Data analysis repository for Kulkarni et al, Age-associated changes in lineage composition of the enteric nervous system regulate gut health and disease

BioRxiv version of our manuscript

Analysis of 6month LMMP scRNA

Raw FASTQs, count matrices, and metadata are available at GSE156146. Cell metadata available in cell_clusters_and_metadata.csv

Library generated with 10xv2 chemistry Tissue prepped from longitudinal muscle myenteric plexus (LMMP) from two 6 month mice

Preprocessing to generate counts with kallisto bustools

Scripts in ./preprocessing/ Scripts run in the following order: get_velo_files_mm10_10xv2.R index_build.sh kallisto_bus_pseudoalign.sh bustools.sh

./preprocessing/run_all.sh will run the 4 scripts above. Path to fastqs (in kallisto_bus_pseudoalign.sh) must be correct

Processing from raw UMI counts, QC, dimensionality reduction

./scripts ./data ./results ./plots hold the relevant info Modular functions held in ./scripts/accessory_functions

Scripts to generate figures and supplemental figures are available in ./scripts/figures

Analysis of public datasets

Elmentaite et al: Spliced and unspliced count matrices for mesenchymal subset of the Gut Cell Atlas were obtained from https://www.gutcellatlas.org/

May-Zhang et al: Adult ileal snRNAseq counts matrices et al were obtained from GEO GSE153192