Boles_et-al_DSS_time-series

A leaky gut dysregulates gene networks in the brain associated with immune activation, oxidative stress, and myelination in a mouse model of colitis (bioRxiv) Jake Sondag Boles1, Maeve E. Krueger, Janna E. Jernigan, Cassandra L. Cole, Noelle K. Neighbarger, Oihane Uriarte Huarte, & Malú Gámez Tansey. 1 Analysis lead and contact ([email protected]) Data: Original bulk RNA-sequencing data: This can be accessed via the NCBI GEO (GSE239820). We have included: Raw FASTQ files from paired-end reads (two files per sample) Raw transcript counts after read mapping and counting. These data are in "raw_counts.csv". The key can be found in the metadata at the GEO entry page. They will also be scraped from the link in 01_counts_cleaning.R for both colon and brain pipelines. Processed and normalized counts after the removal of low-quality genes and samples. These are the data used to arrive at the conclusions in the paper above. These data are separated into colon ("colon_clean_VST_counts.csv") and brain ("brain_clean_VST_counts.csv"). The sample key can be found in the metadata at the GEO entry page. This repository contains the code that was used to generate these cleaned counts from the raw counts.