Evolution of chromosome arm aberrations in breast cancer through genetic network rewiring
Description
These data correspond to manuscript entitled "Evolution of chromosome arm aberrations in breast cancer through genetic network rewiring" by Kuzmin et al Cell Reports Table S1. TCGA copy number and gene expression analysis, Related to Figure 1. (A) GISTIC2.0 Broad deletion analysis in TCGA basal breast cancer cohort. (B) Differential gene expression of chr4p genes in TCGA basal breast cancer cohort with deletion or copy neutral status of chr4p. (C) GISTIC2.0 Broad deletion analysis in TCGA pancancer cohort. (D) Transcriptome-wide differential gene expression in TCGA basal breast cancer cohort with deletion or copy neutral status of chr4p. (E) Aneuploidy in basal breast cancer with different chr4p copy number states. Aneuploidy score as quantified by Chrom.Arm.SCNA.Level median reported by (Davoli et al)20. Table S2. Phylogenetic reconstruction of basal breast cancer, Related to Figure 2. (A) Phylogenetic reconstruction using bulk WGS data of PT/PDX basal breast cancer cohort. (B) Phylogenetic reconstruction using scDNAseq data of PT/PDX GCRC1735 basal breast cancer. Table S3. Chromosome 4p loss is associated with a proliferative state using inferred copy number from scRNAseq, Related to Figure 3. (A) Gene expression and cell clusters as identified from scRNAseq of normal breast epithelial tissue. (B) Relationship between transcriptional programs and inferred copy number changes using scRNAseq data of GCRC1735 PDX. Table S4. Gene overexpression screen for MCF10A and GCRC1335 PDX-derived cell line, Related to Figure 4. Table S5. miniTurboID screen for C4orf19, Related to Figure 5.