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

These are the processed BCR repertoire bulk sequencing data described in Turner & O'Halloran et al., Nature, 2021. The corresponding raw sequencing reads are available on SRA under BioProject PRJNA731610.

Metadata file: WU368_turner_et_al_nature_2021_meta.tsv

Abbreviations:

LN = lymph node

PB = plasmablast

GC = germinal centre

mAb = monoclonal antibody

BCR data file: 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.

BCR data column descriptions

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)