Example data for chromatin interaction predictions using deepC.

This archive contains example files, data and models to run deepC predictions of chromatin interactions from DNA sequence, specifically the tutorials and example commands described in the deepC repository.

https://github.com/rschwess/deepC
https://github.com/rschwess/deepHaem

Copies of the deepC and deepHaem cover are included for continuity.

Please see the deepC publication for details:
Schwessinger, R., Gosden, M., Downes, D. et al. DeepC: predicting 3D genome folding using megabase-scale transfer learning. Nat Methods 17, 1118–1124 (2020). https://doi.org/10.1038/s41592-020-0960-3

Human Hi-C is based on Rao, S. S. P. et al. A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell 159, 1665–1680 (2014).

Mouse Hi-C is based on Bonev, B. et al. Multiscale 3D genome rewiring during mouse neural development. Cell 171, 557–572.e24 (2017).

DNase-seq and CTCF ChIP-seq were retrieved from the ENCODE Data portal (https://www.encodeproject.org/) Bernstein, B. E. et al. An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57–74 (2012).