SARS-CoV-2 mRNA vaccines induce persistent human germinal centre responses

These are the<strong> processed</strong> BCR repertoire bulk sequencing data described in Turner &amp; O'Halloran et al., Nature, 2021 (Fig 3b-d; Extended Data Fig 3; Extended Data Table 6). The corresponding <strong>raw</strong> sequencing reads are available on SRA under BioProject PRJNA731610. <strong>Summary</strong>: Bulk-sorted total plasmablasts from PBMCs and germinal centre B cells at 4 weeks after primary immunization from 3 vaccinees who had no prior history of infection with SARS-CoV-2. <strong>Code: </strong>Code along with Docker container for reproducing the NGS data-based figures and analyses in the published paper can be found on GitHub. <strong>Metadata file</strong>: WU368_turner_et_al_nature_2021_meta.tsv Abbreviations: LN = lymph node PB = plasmablast GC = germinal centre mAb = monoclonal antibody <strong>BCR data file</strong>: WU368_turner_et_al_nature_2021_bcr.tsv.gz In addition to the processed bulk sequences, also included are the heavy chains of 37 mAbs that had been validated to be spike-binding and that were used together with the bulk sequences for clonal lineage inference. The mAbs are annotated as "mab" in the "seq_type" column. <strong>BCR data column descriptions</strong> The columns largely follow the AIRR-C Rearrangement format. The main deviation is that CDR3s are used, as opposed to IMGT-defined "junctions". Non-standard columns are noted below. v_call_genotyped: V gene annotation reassigned after individualized genotyping by TIgGER germline_[vdj]_call: clonal consensus germline sequence reconstructed via `CreateGermlines.py --cloned` using Change-O isotype: IGH[ADEGM] cdr3: CDR3 nucleotide sequence cdr3_length: CDR3 nucleotide sequence length cdr3_aa: CDR3 amino acid sequence collapse_count: number of duplicate IMGT-aligned V(D)J sequences that were collapsed by `alakazam::collapseDuplicates` donor: vaccinee sample: sample ID (arbitrary) timepoint: time point at which sample was collected tissue: tissue from which sample was collected sorting: FACS sorting seq_type: sequence type (mAb or bulk) nuc_RS_19_312: number of replacement and silent mutations between IMGT-numbered nucleotide positions 19-312 along IGHV sequences, calculated by `shazam::calcObservedMutations` nuc_denom_19_312: number of informative nucleotide positions for counting mutations, excluding non-A/T/G/C positions (such as "N", "-", ".") nuc_RS_freq_19_312: nucleotide-level mutation frequency (= nuc_RS_19_312 / nuc_denom_19_312)