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本文件包含本研究发表于《自然·通讯》（Nature Communications）的完整增强子预测分析输出结果，对应论文链接为：https://www.nature.com/articles/s41467-025-57758-x。本次分析采用接触活性模型（Activity by Contact Model, ABC），遵循的分析流程来自https://github.com/broadinstitute/ABC-Enhancer-Gene-Prediction。 本分析所需的全基因组Hi-C相互作用矩阵通过Juicer v1.6生成；各基因的表达计数通过STAR v2.7.10b与Rsubread v2.8.2生成；ATAC-seq与H3K27ac ChIP-seq的序列比对文件则通过NextGenMap v0.5.5生成。所有测序数据均来自SRA数据库下载的原始测序读段：Hi-C（SRR16220088）、RNA-seq（SRR074113与SRR074114）、ATAC-seq（SRR2999996）以及H3K27ac ChIP-seq（SRR358589、SRR358590与SRR358591）。 该数据集采用GRCm38（mm10）基因组组装版本的染色体坐标，基因ID源自ENSEMBL注释数据库。 本研究全部或部分由奥地利科学基金（Austrian Science Fund, FWF）项目[P29713-B28、P32512-B及P36503-B]资助给Roland Foisner，同时获得奥地利科学基金（FWF）资助的博士培养项目[W1261-B28]的支持。 如需获取更多信息，请参阅使用本增强子预测结果的研究论文，其标题为：《MyoD1在核周区的定位通过WFS1与活性增强子的关联介导》