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

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  • TCGA Analysis Network Collaborators
  • Materials and Methods
  • Protocol S1
  • Figs. S1 to S8
  • Caption for Data S1 to S10
  • References
Data S1
Cancer types studied, donor characteristics, and sequencing statistics.
Data S2
Pan-cancer and breast cancer peak calls.
Data S3
Overlap of peaks with Roadmap DNase-seq, peak saturation analysis, and t-SNE positions of all samples.
Data S4
Distal binarization analysis and enrichment of motifs in cluster-specific peak sets.
Data S5
GWAS and eQTL analyses and overlap with peak-to-gene links.
Data S6
TF footprinting analyses and correlation to gene expression.
Data S7
Pan-cancer and breast cancer-specific peak-to-gene links and enhancer-to-gene links.
Data S8
ELMER and Regulon analyses.
Data S9
Peak-to-gene links related to immune response in cancer.
Data S10
Integration of ATAC-seq and WGS to identify noncoding mutations.