Whole genome doubling promotes tumorigenesis through loss of chromatin segregation and compartment repositioning (part 2)

Processed data for the paper "Whole genome doubling promotes tumorigenesis through loss of chromatin segregation and compartment repositioning"

PART 2:

Structure of the repository

chipseq.zip

• chipseq/input_normalized: contains bigwig files of ChIP-seq experiments generated in this study. Files are log2 input normalized tracks. The "bw_signals_attributes.txt" file can be used to add metadata to the tracks for visualization in IGV

scRNAseq.zip

• differential_expression: contains the output of the differential expression analysis. A README file is present explaining the meaning of each column in the table

• expression: gene expression matrix (cell x gene) containing normalized expression value. A table containing metadata of each cell (like sample of origin, uuid) is also available

• infercnv: copy numbers inferred by INFERCNV. Linkage matrix providing the clustering output of the infercnv data is also provided.

copy_numbers.zip

• ControlFREEC_log2_coverage_ratio_10Kb.seg: .seg file (to be loaded in IGV) containing coverage log2 fold-change between samples and control as computed by ControlFREEC for the detection of CNVs
• filtered_cnvs.seg: significant CNVs detected by ControlFREEC
• RPE_cnvs_20wTumors_merged.bed: consensus set of CNVs in RPE TP53-/- 20w post-WGD tumors