Supplementary Data for Doctoral Thesis: Deep Learning Approaches for an Integrated Study of DNA Sequence, Epigenome and Chromatin Architecture

Supplementary Data for Doctoral Thesis: Deep Learning Approaches for an Integrated Study of DNA Sequence, Epigenome and Chromatin Architecture

Appendix A - lists all datasets used in constructing the chromatin feature compendia for the chromatin feature neural network training sets (deepHaem).

Appendix B - lists all CaptureC validation probes.

ctcf_screen_k562_with_motifs_results.txt.gz - lists the results of the CTCF site in silico insertion screen listing chr start and end pf the CTCF site, nine metrics (only "sum.abs.diff" used in thesis) quantifying the chromatin interaction changes, intersections with CTCF ChIP-seq peak calls and presence, orientation and strength of the motifs as well as a naive integrated motif score.