Project description

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

Data source

The data used in this repository were provided by the following contributors from the Julius Wolff Institute of Biomechanics and Musculoskeletal Regeneration:

• Dr. Christian H. Bucher
• Ann-Kathrin Mess
• Dr. Katharina Schmidt-Bleek

Contacts and links

• P.I: Georg Duda, Dieter Beule
• CUBI Contact: [Miha Milek] [mailto:milek@bih-charite.de]

Quick Start

For the preprocessing

• Download the FASTQ files from GEO (data owned by Dr. Christian H. Bucher): 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 used to reproduce the figures—based on data owned by Dr. Christian H. Bucher—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