Oliveira et al. 2024 Processed Data

This is the collection of processed data for the manuscript "Epigenetic heritability of cell plasticity drives cancer drug resistance through one-to-many genotype to phenotype mapping", the accompanyng code is hosted on GitHub at this link, this data is sufficient to regenerate all the figures.

There are 3 cohorts of organoids analyzed in the paper (more details in the manuscript): MSI, MSS batch 1 and MSS batch 2. All the subdirectories are divided accordingly The directory is structured in 6 main branches:

archetype_params: this folder contains results of the archetypal analysis decomposition for RNA and ATAC of each cohort, they are either in tabular format or as MIDAA objects (more info here) 

archr_objects: this folder contains the zipped archR projects for each of the cohort, beware that archR projects have absolute paths, so you might have to change the internal links to make them work, I know the authors of archR are trying to put the possibilities of relative paths. In case you know of a better way to share archR objects please let me know.

barcode_tables: this stores the barcode quantification tables for each cohort: in the MSI and MSS batch 2 case both floating and cellular barcodes are together in the same table (novaseq...etc), while for MSS batch 1 they are dividend into cell and floating tables

copy_number_data: This folder contains the segmentation and the absolute copy number values obtained from lpWGS for each organoid line and treatment combination, and scDNA-seq results for MSI and MSS batch 2 for Parental and CENPE+MPS1 inh 

other_data: this folder contains various processed data. 

congas_fit_final.rds: contains the final fit of CONGAS  on MSS batch1 multiomemedicc_input_congas_final_tree.new: this contains the tree inferred by MEDICC2 on CONGAS outputpalette_MSI.rds: this contains the color palette for MSI organoidpalette_enriched_100.rds: this contains the color paletter for MSS organoid

AKT_mutect2.ann.all_plugins.VEP.tsv: this contains the mutect calls for SNVs in the AKT Trametinib resistant vs Parental Population of MSS batch 1 deep WGSAZD_TRAM_vs_AKT_blood.cnvs.txt: this contains the ASCAT inferred CNV in the AKT Trametinib resistant vs Parental Population of MSS batch 1 deep WGS

seurat_objects: This folder contains the seurat objects for scRNA-seq data