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Anthracyclines induce global changes in cardiomyocyte chromatin accessibility that overlap with cardiovascular disease loci

Authors: E. Renee Matthews, Raodahtullah O. Abodunrin, John D. Hurley, Sayan Paul, Jose A. Gutierrez, Alyssa R. Bogar, Michelle C. Ward

Supplementary Figures 13-21

Code and analysis used for paper:

Immunofluorecence of gamma-H2A.X
Contains macros used to obtain nuclei ROIs and check for positive staining using imageJ.

Quality Checks on Reads and Peaks for ATAC data Also describes how the master peak list was created.

Feature counts matrix analysis

Differential accessibility analysis of ATAC data Incorporates differentially expressed genes from Matthews, et al., 2024.

Integration of TOP2B regions Also does permutation test of adult left ventricle heart ATAC data from ENCSR204PZT, (the ENCF966JZT file) and presents expression data from several genes of interest from later in the paper.

TE enrichment in dataset

Analysis of TSS and CpG islands enrichment

Enrichment of cis Regulatory Elements
Uses data from the SCREEN website

ALL genomic feature enrichment with multiple testing correction

H3K27ac CUT&Tag QC metrics and Differential acetylation analysis

H3K27ac integration with ATAC and RNA data

MEMEsuite xstreme motif enrichment results

GO:BP and KEGG pathway analysis of DEG-associated DARs

Cardiotoxicity associated SNP analysis Utilizes 108 total SNPs obtained from:
Schneider, BP, et al., Genome-Wide Association Study for Anthracycline-Induced Congestive Heart Failure, Clinical Cancer Research, 2017. Link to paper
This data also uses TADs obtained from https://3dgenome.fsm.northwestern.edu/publications.html.
We used the regions generated for Heart, left ventricle data from Leung, et al., Nature, 2015.

GWAS AF, HF, CAD, and IHD SNP analysis Log2 Fold change of regions overlapping AF, HF, CAD, and IHD SNPs

Additional pages of analysis for DAR heatmaps in Supplemental data

Older Analysis pages

Exploratory analysis pages and preprint figures