Data from: Sex-determining 3D regulatory hubs revealed by genome spatial auto-correlation analysis

<p>Mammalian sex is determined by&nbsp;opposing networks of ovarian and testicular genes&nbsp;that are well characterized. However, its epigenetic regulation is still largely unknown, thus limiting our understanding of a fundamental process for species propagation.&nbsp;Here we explore the 3D chromatin landscape of sex determination&nbsp;<em>in vivo</em>, using&nbsp;<em>METALoci</em>, a novel genome spatial auto-correlation analysis.</p> <p><strong>Extended Data File 1: Coordinates for HH metaloci in each sample.</strong></p> <p>The&nbsp;EDFile1_H3K27ac_HH_metaloci_per_gene.zip&nbsp;file contains four files named:</p> <ul> <li>XX10.5_H3K27ac_HH_metaloci_per_gene.bed</li> <li>XX13.5_H3K27ac_HH_metaloci_per_gene.bed</li> <li>XY10.5_H3K27ac_HH_metaloci_per_gene.bed</li> <li>XY13.5_H3K27ac_HH_metaloci_per_gene.bed</li> </ul> <p>Each BED file contains the following columns tab separated:</p> <ul> <li>chr&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Chromosome</li> <li>start&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Start coordinates</li> <li>end&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;End coordinates</li> <li>MetaLociBinNumber&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Number of the bin in the METALoci layout</li> <li>GeneSymbol&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Gene symbol</li> </ul> <p>&nbsp;</p> <p><strong>Extended Data File 2: Coordinates bins in METALoci with ATAC-seq accessible peak targeted by TF.</strong></p> <p>The EDFile2_TF_ATAC_ML_Sites.zip file contains four files named:</p> <ul> <li>XX10.5_TF_ATAC_ML_Sites.tsv</li> <li>XX13.5_TF_ATAC_ML_Sites.tsv</li> <li>XY10.5_TF_ATAC_ML_Sites.tsv</li> <li>XY13.5_TF_ATAC_ML_Sites.tsv</li> </ul> <p>Each TSV file contains the following columns tab separated:</p> <ul> <li>chr&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Motif site chromosome&nbsp;</li> <li>start&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Motif site start coordinates&nbsp;</li> <li>end&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Motif site end coordinates</li> <li>bin &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;Hi-C bin number</li> <li>pchr&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;ATAC site chromosome</li> <li>pstart&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;ATAC site start coordinates</li> <li>pend&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;ATAC site end coordinates</li> <li>gene&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Gene symbol</li> </ul>