Home > Publications Database > Dataset: Complement activation induces excessive T cell cytotoxicity in severe COVID-19: Analysis of single cell data cohort 1 (Berlin), v1.0.0 > print

001     169094
005     20250715105304.0
024 7 _ |a 10.5281/ZENODO.5771937
|2 doi
024 7 _ |a 10.5281/zenodo.5771937
|2 doi
024 7 _ |a 10.5281/zenodo.5771936
|2 doi
037 _ _ |a DZNE-2022-01801
100 1 _ |a Georg, Philipp
|0 0000-0001-9934-7415
|b 0
245 _ _ |a Dataset: Complement activation induces excessive T cell cytotoxicity in severe COVID-19: Analysis of single cell data cohort 1 (Berlin), v1.0.0
260 _ _ |c 2021
|b Zenodo
336 7 _ |a MISC
|2 BibTeX
336 7 _ |a Dataset
|b dataset
|m dataset
|0 PUB:(DE-HGF)32
|s 1752569547_3120
|2 PUB:(DE-HGF)
336 7 _ |a Chart or Table
|0 26
|2 EndNote
336 7 _ |a Dataset
|2 DataCite
336 7 _ |a DATA_SET
|2 ORCID
336 7 _ |a ResearchData
|2 DINI
520 _ _ |a 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.
536 _ _ |a 354 - Disease Prevention and Healthy Aging (POF4-354)
|0 G:(DE-HGF)POF4-354
|c POF4-354
|f POF IV
|x 0
588 _ _ |a Dataset connected to DataCite
650 _ 7 |a COVID-19
|2 Other
650 _ 7 |a single cell analysis
|2 Other
650 _ 7 |a clustering
|2 Other
650 _ 7 |a CyTOF
|2 Other
650 _ 7 |a scRNA-seq
|2 Other
700 1 _ |a Astaburuaga-García, Rosario
|0 0000-0003-1179-4080
|b 1
700 1 _ |a Bonaguro, Lorenzo
|0 P:(DE-2719)9001512
|b 2
|u dzne
700 1 _ |a Blüthgen, Nils
|0 0000-0002-0171-7447
|b 3
700 1 _ |a Sawitzki, Birgit
|0 0000-0001-8166-8579
|b 4
773 _ _ |a 10.5281/zenodo.5771936
909 C O |p VDB
|o oai:pub.dzne.de:169094
910 1 _ |a Deutsches Zentrum für Neurodegenerative Erkrankungen
|0 I:(DE-588)1065079516
|k DZNE
|b 2
|6 P:(DE-2719)9001512
913 1 _ |a DE-HGF
|b Gesundheit
|l Neurodegenerative Diseases
|1 G:(DE-HGF)POF4-350
|0 G:(DE-HGF)POF4-354
|3 G:(DE-HGF)POF4
|2 G:(DE-HGF)POF4-300
|4 G:(DE-HGF)POF
|v Disease Prevention and Healthy Aging
|x 0
914 1 _ |y 2021
920 1 _ |0 I:(DE-2719)1013038
|k AG Schultze
|l Clinical Single Cell Omics (CSCO) / Systems Medicine
|x 0
980 _ _ |a dataset
980 _ _ |a VDB
980 _ _ |a I:(DE-2719)1013038
980 _ _ |a UNRESTRICTED

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