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

<p>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 &quot;Complement activation induces excessive T cell cytotoxicity in severe COVID-19&quot;. Additionally, here we&nbsp;include&nbsp;the necessary CyTOF data to reproduce this&nbsp;analysis.</p> <p>CyTOF data:</p> <ul> <li>The debarcoded fcs files (before batch-correction) can be found in&nbsp;<a href="https://flowrepository.org/id/FR-FCM-Z4P5">https://flowrepository.org/id/FR-FCM-Z4P5</a>. \</li> <li>Here you can find the necessary data to reproduce the analysis (cytof_analysis.Rmd, cytof_analysis.html): <ul> <li>data_norm_all.csv: single-cell protein expression data (after batch-normalization and in linear scale).</li> <li>data_Tcells_annotated.csv: single-cell protein expression of gated T cells with cluster annotation.</li> <li>phenograph_CD4_k30.csv, phenograph_CD8_k30.csv, phenograph_TCRgd_k30.csv: output from Louvain Clustering computed with PhenoGraph (<a href="https://github.com/jacoblevine/PhenoGraph">https://github.com/jacoblevine/PhenoGraph</a>) per T cell compartment.</li> <li>clusterannotation.csv: annotation for each cluster and metacluster</li> </ul> </li> </ul> <p>scRNA-seq data:</p> <ul> <li>The raw data can be found in&nbsp;<a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE175450">https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE175450</a></li> <li>Other files&nbsp;to reproduce the analysis (scRNAseq_analysis_1preprocessing.Rmd, scRNAseq_analysis_2clustering.Rmd, scRNAseq_analysis_3convalescent.Rmd): <ul> <li><a href="https://zenodo.org/api/files/76286c93-628d-4251-9118-52130d4a75c6/scRNAseq_Sawitzki_RECAST_09_2021.xlsx">scRNAseq_Sawitzki_RECAST_09_2021.xlsx</a>: Single-cell metadata.</li> <li>scRNAseq_samples.tsv: Samples metadata.</li> <li><a href="https://zenodo.org/api/files/76286c93-628d-4251-9118-52130d4a75c6/scRNAseq_genelist_annotation.xlsx">scRNAseq_genelist_annotation.xlsx</a>:&nbsp;<a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE175450">G</a>ene list for the annotation of T cells (Also in Mendeley, see&nbsp;Data and Code Availability).</li> <li><a href="https://zenodo.org/api/files/76286c93-628d-4251-9118-52130d4a75c6/scRNAseq_GO_RESPONSE_TO_TYPE_I_INTERFERON.txt">scRNAseq_GO_RESPONSE_TO_TYPE_I_INTERFERON.txt</a>,&nbsp;<a href="https://zenodo.org/api/files/76286c93-628d-4251-9118-52130d4a75c6/scRNAseq_GO_DEFENSE_RESPONSE_TO_VIRUS.txt">scRNAseq_GO_DEFENSE_RESPONSE_TO_VIRUS.txt</a>,&nbsp;,&nbsp;<a href="https://zenodo.org/api/files/76286c93-628d-4251-9118-52130d4a75c6/scRNAseq_GO_T_CELL_MEDIATED_CYTOTOXICITY.txt">scRNAseq_GO_T_CELL_MEDIATED_CYTOTOXICITY.txt</a>: Gene lists for the signatures &ldquo;Response to Type I Interferon&rdquo; , &ldquo;Defense Response to virus&rdquo; and &ldquo;Cytotoxicity&rdquo; used for GSEA. (Also in&nbsp;Table S2).</li> <li><a href="https://zenodo.org/api/files/76286c93-628d-4251-9118-52130d4a75c6/scRNAseq_traj18_trav10.txt">scRNAseq_traj18_trav10.txt</a>,<a href="https://zenodo.org/api/files/76286c93-628d-4251-9118-52130d4a75c6/scRNAseq_trbv25.txt">scRNAseq_trbv25.txt</a>: sequences to determine&nbsp;the proportion of TRAV10-TRAJ18-TRBV25 pairing T cell clones across all T cell clusters.</li> </ul> </li> </ul>