This is the repository for scripts and resources for the analysis and figure production of the manuscript titled as "Modeling host-microbe interactions in immunocompetent engineered human gut tissues" (López-Sandoval, Harter, Yu et al)
The accession number for the fastq files of non-sorted scRNA-seq and scMultiome data reported in this paper is ArrayExpress:E-MTAB-16821. The raw and processed sorted infection scRNA-seq and VASA-seq data could be accessed via E-MTAB-17487 and E-MTAB-17486.
Additional supporting materials, including processed single cell data with cell type annotation, statistically significant differentially accessible chromatin regions upon S.Tm infection and TF-target regulomes inferred by Pando based on the S.Tm infection dataset are available at Mendeley Data doi: 10.17632/3jpvw4t4gr. Fragment files of scMultiome are available at Mendeley Data doi: 10.17632/8pt6w6fc7m.
Public adult intestine multi-region scRNA-seq datasets were retrieved from an interactive website of the Space-Time Gut Cell Atlas (https://www.gutcellatlas.org/) {PMID: 34497389}, ArrayExpress (E-MTAB-10187) {PMID: 34019796} and Gene Expression Omnibus (GSE185224) {PMID: 35176508}.
Modeling host-microbe interactions in immunocompetent engineered human gut tissues, López-Sandoval, Harter, Yu et al, bioRxiv, 2025. doi:10.1101/2025.05.02.651468