Scripts and resources for the manuscript titled as Recent evolution of the developing human intestine impacts metabolic and barrier functions (Yu, Kilik, Secchia et al)
DEG_and_DAR: scripts to identified differentially expressed genes (DEGs) and differentially accessible regions (DARs) between human, chimpanzee and mouse.
Data_preprocessing_integration_and_annotation: scripts to construct customized reference for read alignments where applicable, preprocessing, integration and cell type annotation for scRNA-seq and scATAC-seq data.
Deep_learning: scripts to perform sequence variation modeling based on ChromBPNet and the derived models.
Evolutionary_force: scripts and resources for deepest evolutionary ancestry assignment for regulatory elements and calculation of dN/dS.
Plotting: plotting scripts, including script to generate willow plot for visualization of hierarchy of enriched GO terms and parent terms and coverage plots with overlapping genomic signature.
scSTARRseq: scripts to construct customized reference for read alignments, preprocessing and downstream analysis.
Most processed data are accessible via Mendeley Data https://doi.org/10.17632/W4MKDMWVN6 scATAC-seq fragment files are accessible via Zenodo https://doi.org/10.5281/zenodo.15923365 Seurat objects of scATAC-seq data of all PSC derived HIOs/CIOs are accessible via ArrayExpress with accession number E-MTAB-15112
In this manuscript, Stefano Secchia established the workflow for scSTARRseq data analysis, Christiana Fauci established the workflow for deepest evolutionary ancestry assignment; Jasper Janssens established the workflow of deep learning. Qianhui Yu established the other workflows and are responsible for the maintenance.