mouseCMS_Scripts

Scripts for regenerating figures in the paper entitled:"Enterocyte-like differentiation defines the metabolic phenotype of CMS3 colorectal cancers and provides a therapeutic vulnerability." Download data from https://www.synapse.org/#!Synapse:syn53040345/ to run the scripts.

Data description:

• organoids.RData: in vitro mouse models generated in this study and available at GSE223323
• invivo.organoids.RData (in vivo mouse models generated in this study and available at GSE270929)
• CellLine.GSE248558.RData (CRC cell lines treated with CPS1 inhibition and untreated controls available at GSE248558)
• Synapse.RData (human gene expression datasets proflied using U133 Plus 2.0 platform collected in the work of Guinney et al.)
• Synapse.High.RData (human gene expression datasets proflied using U133 Plus 2.0 platform collected in the work of Guinney et al. + TCGA CRC samples)
• scRNAseq.colon.GSE125970.RData (single cell data of normal colon collected from GSE125970)
• msigdb.v7.4.symbols.gmt (gene signatures obtained from Broad Institute)
• Synapse.genesets.gmt (gene signatures obtained from work of Guinney et al.)
• jem_20191130_tables2.xlsx (gene signatures of human cell types developed by Wang et al.)
• Haber.Combine.All.xlsx (gene signatures of mouse SI cell types developed by Haber et al.)
• GSE146476_Intestinal-region-specific-Wnt-signalling_gene_counts.txt (count data directly obtained from publicly available data at GSE146476)

Scripts to process raw fastq files available in GEO to count data:

• fastq2count.organoids.GSE223323.txt (GSE223323 and GSE270929)
• fastq2count.cellline.GSE248558.txt (GSE248558)

Scripts to normalize/remove batch effect in count data and their final file names.

In the final files both count data and normalized data are available:

• data.handling.organoids.R --> organoids.RData (GSE223323)
• data.handling.invivo.organoids.R --> invivo.organoids.RData (GSE270929)
• data.handling.cellLine.GSE248558.R --> CellLine.GSE248558.RData (GSE248558)

Scripts for conducted analyses and figures:

Human gene expression datasets:

• Scripts: data.handling.Synapse.R

GSEA in patient samples:

• Scripts: Fig.4C.Synapse.Enterocyte.R, Fig.S4C.GSEA.KRAS.MUTvsWT.R
• Datasets: Synapse.RData, msigdb.v7.4.symbols.gmt

GSEA in CRC cell lines:

• Scripts: Fig.6E.S5A.GSEA.CPS1.Inhibition.R
• Datasets: CellLine.GSE248558.RData, msigdb.v7.4.symbols.gmt, jem_20191130_tables2.xlsx

GSEA in scRNAseq data:

• Scripts: Fig.4B.CellType.Metabolism.R
• Datasets: scRNAseq.colon.GSE125970.RData, msigdb.v7.4.symbols.gmt

GSEA in mouse organoids:

• Scripts: Fig.4A.Genotype.Cell.All.R, Fig.3C.gsplot.cms.R
• Datasets: organoids.RData, Haber.Combine.All.xlsx, Synapse.genesets.gmt, msigdb.v7.4.symbols.gmt

DE analysis in wild type colon and small intestine organoids:

• Scripts: Fig.S2.R
• Datasets: GSE146476_Intestinal-region-specific-Wnt-signalling_gene_counts.txt, organoids.RData

CMS classifier for mouse models:

• Scripts: First.CMS.Stratification.R, Training.Mouse.Classifier.R, Fig.S3DE.Classifier.Coef.R, https://github.com/atorang/mouseCMS
• Datasets: organoids.RData, Synapse.genesets.gmt, msigdb.v7.4.symbols.gmt

CMS stratification of mouse organoids:

• Scripts: Fig.3B.classification.R, https://github.com/atorang/mouseCMS
• Datasets: organoids.RData

Metabolic and enterocyte scoring:

• Scripts: Fig.4D.Met.Ent.Scores.R
• Datasets: Synapse.High.RData, msigdb.v7.4.symbols.gmt

ssGSEA:

• Scripts: Fig.S4B.ssGSEA.organoids.R, Fig.6B.ssGSEA.CellLines.R
• Datasets: organoids.RData, Synapse.genesets.gmt, msigdb.v7.4.symbols.gmt