An integrative single-nucleus multiomic atlas of the human left ventricle identifies gene regulatory network dynamics across development, aging, and disease

An integrative single-nucleus multiomic atlas of the human heart identifies gene regulatory network dynamics across cardiac development, aging, and disease This repository contains the scripts used for the analysis of the human cardiac snRNA-seq, snATAC-seq, and spatial transcriptomic datasets in the manuscript titled "An integrative single-nucleus multiomic atlas of the human heart identifies gene regulatory network dynamics across cardiac development, aging, and disease"). For any questions regarding these scripts, please reach out to william.gao@pennmedicine.upenn.edu. This repository includes several subdirectories. For each subdirectory, there is a README.md file describing the contents of the directory, and the order of the commands used to generate the paper figures. Some of the scripts are run in the command line; others are interactive Jupyter notebooks. To run these notebooks/scripts, there are some R/python libraries that need to be downloaded, which will be indicated in the scripts/notebooks. Because some files are too large, they are not included in this directory, but can be reproduced using the scripts, as described in the README.md files within each directory. These large files include .h5ad (anndata format) objects with snRNA-seq + snATAC-seq + spatial objects, and FASTQ files. For example, for any directories that specify raw data, please download these either from the external links for datasets from other studies, or GEO for the datasets generated in this study. The new samples generated as part of this study (19 snRNA-seq donors, 11 snATAC-seq donors) are deposited as raw FASTQ files in GEO under the accession number GSE290367, and will be released upon manuscript publication. Here is the structure of this directory. The immediate subdirectories are ATAC: the snATAC-seq scripts RNA: includes scRNA-seq analysis (internal_datasets, external_datasets, aggregated_analysis and spatial RNA-seq analysis is spatial_RNA. human_genome: includes information related to gene features in the human genome The corresponding web browser for this multiomic atlas is hosted by UCSC Cell Browser.