This is a public repository containing scripts used in the publication:
Frede A*, Czarnewski P*, Monasterio G* et al. (* co-first authors)
B cell expansion hinders the stomal-epithelium regenerative crosstalk during mucosal healing
Immunity 02 Dec 2022. DOI: https://doi.org/10.1016/j.immuni.2022.11.002
The analysis scripts are available in the code folder and is empty by default.
The data folder is used to host the raw counts and other files used for the analysis.
Some datasets require manual download and should be placed in the corresponding folder. The results folder,
also empty by default, will store the output from analysis performed.
The analysis done herein can be reproduced by installing CONDA and running:
- Clone this repository\
git clone https://github.com/czarnewski/b_cell_in_mucosal_healing.git
- Create and activate the conda environment\
cd b_cell_in_mucosal_healing
conda activate base
conda install -c conda-forge mamba
mamba env create -n b_cell_mh -f env_b_cell_mh.yml
conda activate b_cell_mh
The list of all datasets used in the manuscript are depicted below:
| Technology | Dataset | source publication | Accession no |
|---|---|---|---|
| 10X scRNAseq | B cells, DSS d0 and d14 | this manuscript | GSE163637 |
| 10X scRNAseq | stromal and epithelial, BCD and Ctrl, DSS d14 | this manuscript | GSE163638 |
| bulk-RNAseq | Colon tissue (BCD and Ctrl, DSS d14) | this manuscript | GSE207178 |
| bulk-RNAseq | Colon tissue (DSS d0/2/4/6/7/8/10/12/14) | Czarnewski et al 2019 Nat Commun | GSE131032 |
| 16S sequencing | Microbiota (BCD and Ctrl, DSS d14) | this manuscript | PRJEB54765 |
| 10X Visium | Colon (DSS d0 and. d14) | Parigi et al. 2021 Nat Commun | GSE169749 |
| 10X Visium | Colon (BCD and Ctrl, DSS d14) | this manuscript | GSE190595 |
| 10X scRNAseq | Single cell, colon, human, ulcerative colitis | Smillie et al 2019 Cell | SCP259 |
| 10X scRNAseq | Bone marrow from Tabula Muris | TMC et al 2018 Nature | GSE109774 |