Project description

The scripts for Tchouto et. al paper on pronounced B cell impairment in adult immune-experienced mice link to article.

Contacts and links

• P.I: Georg Duda, Dieter Beule
• CUBI Contact: [Miha Milek] [mailto:[email protected]]

Quick Start

For the preprocessing

• Download the fastq files from GEO: GSE273792.
• Run under Preprocessing: cellranger
• Run under Pre-processing: the single cell pipeline

For the processing:

Run the scripts under the processing folder to correct for any batch effects and integrate the data

Figures in the publication

The seurat object to reproduce the figures can be downloaded from "zenodo link":

• git clone "repo"
• cd .../Figures
• Add the downloaded seurat objet to the folder Figures/data. To install all the packages that are useful for creating the figures, use the already created environments in Figures/envs
• run Figures/Scripts/fig1.rmd ... Figures/Scripts/fig5.rmd to generate figure 2-6 and supplemental figures of the maunscript. Input data for the figures are found in the folder Figures/data except for fig1a which is in Figures/images/fig1a.svg