showing the number of chemo-naïve and post-CTX samples belonging to a defined AJCC (8th Edition) Stage19 in either the PDAC-HD RNAseq or PDAC-HD IF sample cohorts. Stage (I-IV) and corresponding sample number (n) are shown at the bottom of each plot. A Pearson χ2-test of independence (two-sided) is provided at the top of each plot and P-values from a one sample proportions test are displayed on the top of each bar (two-sided). P-values are not adjusted for multiple testing. b) Heatmap showing Moffitt classification of chemo-naïve PDAC-HD samples using established subtyping schemes. The heatmap is annotated with Bailey, Collisson and Notta subtyping designations and PurIST scores. c) Kaplan Meier survival analysis of chemo-naive PDAC-HD samples stratified by the Bailey, Collisson and Notta subtyping schemes. The number of patients falling into one of the designated subtypes is shown in the ‘Number at risk’ table. Log-rank test (two-sided) P-values are provided for each comparison. Log-rank P-values are not adjusted for multiple correction. d) Bar stat plots showing the number of patient samples belonging to a Moffitt subtype and grouped by AJCC Stage. Stage (I-IV) and corresponding sample number (n) are shown at the bottom of each plot. Separate plots are provided for chemo-naïve and post-CTX samples. As above, a Pearson χ2-test of independence (two-sided) is provided at the top of each plot and P-values from a one sample proportions test (two-sided) are displayed on the top of each bar. P-values are not adjusted for multiple testing. e) WGCNA dendrogram of co-expressed genes showing dissimilarity based on topological overlap and assigned gene module colours. f) Heatmap showing the enrichment of gene programs in chemo-naïve and post-CTX patient samples. Samples are clustered by module eigengene values with higher values (red) associated with increased enrichment and lower values (blue) associated with decreased enrichment of a gene module in a sample. The gene modules presented are all significantly enriched. LCM patient samples were removed from the analysis to provide a direct comparison of chemo-naïve and post-CTX bulk RNAseq samples.
