In this study, we analyze the effect of a three-shot vaccination regime against SARS-CoV-2 on the human immune response repertoire. This repository contains the single-cell analysis of T cell receptor (TCR), Gene expression, Surface Proteins (Antibody Captured), and dextramer staining as well as reverse phenotyping.
- The raw sequencing data can be downloaded from GEO GSE249998 for the dextramer dataset and GSE310441 and GSE310442 for the reverse phenotyping dataset.
- The processed and annotated data can be downloaded from Zenodo (???) and stored as
./data/dex/02_dex_annotated_cd4.h5ad,./data/dex/02_dex_annotated.h5ad,./data/dex/02_dex_annotated_cd8.h5ad,./data/reverse_phenotyping/02_rv_annotated_cd4.h5ad,./data/reverse_phenotyping/02_rv_annotated.h5ad,./data/combined/02_joint_annotated_cd4.h5ad(entry point notebooks 03)
Additionally, we use the following external resources (not provided by us, store in ./data/scores/):
- Genes for various T cell scores by Szabo et al. (Nature Communications, 2019) (https://static-content.springer.com/esm/art%3A10.1038%2Fs41467-019-12464-3/MediaObjects/41467_2019_12464_MOESM7_ESM.xlsx)
- Genes for Cell Scores by Meckiff et al. (Cell, 2020) (https://ars.els-cdn.com/content/image/1-s2.0-S0092867420313076-mmc3.xlsx)
To recreate the results of the paper:
git clone https://github.com/SchubertLab/CovidVac_CD4.git
cd CovidVac_CD4
conda env create -f requirements.yml
Following, the notebooks in analysis/01_reverse_phenotyping/, analysis/02_dextramer/, and analysis/03_combined/ must be run (ideally in this order). Note, that there are issues with reproducing UMAPs across different machines, even when the same seeds and package versions are used. Results might therefore look slightly different. To fully reproduce the paper results, use the annotated data.
If you refer to this work, please consider citing the following paper:
TODO upon publication