Signature of long-lived memory CD8+ T cells in acute SARS-CoV-2 infection

<p>The datasets uploaded in this Zenodo entry were generated in the single cell RNA sequencing part of the project.</p> <p>For the scRNAseq analysis, cells from ten patients and the same time point were pooled together, generating four individual sample sets in total: (1) patients CoV2_T001- CoV2_T010, acute; (2) patients CoV2_T001- CoV2_T010, six months post-infection; (3) patients CoV2_T011- CoV2_T020, acute; (4) patients CoV2_T011- CoV2_T011-20, six months post-infection.</p> <p>We additionally generated two more sample sets: using 5000 unsorted PBMCs from each patient&rsquo;s sample: (5) patients CoV2_T001- CoV2_T010, six months post-infection unsorted; (6) patients CoV2_T011- CoV2_T020, six months post-infection unsorted. The cells in these two sample sets were hashed.</p> <p>Finally, using PBMCs from four healthy donors, we generated sample set (7) by sorting and pooling 2000 CD8+ T cells from each healthy donor sample.</p> <p>We are here providing the pre-processed&nbsp;sets for each sample set (1-7), i.e. :<br> - &quot;filtered feature bc matrix&quot; files, as output from the &lsquo;cellranger multi&rsquo; pipeline (Cell Ranger version 5.0.0), containing cell-RNA count matrices and cell-ADT matrices. ADTs comprise&nbsp;counts for TotalSeq antibodies and dCODE Dextramers.<br> - &quot;filtered_contig_annotations.csv&quot; files, as output from the &lsquo;cellranger multi&rsquo; pipeline (Cell Ranger version 5.0.0), containing High-level annotations of each high-confidence, cellular contig for TCR clonal analysis. This file is not present for sets 5 and 6, because we did not perform TCR profiling for these samples.<br> - &quot;clusters.tsv&quot; files, as output from the souporcell SNP analysis (version 2). To cluster cells based on their patient specific genetic variants, we merged sample sets 1, 2 &nbsp;and 5 (comprising sorted cells from both time points of patients CoV2_T001- CoV2_T010 and unsorted cells of the same patients) and sets 3, 4 and 6 (comprising cells from both time points of patients CoV2_T011- CoV2_T020 and unsorted cells of the same patients). Then, we executed the souporcell pipeline with option <em>k=10 </em>(number of clusters to be determined) for each of the two merged sample sets.</p> <p>Together, these files allow to reproduce the analysis as reported in the paper.</p> <p>Additionally, we provide the Seurat Objects &quot;Integrated.h5seurat&quot;&nbsp; and &quot;Integrated_NA_filtered.h5seurat&quot; which can be used to skip the pre-processing steps of the data analysis. See the code provided on&nbsp;https://github.com/Moors-Code/SARS-CoV-2-Tcell-Boyman-collaboration for details.</p> <p>&nbsp;</p>