Dataset

DZNE-2022-01801

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Dataset: Complement activation induces excessive T cell cytotoxicity in severe COVID-19: Analysis of single cell data cohort 1 (Berlin), v1.0.0

Georg, P. ; Astaburuaga-García, R. ; Bonaguro, L.DZNE* ; Blüthgen, N. ; Sawitzki, B.

2021
Zenodo

This record in other databases:

Please use a persistent id in citations: doi:10.5281/ZENODO.5771937  doi:10.5281/zenodo.5771937  doi:10.5281/zenodo.5771936

Abstract: 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 : Metadata scRNAseq_genelist_annotation.xlsx : G ene 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.

Keyword(s): COVID-19 ; single cell analysis ; clustering ; CyTOF ; scRNA-seq

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Contributing Institute(s):

1. Clinical Single Cell Omics (CSCO) / Systems Medicine (AG Schultze)

Research Program(s):

1. 354 - Disease Prevention and Healthy Aging (POF4-354) (POF4-354)

Appears in the scientific report 2021

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Linked articles:

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Journal Article Georg, P. ; Astaburuaga-García, R. ; Bonaguro, L.DZNE* ; et al
Complement activation induces excessive T cell cytotoxicity in severe COVID-19.
Cell 185(3), 493 - 512.e25 (2022) [10.1016/j.cell.2021.12.040]2022   Files  Fulltext by Pubmed Central BibTeX | EndNote: XML, Text | RIS

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