{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Joseph Ng"],"organism":["Homo sapiens"],"software":["cellranger v6.1.2"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16531"],"description":["We generated single-cell transcriptomic and BCR sequencing data of B cells from peripheral blood samples taken from a SARS-CoV-2-antigen-naive cohort being vaccinated with the SARS-CoV-2 mRNA-1273 vaccine. Blood samples were collected at the baseline timepoint D-1 (i.e. one day prior to the initial vaccination), D+5, D+9, D+12, W8 (taken just before the second immunization), W10 and M6 post first vaccination dose. This dataset, in conjunction with other multi-omic data generated from other samples in the study, allowed us to finely map B cell, Class switch recombination (CSR) and antibody production dynamics during primary immunization in the context of vaccine-derived antigen-specific B cells."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Nucleic Acid Extraction - For timepoints D-1, D+5, D+9, D+12, W8 and W10 a pool of all S1+ B cells, 60% S1- B cells, 20% CD19- lymphocytes, 20% innate immune cells was performed. For M6 samples, a pool of all S1+ B cells with the addition of S1- B cells up to 100% was performed. All samples were run in multiple 10X reactions lanes for 5000 cells in each reaction. Cells were centrifuged (500g 5 minutes at 4°C) and resuspended in PBS with non-acetylated BSA to the desired concentration and run on the 10X chromium controller utilizing the Chromium Next GEM Single cell 5’ reagent kit v2 (Dual Index) (document number: CG00030 Rev F) producing the GEX, VDJ sequencing and cell surface protein libraries according to the manufacturer’s instructions.","Sequencing - Libraries were sequenced on a HiSeq2000 or NovaSeq X Plus Series (PE150) at 50,000 reads per cell for GEX libraries and 5,000 read per cell for VDJ/Cell surface protein libraries.","Sample Collection - Healthy adults were immunized with the mRNA-1273 vaccine formulating mRNA molecules encoding for the full length of the spike (S) protein of the original SARS-CoV-2 strain, during the spring of 2021 as part of the national (United Kingdom) vaccination program. Informed consent was asked of all participants prior to the start of the study. Participants were surveyed for previously known SARS-CoV-2 infection and other relevant (immune-related) co-morbidities at the start and at the end of the study. Whole blood was collected in sodium heparin tubes (455051, Greiner Bio-One). Non-coagulated whole blood from heparin tubes was diluted 1:1 in PBS (14040-091, Gibco) with 2% heat-inactivated fetal bovine serum (FBS, FCS-SA/500-22512, Labtech). Density gradient centrifugation using SepMate tubes (85450, STEMCELL Technologies) was used to isolate peripheral blood mononuclear cells (PBMCs) according to the manufacturer’s instructions. PBMCs were counted and viability estimated using a trypan blue exclusion assay. Cells were then resuspended at 10^7 viable cells per ml in FBS containing 10% DMSO (20688, ThermoScientific) and stored in liquid nitrogen. Vaccine-derived antigen-specific B cells were identified by tagging them with the subunit 1 (S1) of the spike protein (S) of the ancestral SARS-CoV-2 and the RBD (M6 timepoint only included S1 tagging). Biotin-conjugated S1 was coupled with two fluorochrome/oligomer dual-labelled streptavidin to form two different S1-fluorochome/oligomer conjugates. In this way, antigen-specific B cells were sorted via flow cytometry assisted sorting (FACS) with nucleotide oligomers to be sequenced as feature barcodes for posterior bioinformatic identification of antigen-specific B cells.","Library Construction - To generate feature barcode libraries tagging antigen-specific B cells for each timepoint, S1-specific B cells were tagged using Totalseq™ streptavidin-PE (405261, Biolegend) and Totalseq™ streptavidin-APC (405283, Biolegend) separately. RBD-specific B cells were tagged using Totalseq™ streptavidin-oligomer (405271, Biolegend). For timepoints before M6, cells from the same donors but collected from different timepoints were multiplexed using TotalSeq hashtags (Biolegend 294661, 394663, 394665, 394667, 394669, 394671). For the M6 timepoint, cells from different donors were multiplexed using the same TotalSeq hashtags (Biolegend) listed above for multiplexing. Hashtagged libraries were generated according to 10X Genomics instructions. Libraries were labelled ‘A’, ‘B’, etc. for cells run on different reaction lanes on the 10X Chromium controller."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","MAGE-TAB Files"],"data_protocol":["Sequence Alignment - Matching 10X genomics gene expression, BCR and feature barcode/cell surface protein libraries were processed using the ‘cellranger multi’ command from cellranger version 6.1.2. The following reference genome versions were downloaded from the cellranger website for sequence alignment and annotation: refdata-gex-GRCh38-2020-A (for gene expression libraries) and refdata-cellranger-vdj-GRCh38-alts-ensembl-5.0.0 (for BCR libraries)"],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina HiSeq 2000"],"study_type":["RNA-seq of coding RNA from single cells"],"species":["Homo sapiens"],"pubmed_title":["Multi-step antibody class switching in a primary human response is restricted after IGHG2 and dependent on B cell maturation stage"],"pubmed_authors":["Joseph Ng","Guillem Montamat Garcia","Guillem Montamat Garcia, Joseph C. F. Ng, Alexander T. Stewart, Emma Sinclair, Paul Blair, Diana Kateregga, Amir Gander, David Kipling, Dongjun Guo, Lutecia Servius, Christopher J. M. Piper, Zara Baig, Franca Fraternali, Claudia Mauri, Deborah K. Dunn-Walters"],"additional_accession":[]},"is_claimable":false,"name":"Single-cell RNA and B cell receptor profiling of B cell response to SARS-CoV-2 vaccination","description":"We generated single-cell transcriptomic and BCR sequencing data of B cells from peripheral blood samples taken from a SARS-CoV-2-antigen-naive cohort being vaccinated with the SARS-CoV-2 mRNA-1273 vaccine. Blood samples were collected at the baseline timepoint D-1 (i.e. one day prior to the initial vaccination), D+5, D+9, D+12, W8 (taken just before the second immunization), W10 and M6 post first vaccination dose. This dataset, in conjunction with other multi-omic data generated from other samples in the study, allowed us to finely map B cell, Class switch recombination (CSR) and antibody production dynamics during primary immunization in the context of vaccine-derived antigen-specific B cells.","dates":{"release":"2026-05-08T00:00:00Z","modification":"2026-05-08T09:15:44.753Z","creation":"2026-01-16T18:21:45.877Z"},"accession":"E-MTAB-16531","cross_references":{"ENA":["ERP187667"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005684","EFO_0004917","EFO_0005518","EFO_0004184"],"doi":["10.1101/2025.05.07.652638"]}}