Complement activation induces excessive T cell cytotoxicity in severe COVID-19: Analysis of single cell data cohort 1 (Berlin).

This repository contains the R Markdown files with the analysis of CyTOF and scRNA-seq data corresponding to cohort 1 (Berlin) analysed in Georg et al. 2021 "Complement activation induces excessive T cell cytotoxicity in severe COVID-19". Additionally, here we include the necessary CyTOF data to reproduce this analysis.

CyTOF data:

• The debarcoded fcs files (before batch-correction) can be found in https://flowrepository.org/id/FR-FCM-Z4P5. \
• Here you can find the necessary data to reproduce the analysis (cytof_analysis.Rmd, cytof_analysis.html):
  • data_norm_all.csv: single-cell protein expression data (after batch-normalization and in linear scale).
  • data_Tcells_annotated.csv: single-cell protein expression of gated T cells with cluster annotation.
  • phenograph_CD4_k30.csv, phenograph_CD8_k30.csv, phenograph_TCRgd_k30.csv: output from Louvain Clustering computed with PhenoGraph (https://github.com/jacoblevine/PhenoGraph) per T cell compartment.
  • clusterannotation.csv: annotation for each cluster and metacluster

scRNA-seq data:

• The raw data can be found in https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE175450
• Other files to reproduce the analysis (scRNAseq_analysis_1preprocessing.Rmd, scRNAseq_analysis_2clustering.Rmd, scRNAseq_analysis_3convalescent.Rmd):
  • scRNAseq_Sawitzki_RECAST_09_2021.xlsx: Single-cell metadata.
  • scRNAseq_samples.tsv: Samples metadata.
  • scRNAseq_genelist_annotation.xlsx: Gene list for the annotation of T cells (Also in Mendeley, see Data and Code Availability).
  • scRNAseq_GO_RESPONSE_TO_TYPE_I_INTERFERON.txt, scRNAseq_GO_DEFENSE_RESPONSE_TO_VIRUS.txt, , scRNAseq_GO_T_CELL_MEDIATED_CYTOTOXICITY.txt: Gene lists for the signatures “Response to Type I Interferon” , “Defense Response to virus” and “Cytotoxicity” used for GSEA. (Also in Table S2).
  • scRNAseq_traj18_trav10.txt,scRNAseq_trbv25.txt: sequences to determine the proportion of TRAV10-TRAJ18-TRBV25 pairing T cell clones across all T cell clusters.