000169094 001__ 169094
000169094 005__ 20250715105304.0
000169094 0247_ $$2doi$$a10.5281/ZENODO.5771937
000169094 0247_ $$2doi$$a10.5281/zenodo.5771937
000169094 0247_ $$2doi$$a10.5281/zenodo.5771936
000169094 037__ $$aDZNE-2022-01801
000169094 1001_ $$00000-0001-9934-7415$$aGeorg, Philipp$$b0
000169094 245__ $$aDataset: Complement activation induces excessive T cell cytotoxicity in severe COVID-19: Analysis of single cell data cohort 1 (Berlin), v1.0.0
000169094 260__ $$bZenodo$$c2021
000169094 3367_ $$2BibTeX$$aMISC
000169094 3367_ $$0PUB:(DE-HGF)32$$2PUB:(DE-HGF)$$aDataset$$bdataset$$mdataset$$s1752569547_3120
000169094 3367_ $$026$$2EndNote$$aChart or Table
000169094 3367_ $$2DataCite$$aDataset
000169094 3367_ $$2ORCID$$aDATA_SET
000169094 3367_ $$2DINI$$aResearchData
000169094 520__ $$aThis repository contains the R Markdown files with the analysis of CyTOF and scRNA-seq data corresponding to cohort 1 (Berlin) analysed in Georg et al. 2021 'Complement activation induces excessive T cell cytotoxicity in severe COVID-19'. Additionally, here we include the necessary CyTOF data to reproduce this analysis. CyTOF data: The debarcoded fcs files (before batch-correction) can be found in https://flowrepository.org/id/FR-FCM-Z4P5 . \ Here you can find the necessary data to reproduce the analysis (cytof_analysis.Rmd, cytof_analysis.html): data_norm_all.csv: single-cell protein expression data (after batch-normalization and in linear scale). data_Tcells_annotated.csv: single-cell protein expression of gated T cells with cluster annotation. phenograph_CD4_k30.csv, phenograph_CD8_k30.csv, phenograph_TCRgd_k30.csv: output from Louvain Clustering computed with PhenoGraph ( https://github.com/jacoblevine/PhenoGraph ) per T cell compartment. clusterannotation.csv: annotation for each cluster and metacluster scRNA-seq data: The raw data can be found in https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE175450 Other files to reproduce the analysis (scRNAseq_analysis_1preprocessing.Rmd, scRNAseq_analysis_2clustering.Rmd, scRNAseq_analysis_3convalescent.Rmd): scRNAseq_Sawitzki_RECAST_09_2021.xlsx : Metadata scRNAseq_genelist_annotation.xlsx : G ene list for the annotation of T cells (Also in Mendeley, see Data and Code Availability). scRNAseq_GO_RESPONSE_TO_TYPE_I_INTERFERON.txt , scRNAseq_GO_DEFENSE_RESPONSE_TO_VIRUS.txt , , scRNAseq_GO_T_CELL_MEDIATED_CYTOTOXICITY.txt : Gene lists for the signatures “Response to Type I Interferon” , “Defense Response to virus” and “Cytotoxicity” used for GSEA. (Also in Table S2). scRNAseq_traj18_trav10.txt , scRNAseq_trbv25.txt : sequences to determine the proportion of TRAV10-TRAJ18-TRBV25 pairing T cell clones across all T cell clusters.
000169094 536__ $$0G:(DE-HGF)POF4-354$$a354 - Disease Prevention and Healthy Aging (POF4-354)$$cPOF4-354$$fPOF IV$$x0
000169094 588__ $$aDataset connected to DataCite
000169094 650_7 $$2Other$$aCOVID-19
000169094 650_7 $$2Other$$asingle cell analysis
000169094 650_7 $$2Other$$aclustering
000169094 650_7 $$2Other$$aCyTOF
000169094 650_7 $$2Other$$ascRNA-seq
000169094 7001_ $$00000-0003-1179-4080$$aAstaburuaga-García, Rosario$$b1
000169094 7001_ $$0P:(DE-2719)9001512$$aBonaguro, Lorenzo$$b2$$udzne
000169094 7001_ $$00000-0002-0171-7447$$aBlüthgen, Nils$$b3
000169094 7001_ $$00000-0001-8166-8579$$aSawitzki, Birgit$$b4
000169094 773__ $$a10.5281/zenodo.5771936
000169094 909CO $$ooai:pub.dzne.de:169094$$pVDB
000169094 9101_ $$0I:(DE-588)1065079516$$6P:(DE-2719)9001512$$aDeutsches Zentrum für Neurodegenerative Erkrankungen$$b2$$kDZNE
000169094 9131_ $$0G:(DE-HGF)POF4-354$$1G:(DE-HGF)POF4-350$$2G:(DE-HGF)POF4-300$$3G:(DE-HGF)POF4$$4G:(DE-HGF)POF$$aDE-HGF$$bGesundheit$$lNeurodegenerative Diseases$$vDisease Prevention and Healthy Aging$$x0
000169094 9141_ $$y2021
000169094 9201_ $$0I:(DE-2719)1013038$$kAG Schultze$$lClinical Single Cell Omics (CSCO) / Systems Medicine$$x0
000169094 980__ $$adataset
000169094 980__ $$aVDB
000169094 980__ $$aI:(DE-2719)1013038
000169094 980__ $$aUNRESTRICTED