Whole genome doubling drives oncogenic loss of chromatin segregation (part 1)

Whole genome doubling drives tumorigenesis by loss of chromatin segregation

Ruxandra A. Lambuta, Luca Nanni, Yuanlong Liu, Juan Diaz-Miyar, Arvind Iyer, Daniele Tavernari, Natalya Katanayeva, Giovanni Ciriello and Elisa Oricchio

Supplementary data (part 1)

HOW TO DOWNLOAD

The data is distributed in two Zenodo repositories (part 1 and 2) as a multi-split zip archive.

• Part 1: https://doi.org/10.5281/zenodo.7351767
• Part 2: https://doi.org/10.5281/zenodo.7351776

Please, download both repositories and place both files in the same directory. Then run

zip -F Lambuta_Nanni_et_al_2022.zip --out full.zip
unzip full.zip

to first merge the files together and then decompress the archive.

CHECKSUM

• Lambuta_Nanni_et_al_2022.z01: 437feb02ae5ba29ff80f3702d4f4a3cb
• Lambuta_Nanni_et_al_2022.zip: 25670707142557423881ea5ddc57b0d9

STRUCTURE OF THE REPOSITORY

- chipseq
    - chipseq/peaks: consensus ChIP-seq peaks as computed by MACS3 for each cell line and TF/histone
    - chipseq/signals: bigwig signal files for ChIP-seq experiments for each sample and TF/histone
- hic
    - hic/compartment_domains: bed files containing Calder calls for each Hi-C sample
    - hic/cscores: compartment segregation scores for each genomic position for each sample
    - hic/hicdc
        - hic/hicdc/HiC_DC_p_values.Rdata: HiC-DC signficant interactions in the specified samples.
    - hic/insulation_boundaries: insulation boundaries detected by the insulation score computed on the Hi-C samples
    - hic/insulation_scores: insulation scores computed on the Hi-C samples
    - hic/inter_chromosomal: Inter-chromosomal Hi-C interactions for each sample
    - hic/maps: Hi-C samples in .hic format
    - hic/phasing
        - hic/phasing/all_sample_phasing_stats.xlsx: number of phased interactions for each class (MM, PP, MX, PX, XX, ...)
        - hic/phasing/RPE_TP53_20w0T[1,2,3]_mega_hap[1,2]_2000000bp_coverage.bedGraph: phased Hi-C coverage tracks for RPE TP53-/- 20 weeks post-WGD tumors
- rnaseq
    - rnaseq/rnaseq_gene_tpm.tsv: number of RNA-seq reads mapping to each transcript, for each sample
    - rnaseq/rnaseq_gene_counts.tsv: number of RNA-seq reads mapping to each gene, for each sample
- schic
    - schic/maps: for each sc-hic sample, the interactions at 500Kb resolution
- scRNAseq
    - scRNAseq/differential_expression
        - scRNAseq/differential_expression/diff_genes_with_contextual_info_MAST_fc_0.3_pval_0.001.tsv: differential expression analysis of 20 weeks post-WGD tumors
        - scRNAseq/differential_expression/README.txt: meaning of each column in the differential expression file
    - scRNAseq/expression
        - scRNAseq/expression/RPE_gene_expression.tsv: cell x gene expression matrix calculated by cell-ranger from scRNAseq data
        - scRNAseq/expression/RPE_cells_metadata.tsv: metadata about each cell in scRNAseq data
    - scRNAseq/infercnv
        - scRNAseq/infercnv/RPE_TP53_inVitro: infercnv results in RPE TP53-/- in-vitro samples
            - scRNAseq/infercnv/RPE_TP53_inVitro/cell_info.tsv: metadata about each cell
            - scRNAseq/infercnv/RPE_TP53_inVitro/gene_info.tsv: metadata about each gene
            - scRNAseq/infercnv/RPE_TP53_inVitro/linkage_matrix.npy: cell clustering matrix
            - scRNAseq/infercnv/RPE_TP53_inVitro/raw_data.tsv: residual matrix computed by infer-cnv
        - scRNAseq/infercnv/RPE_TP53_20wTumors: same structure as for RPE_TP53_inVitro, but for RPE TP53-/- 20 weeks post-WGD tumors
    - scRNAseq/scenic
        - scRNAseq/scenic/adj.csv: adjacency matrix of each gene as computed by scenic
        - scRNAseq/scenic/diff_regulon_analysis.tsv: differential regulon analysis between each sample and control
        - scRNAseq/scenic/pyscenic_output_BOTH.csv: for each cell, scores for both positive and negative regulators
        - scRNAseq/scenic/reg_BOTH.csv: informations about regulons and target genes
        - scRNAseq/scenic/thresholds.csv: thresholds computed by scenic
- wgs
    - wgs/copy_numbers
        - wgs/copy_numbers/ControlFREEC_log2_coverage_ratio_10Kb.seg: Log2 coverage ratio between each sample and control, computed from whole-genome sequence
        - wgs/copy_numbers/RPE_cnvs_20wTumors_merged.bed: consensus CNVs for RPE TP53-/- 20 weeks post-WGD tumors
        - wgs/copy_numbers/RPE_filtered_cnvs.seg: detected CNVs by ControlFREEC for each whole-genome sequencing sample
    - wgs/mutations
        - wgs/mutations/RPE_somatic_all.maf: all mutations detected in RPE TP53-/- samples
        - wgs/mutations/RPE_somatic_all_FILTER_PASS.tsv: all mutations detected in RPE TP53-/- samples passing the filtering requirements