Gene Enhancer Predictions in C2C12 (Mouse Myoblast)

This file contains the complete enhancer prediction output of the analysis done in this study published on Nature Communications:

https://www.nature.com/articles/s41467-025-57758-x

using the Activity by Contact Model following the pipeline described here: https://github.com/broadinstitute/ABC-Enhancer-Gene-Prediction

To be used in this analysis, a genomewide Hi-C interaction matrix was generated with Juicer  v1.6, expression counts for each gene were generated with STAR v2.7.10b and Rsubread v2.8.2, and the sequence alignment maps of ATAC-seq and H3K27ac ChIP-seq were generated with NextGenMap v0.5.5, all using raw sequencing reads downloaded from SRA: Hi-C (SRR16220088), RNA-seq (SRR074113 and SRR074114), ATAC-seq (SRR2999996) and H3K27ac ChIP-seq (SRR358589, SRR358590, and SRR358591).

The chromosome coordinates are of the GRCm38 - mm10 assembly, and the gene IDs are from ENSEMBL annotation.

This research was funded in whole or in part by the Austrian Science Fund (FWF) [P29713-B28, P32512-B and P36503-B] to Roland Foisner and a doctorate program funded by the Austrian Science Fund (FWF) [W1261-B28].

For more information please refer to our publication that used these enhancer predictions titled:

MyoD1 localization at the nuclear periphery is mediated by association of WFS1 with active enhancers