🎉 Welcome to the GitHub repository for our manuscript entitled "Enhanced Chromatin Accessibility Contributes to X-chromosome Dosage Compensation in Mammals" published in Genome Biology.
As a resource to community we provide .loom files that contain UMAP-clustering, cluster annotation, expression and gene regulatory data from datasets analyzed in the manuscript.
Loom files can be downloaded here: GSE153846 using the http links at the bottom of the page. After unzipping, you can browse interactively using SCope platform. In order to browse the datasets, upload loom files by clicking on "Upload new dataset" in the menu on the left-side of SCope website. Uploading may take a few minutes. Successful upload will activate a private, temporary session for the user. Each session expires after 5 days, but can be renewed by re-uploading the loom file.
Standalone SCope apps for macOS and Linux can be downloaded from here.
SCope was developed and is maintained by Aerts lab.
The GEO SuperSeries with all data deposited that relates to the article can be found in GEO under the accession number GSE153847.
The reprogramming smart-seq2 single-cell RNA-seq data have been deposited in GEO under the accession number GSE153846.
The iPSCs (XX/XO) smart-seq2 single-cell RNA-seq data have been deposited in GEO under the accession number GSE184987.
The reprogramming 10X single-cell RNA-seq data have been deposited in GEO under the accession number GSE153845.
The bulk ATAC-seq data have been deposited in GEO under the accession number GSE153844.
Scripts related to the manuscript are available in this GitHub repository in Notebooks directory.