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

Whole genome doubling promotes tumorigenesis through loss of chromatin segregation and compartment repositioning

PART 2

hic_maps_K562.zip: Hi-C maps (.hic format) of K562 samples

hic_features.zip

• hic_features/compartment_domains: contains, for each of the hic matrices, the compartment domains imputed by Calder in BED format
• hic_features/compartment_domain_boundaries: boundaries between adjacent compartment domains in Control and WGD samples from RPE TP53-/- cell line
• hic_features/compartment_scores: for each compartment domain in Control and WGD samples from RPE TP53-/- cell line it reports its C-score
• hic_features/insulation_scores: for each of the Hi-C matrices, the insulation scores computed at 50 Kb resolution, in bigwig format
• ihic_features/nsulation_boundaries: TAD boundaries detected using the insulation score, for each Hi-C sample

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

mutations.zip

• RPE_somatic_all.maf: MAF file of mutations detected by Mutect2 on RPE TP53-/- sample
• RPE_somatic_all_FILTER_PASS.tsv: mutations passing the quality filters