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. Please use the Version 3, and for more information please refer to our publication that used these enhancer predictions.