{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Sunil Raghav"],"organism":["Homo sapiens"],"software":["Cellranger (v5)"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-10636"],"description":["We selected COVID-19 positive individuals, their direct contacts, and unmatched controls. CD3+ and CD19+ cells were sorted from PBMCs and they were analyzed for surface expression, 5' gene expression, and TCR/BCR profiling at single-cell resolution. For each group, three samples were pooled using Biolegend hashtag antibodies (TotalSeq™-C C0251, TotalSeq™-C C0252, and TotalSeq™-C C0253 ) and multiple runs were performed per library. The raw data for each run will be provided upon request."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Nucleic Acid Extraction - The sorted single cell suspension was converted to single-cell gel beads in the emulsion (GEMs) by using the Chromium Single Cell 5′ Library and Gel Bead kit, and Chromium Single Cell G Chip kit (10x Genomics) according to the manufacturer’s protocol.","Library Construction - scRNA-seq libraries were constructed using a Single Cell 5′ Library and Gel Bead kit, Single Cell V(D)J Enrichment kit, Human T Cell and a Single Cell V(D)J Enrichment kit, Human B Cell according to manufacturer's protocol. The control, contact and patient sample groups contain 3 individuals each which were tagged using TotalSeq™-C antibodies (C0251, C0252, C0253) respectively.","Sample Collection - PBMCs were extracted from 5ml of blood by density gradient centrifugation with the help of Lymphoprep. PBMCs were stained with surface markers CD3 FITC and CD19 PB. Cells were sorted in FACS melody.","Sequencing - The libraries were sequenced using an Illumina NextSeq550 platform."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - The raw BCL files were first processed using cellranger mkfastq command. Further the obtained fastq files were analyzed for V(D)J and gene expression/feature barcode using cellranger multi (cellranger v5)"],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["FACS Melody","NextSeq 550"],"study_type":["RNA-seq of coding RNA from single cells"],"species":["Homo sapiens"],"pubmed_authors":["Sunil Raghav"],"additional_accession":[]},"is_claimable":false,"name":"Single-cell V(D)J-seq of CD3+ and CD19+ lymphocytes from PBMCs of COVID-19 patients","description":"We selected COVID-19 positive individuals, their direct contacts, and unmatched controls. CD3+ and CD19+ cells were sorted from PBMCs and they were analyzed for surface expression, 5' gene expression, and TCR/BCR profiling at single-cell resolution. For each group, three samples were pooled using Biolegend hashtag antibodies (TotalSeq™-C C0251, TotalSeq™-C C0252, and TotalSeq™-C C0253 ) and multiple runs were performed per library. The raw data for each run will be provided upon request.","dates":{"release":"2025-12-03T00:00:00Z","modification":"2026-05-27T14:04:24.813Z","creation":"2025-11-28T16:15:51.233Z"},"accession":"E-MTAB-10636","cross_references":{"ENA":["ERP185807"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005684","EFO_0005518","EFO_0003816","EFO_0004184"]}}