Gene Enhancer Predictions in C2C12 (Mouse Myoblast)

<p>This file contains the complete enhancer prediction output of the analysis done in this study published on Nature Communications:</p> <p><a href="https://www.nature.com/articles/s41467-025-57758-x" target="_blank" rel="noopener">https://www.nature.com/articles/s41467-025-57758-x</a></p> <p>using the Activity by Contact Model following the pipeline described here: <a href="https://github.com/broadinstitute/ABC-Enhancer-Gene-Prediction">https://github.com/broadinstitute/ABC-Enhancer-Gene-Prediction</a></p> <p>To be used in this analysis, a genomewide Hi-C interaction matrix was generated with&nbsp;<a>Juicer&nbsp;</a>&nbsp;v1.6, expression counts for each gene were generated with STAR v2.7.10b and&nbsp;<a>Rsubread</a>&nbsp;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&nbsp;<a>SRA</a>: Hi-C (SRR16220088), RNA-seq (SRR074113 and SRR074114),&nbsp;<a>ATAC-seq (SRR2999996) and H3K27ac ChIP-seq (SRR358589, SRR358590, and SRR358591).</a></p> <p><a>The chromosome coordinates are of the GRCm38 - mm10 assembly, and the gene IDs are from ENSEMBL annotation.</a></p> <p>&nbsp;</p> <p>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].</p> <p>&nbsp;</p> <p>For more information please refer to our publication that used these enhancer predictions titled:</p> <p>MyoD1 localization at the nuclear periphery is mediated by association of WFS1 with active enhancers</p>