GDG_2025 data supplement

This repository contains data for the manuscript "Unexpected XIST Expression in Male Hearts Associates with Disease."

The files are generated by notebooks in the GitHub repository.

The human folder contains pseudobulks from human data. The files gg_250327_heart_celltype_psbulks.p and gg_250821_heart_data_split_by_xist.p are pickled Python dicts containing AnnData structures. The files gg_250821_female_glia_deseq.anndata.p and gg_250821_male_glia_deseq.anndata.p are pickled AnnData structures.

The bam folder contains are XIST-localized aligned reads from Larson and Chin.

The files in de_tables are tables of differential expression for various PyDESeq2 contrasts.

The files in nonhuman are scVI-clustered macaque, mouse, and pig heart datasets. 

The genome folder contains a gtf file with putative M. mulatta XIST lifted over to M. fascicularis, as well as the putative S. scrofa XIST lifted over from RefSeq 10.2 to Ensemble 11.1.

The  longread folder contains data related to the Pan et al. long-read dataset: disclosed counts and cell identities (from GSE288222 and the supplements of the original publication), kb-quantified and scVI-clustered data, a small genome reference immediately surrounding the XIST/TSIX pair, and reads that align in this region in a variety of formats.