hongduosun / eosinophils_scrnaseq

Codes for analyses in the titled "Active eosinophils regulate host defense and immune responses during intestinal inflammation"

Eosinophils_scRNASeq

This is a resource for the article: "Active eosinophils regulate host defense and immune responses in colitis", from the Arnold and Moor labs. It includes all code used for the analysis of single cell RNA sequencing data, bulk RNA sequencing data and genome wide CRISPR inhibition screening data.

1. Packages and functions for the scRNASeq analysis
2. Preprocessing of scRNASeq data (after count matrix generation on the Igor SB Genomics Platform)
3. Analysis of the steadystate scRNASeq datasets (Fig.1)
4. Analysis of the H.pylori and C.Rodentium infection scRNASeq datasets (Fig.2)
5. Integration of DSS dataseta (Schwarzfischer et al, in revision) and plotting of bulk DSS data from https://pubmed.ncbi.nlm.nih.gov/31253778/ (Fig.2)
6. Analysis of CRISPR-i screen, scRNASeq of colonic eosinophils upon in vivo INFg neutralization and bulk RNASeq of conditioned BM-eos (Fig.3 and 4)

The publication can be accessed from here: https://www.nature.com/articles/s41586-022-05628-7

The scRNAseq datasets are available here: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18200 (fastqs) and here https://doi.org/10.5281/zenodo.10225349 (processed R objects).