Whole genome doubling drives oncogenic loss of chromatin segregation (part 2)
Year: 2022
Type: article
Abstract: 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
Authors: Lambuta, Ruxandra A., Nanni, Luca, Yuanlong Liu, Diaz-Miyar, Juan, Iyer, Arvind, Tavernari, Daniele, Katanayeva, Natalya, Ciriello, Giovanni, Oricchio, Elisa
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: green
OpenAlex ID: W6931379651