Supplementary Materials
The chromatin accessibility landscape of primary human cancers
M. Ryan Corces, Jeffrey M. Granja, Shadi Shams, Bryan H. Louie, Jose A. Seoane, Wanding Zhou, Tiago C. Silva, Clarice Groeneveld, Christopher K. Wong, Seung Woo Cho, Ansuman T. Satpathy, Maxwell R. Mumbach, Katherine A. Hoadley, A. Gordon Robertson, Nathan C. Sheffield, Ina Felau, Mauro A. A. Castro, Benjamin P. Berman, Louis M. Staudt, Jean C. Zenklusen, Peter W. Laird, Christina Curtis, The Cancer Genome Atlas Analysis Network, William J. Greenleaf, Howard Y. Chang
Materials/Methods, Supplementary Text, Tables, Figures, and/or References
- TCGA Analysis Network Collaborators
- Materials and Methods
- Protocol S1
- Figs. S1 to S8
- Caption for Data S1 to S10
- References
- Cancer types studied, donor characteristics, and sequencing statistics.
- Pan-cancer and breast cancer peak calls.
- Overlap of peaks with Roadmap DNase-seq, peak saturation analysis, and t-SNE positions of all samples.
- Distal binarization analysis and enrichment of motifs in cluster-specific peak sets.
- GWAS and eQTL analyses and overlap with peak-to-gene links.
- TF footprinting analyses and correlation to gene expression.
- Pan-cancer and breast cancer-specific peak-to-gene links and enhancer-to-gene links.
- ELMER and Regulon analyses.
- Peak-to-gene links related to immune response in cancer.
- Integration of ATAC-seq and WGS to identify noncoding mutations.
