Code to reproduce scRNA-seq results contained in

Sacirbegovic F, Günther M, Greco A, Zhao D, Wang X, Zhou M, Rosenberger S, Oberbarnscheidt MH, Held W, McNiff J, Jain D, Höfer T, Shlomchik WD. Graft-versus-host disease is locally maintained in target tissues by resident progenitor-like T cells. Immunity. 2023 Feb 14;56(2):369-385.e6. doi: 10.1016/j.immuni.2023.01.003. Epub 2023 Jan 30. PMID: 36720219.

The repository contains two folders: code and data.

• Scripts in code/ are numbered based on the order of execution. The working directory for running the scripts is the one containing both code/ and data/ . In order to run the analysis, please generate count matrices for GEX and HTO matrices using standard Seurat::Read10X or Bioconductor equivalent DropletUtils::read10xCounts pipeline.
• Data needs to be downloaded from GEO under the accession number GSE207485. In the data/other/ folder, you’ll find a list of useful files for the analysis:
  • Information about the R version and relative libraries, in data/other/renv.lock . Instructions on how to use this file and recreate the R environment are here
  • scGSEA_cycle file contain cell cycle estimated as explained in this paper
  • dissociation_genes.txt contains a list of genes associated with dissociation, they are used in the analysis to remove poor quality cells from the skin

Scripts used to generate figures

Figure	Content	script
6A	global UMAP by tissue (colon not split)	02_preprocess_all_tissues
S6A	global UMAP by proliferation	02_preprocess_all_tissues
S6B	global UMAP split by tissue (colon not split)	02_preprocess_all_tissues
S6C	Heatmap: cluster vs tissue (colon not split)	02_preprocess_all_tissues
6B	Heatmap: tissue markers	03.figure_tissue_markers
6C	UMAP of tissues clustered	05.figure_6c_tissues
6D	Proliferation vs Tcf7	03.figure_tcf_proliferation
6E	Markers overlap	06_markers_overlap
6F	Markers overlap (p-value)	06_markers_overlap
S6D	LPL-IEL annotation (Small intestine) - UMAP + clusters	03_annotate_LP_IEL
S6E	LPL-IEL annotation (Colon) - UMAP + clusters	03_annotate_LP_IEL
S6F	global UMAP by tissue (colon split)	03_annotate_LP_IEL
S6G	Heatmap: cluster vs tissue (colon split)	03.figure_tissue_markers