Data from: Sex-determining 3D regulatory hubs revealed by genome spatial auto-correlation analysis
Authors/Creators
- 1. MDC
- 2. CNAG-CRG
Description
Mammalian sex is determined by opposing networks of ovarian and testicular genes that are well characterized. However, its epigenetic regulation is still largely unknown, thus limiting our understanding of a fundamental process for species propagation. Here we explore the 3D chromatin landscape of sex determination in vivo, using METALoci, a novel genome spatial auto-correlation analysis.
Extended Data File 1: Coordinates for HH metaloci in each sample.
The EDFile1_H3K27ac_HH_metaloci_per_gene.zip file contains four files named:
- XX10.5_H3K27ac_HH_metaloci_per_gene.bed
- XX13.5_H3K27ac_HH_metaloci_per_gene.bed
- XY10.5_H3K27ac_HH_metaloci_per_gene.bed
- XY13.5_H3K27ac_HH_metaloci_per_gene.bed
Each BED file contains the following columns tab separated:
- chr Chromosome
- start Start coordinates
- end End coordinates
- MetaLociBinNumber Number of the bin in the METALoci layout
- GeneSymbol Gene symbol
Extended Data File 2: Coordinates for all TFs assessed by TOBIAS to bind an ATAC-seq accessible peak within a metaloci in each sample.
The TEDFile2_TF_ATAC_ML_Sites.zip file contains four files named:
- XX10.5_TF_ATAC_ML_Sites.tsv
- XX13.5_TF_ATAC_ML_Sites.tsv
- XY10.5_TF_ATAC_ML_Sites.tsv
- XY13.5_TF_ATAC_ML_Sites.tsv
Each TSV file contains the following columns tab separated:
- chr Motif site chromosome
- start Motif site start coordinates
- end Motif site end coordinates
- tfscore TOBIAS transcription factor score
- strand Motif site strand
- pchr ATAC site chromosome
- pstart ATAC site start coordinates
- pend ATAC site end coordinates
- samplescore TOBIAS sample score
- bchr METALoci chromosome
- bstart METALoci start coordinates
- bend METALoci end coordinates
- bin METALoci bin
- gene Gene symbol
- tf Transcription Factor
- motif Motif id
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