Processed and annotated scRNAseq dataset: CD8+ T cell-mediated immune pressure shapes the diversification of Helicobacter pylori CagA

This repository contains the processed data of the single-cell T cell analysis connected to the manuscript "CD8+ T cell responses targeting CagA derived epitopes on epithelial cells shape human anti Helicobacter pylori immunity" from Koch et al. The data is stored in the AnnData (Scanpy+Scirpy) format and can be reproduced with the notebooks also provided here from the raw data stored under GEO accession number GSE308728. Pre-processing includes: Exclusion of low quality events; Normalization and log data; Hashsolo-based Demultiplexing and elimination of unclear events. Concatination of 10X-reactions; Adding metadata of samples. Clonotype analysis and exclusion of cells that don't show V(D)J expression; Re-assignment of clones that were not identified as one due to secondary chain expression. Correction for hash-misassignment based on clonal and Y-Chromosome-gene analysis. Elimination of non-T cells. Defining CD8 and CD4 T cells, gammadelta, MAIT cells and creating sub-datasets. UMAP and Leiden clustering, celltypist annotation.