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Germinal centre-driven maturation of B cell response to SARS-CoV-2 mRNA vaccination

These are the processed BCR repertoire and transcriptomics data described in <a href="https://doi.org/10.1038/s41586-022-04527-1">Kim & Zhou et al., Nature, 2022</a>. The raw sequencing data new to this study are available on SRA under BioProject <a href="https://www.ncbi.nlm.nih.gov/sra/?term=PRJNA777934">PRJNA777934</a>. This study also used BCR repertoire data from <a href="https://doi.org/10.1038/s41586-021-03738-2">Turner & O'Halloran et al., Nature, 2021</a> (<a href="https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA731610">PRJNA731610</a>) and <a href="https://doi.org/10.1016/j.immuni.2021.08.013">Schmitz, Turner & Liu et al., Immunity, 2021</a> (<a href="https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA741267">PRJNA741267</a>).   Code Code along with Docker containers for reproducing the NGS data-based figures and analyses in the published paper can be <a href="https://github.com/julianqz/wustl_published/tree/main/nature_2022">found on GitHub</a>.   Metadata File: WU368_kim_et_al_nature_2022_meta.tsv Notes: <ul> <li>Sample breakdown by `sequence_type` (132 total) <ul> <li>73 bulk BCR sequencing samples (`bulk`) <ul> <li>57 new</li> <li>5 from <a href="https://doi.org/10.1038/s41586-021-03738-2">Turner & O'Halloran et al., Nature, 2021</a></li> <li>11 from <a href="https://doi.org/10.1016/j.immuni.2021.08.013">Schmitz, Turner & Liu et al., Immunity, 2021</a>.</li> </ul> </li> <li>56 10x Genomics single-cell VDJ + 5' gene expression samples (`tgx`)</li> <li>3 samples from <a href="https://doi.org/10.1038/s41586-021-03738-2">Turner & O'Halloran et al., Nature, 2021</a> (`mab`) corresponding to a total of 37 S-binding mAbs previously reported. These are not the same as the 2099 recombinant mAbs generated in this study (see below).</li> </ul> </li> <li>Sample collection time was originally recorded in days in the `timepoint` column. Timepoints were referenced in weeks in the manuscript, as shown in the `timepoint_ms` column.</li> <li>`bio_rep` and `tech_rep` = biological replicate and technical replicate respectively.</li> </ul> Abbreviations: <ul> <li>LN = lymph node</li> <li>BM = bone marrow</li> <li>PB = plasmablast</li> <li>GC = germinal centre</li> <li>LLPC = long-lived plasma cell</li> <li>NS = no sorting</li> <li>mAb = monoclonal antibody</li> </ul>   Information on the 2099 recombinant mAbs generated in this study File: WU368_kim_et_al_nature_2022_mabs.tsv Notes on columns: <ul> <li>`h_sequence_id` and `l_sequence_id`: Sequence IDs of the heavy and light chains respectively.</li> <li>`elisa`: ELISA results for binding to SARS-CoV-2 S (`TRUE` = positive).</li> </ul>   Processed BCR data - heavy chains File: WU368_kim_et_al_nature_2022_bcr_heavy.tsv Analysis was based on heavy chain-based clonal inference. Notes on columns: The columns largely follow the <a href="https://changeo.readthedocs.io/en/stable/standard.html">AIRR-C Rearrangement format</a>. The main deviation is that CDR3s were used, as opposed to IMGT-defined "junctions". Nonetheless, junction-related columns are included here as some repositories such as <a href="https://gateway.ireceptor.org/login">iReceptor</a> use these. Non-standard columns are noted below. <ul> </ul> <ul> <li>`cell_id`: Only sequences from single-cell samples and the 37 mAbs from Turner & O'Halloran et al., Nature, 2021 have cell IDs following the format `[donor]_[sample]@[id]`. `NA` for bulk sequences.</li> <li>`sequence_id`: Sequence IDs follow the format `[donor]_[sample]@[id]`.</li> <li>`v_call_genotyped`: V gene annotation reassigned after individualized genotyping by <a href="https://tigger.readthedocs.io/en/stable/">TIgGER</a>.</li> <li>`germline_[vdj]_call`: Clonal consensus germline calls after corresponding clonal consensus sequence were reconstructed via <a href="https://changeo.readthedocs.io/en/stable/methods/germlines.html">`CreateGermlines.py --cloned` from Change-O</a>.</li> <li>`isotype`: IGH[ADEGM].</li> <li>`cdr3`: CDR3 nucleotide sequence.</li> <li>`cdr3_length`: CDR3 nucleotide sequence length.</li> <li>`cdr3_aa`: CDR3 amino acid sequence.</li> <li>`collapse_count`: Number of duplicate IMGT-aligned V(D)J sequences that were collapsed by <a href="https://alakazam.readthedocs.io/en/stable/topics/collapseDuplicates/">`alakazam::collapseDuplicates`</a>.</li> <li>`donor`, `timepoint`, `tissue`, `sorting`, `seq_type`: Propagated as is from the metadata file. <ul> <li>In `seq_type`, `tgx` corresponds to 10x Genomics data; `mab` corresponds specifically to the 37 S-binding mAbs from Turner & O'Halloran et al., Nature, 2021.</li> </ul> </li> <li>`timepoint_2`: Same as `timepoint`, except that `d28+d35` and `d201+d208` were treated as `d28` (week 4) and `d201` (week 29) respectively as described in Materials & Methods.</li> <li>`gex_anno`: Cell type identity annotation based on transcriptomic profiles. Mapped from `anno_leiden_0.18` from WU368_kim_et_al_nature_2022_gex_b_cells.h5ad.</li> <li>`compartment`: B cell compartment. <ul> <li>ABC = activated B cell. LNPC = lymph node plasma cell. RMB = resting memory B cell.</li> <li>Minor differences in terminology <ul> <li>The manuscript refers to the memory compartment as MBCs, whereas the terminology used in the data is RMB. As described in Materials & Methods, analysis involving the memory compartment used specifically d201 bulk-sequenced memory sorts from blood. To get these sequences, subset `s_pos_clone`, `seq_type`, `compartment`, and `timepoint_2` to, respectively, `TRUE`, `bulk`, `RMB`, and `d201`. </li> <li>The manuscript uses the term BMPC (bone marrow plasma cell), whereas the data uses the term LLPC.</li> </ul> </li> </ul> </li> <li>`clone_id`: B cell clonal lineage IDs follow the format `[donor]@[id]`.</li> <li>`s_pos_clone`: `TRUE` if a sequence belonged to a B cell clone that was designated as S-binding by virtue of containing one of the recombinant mAbs that tested positive via ELISA or one of the S-binding mAbs from Turner & O'Halloran et al., Nature, 2021.</li> <li>`expressed_id`: mAb IDs for the 2099 recombinant mAbs generated in this study (mapped from `mab_id` from WU368_kim_et_al_nature_2022_mabs.tsv) and the 37 mAbs from Turner & O'Halloran et al., Nature, 2021. `NA` for everything else.</li> <li>`elisa`: ELISA results for binding of recombinant mAbs to SARS-CoV-2 S. `TRUE` if positive. `NA` if not tested.</li> <li>`nuc_RS_19_312`: number of replacement and silent mutations between IMGT-numbered nucleotide positions 19-312 along IGHV sequences, calculated by <a href="https://shazam.readthedocs.io/en/stable/topics/calcObservedMutations/">`shazam::calcObservedMutations`</a>.</li> <li>`nuc_denom_19_312`: number of informative nucleotide positions for counting mutations, excluding non-A/T/G/C positions (such as "N", "-", ".").</li> <li>`nuc_RS_freq_19_312`: nucleotide-level mutation frequency (= nuc_RS_19_312 / nuc_denom_19_312).</li> </ul>   Processed BCR data - light chains File: WU368_kim_et_al_nature_2022_bcr_light.tsv Light chains were not used for heavy chain-based clonal inference or analysis.   Processed transcriptomics data Files: <ul> <li>WU368_kim_et_al_nature_2022_gex_all_cells.h5ad (clustering all cells)</li> <li>WU368_kim_et_al_nature_2022_gex_b_cells.h5ad (re-clustering only the B cells)</li> </ul> Notes: <ul> <li>The `h5ad` files can be imported into <a href="https://scanpy.readthedocs.io/en/stable/index.html">Scanpy</a> as an <a href="https://scanpy.readthedocs.io/en/stable/usage-principles.html#anndata">AnnData object</a>.</li> <li>Each `AnnData` object has 3 `.layers`, each representing a version of the count matrix. <ul> <li>`raw_counts`: Imported from `<a href="https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/6.0/using/aggregate">cellranger aggr</a>` output by `scanpy.read_10x_mtx`.</li> <li>`log_norm`: Log-noramlized expression values outputted by `scanpy.pp.normalize_total` followed by `scanpy.pp.log1p`.</li> <li>`scaled`: The `log_norm` layer scaled to unit variance and zero mean by `scanpy.pp.scale`. </li> </ul> </li> <li>The `gene_name` and `biotype` columns in `.var` were extracted from GENCODE v32 GTF.</li> <li>Columns in `.obs` (each row corresponds to a cell) <ul> <li>`n_feature`: The `n_genes_by_counts` column produced by `scanpy.pp.calculate_qc_metrics`, renamed. The number of genes expressed. This is before subsetting the genes.</li> <li>`n_umi`: The `total_counts` column produced by `scanpy.pp.calculate_qc_metrics`, renamed. The total UMI counts in a cell.</li> <li>`pct_mt`: The `pct_counts_mt` column produced by `scanpy.pp.calculate_qc_metrics`, renamed. The percentage of counts in mitochondrial genes.</li> <li>`n_hkg`: The number of housekeeping genes for which expression was detected.</li> <li>`n_gene_expressed`: The total number of genes for which expression was detected. This is after subsetting the genes.</li> <li>`pre_qc_bcr`: `TRUE` if a cell also had paired BCR data available. Produced by cross-referencing the cellular barcodes in `cell_barcodes.json` outputted by `cellranger vdj`. At this point the BCR data had not gone through the QC process in the BCR processing pipeline (hence `pre_qc`). </li> <li>`leiden_[resolution]`: Cluster assignment by `scanpy.tl.leiden`.</li> <li>`anno_leiden_[resolution]`: Cell type identity annotations based on transcriptomic profiles. This was mapped onto the `gex_anno` column in the processed heavy chain BCR data.</li> </ul> </li> <li>UMAP coordinates can be found in `.obsm["X_umap"]`.</li> <li>`.X` has been set to `None` in order to reduce file size.</li> </ul> In addition, the preprocessed count matrix outputted by `<a href="https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/6.0/using/aggregate">cellranger aggr</a>` is available from <a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE195673">GEO under BioProject PRJNA777934</a>.

ShareScore

40/100

Overall dataset sharing score

Score breakdown

These five areas show where the dataset supports — or may limit — practical reuse.

Stewardship: 8
Harmonization: 4
Access: 20
Reuse readiness: 8
Engagement: 0

Topics

B cell repertoire Antibody AIRR-seq COVID-19 vaccination