PRJNA638224 - BCR repertoire sequencing from COVID-19 patients

Description

These are the processed BCR repertoire sequence data that accompany the following manuscript: “Deep sequencing of B cell receptor repertoires from COVID-19 patients reveals strong convergent immune signatures”. The manuscript preprint is available at doi: https://doi.org/10.1101/2020.05.20.106294. The raw sequence data are available on SRA under the BioProject PRJNA638224

Sequence processing

The Immcantation framework (docker container v3.0.0) was used for sequence processing. Briefly, paired-end reads were joined based on a minimum overlap of 20 nt, and a max error of 0.2, and reads with a mean phred score below 20 were removed. Primer regions, including UMIs and sample barcodes, were then identified within each read, and trimmed. Together, the sample barcode, UMI, and constant region primer were used to assign molecular groupings for each read. Within each grouping, usearch, was used to subdivide the grouping, with a cutoff of 80% nucleotide identity, to account for randomly overlapping UMIs. Each of the resulting groupings is assumed to represent reads arising from a single RNA. Reads within each grouping were then aligned, and a consensus sequence determined. For each processed sequence, IgBlast was used to determine V, D and J gene segments, and locations of the CDRs and FWRs. Isotype was determined based on comparison to germline constant region sequences. Sequences annotated as unproductive by IgBlast were removed.

Sequence data column description

sample_id         Unique identifier for each sequencing library

sequence_id         Unique identifier for a sequence within a sample_id

sequence_alignment         IMGT gapped nucleotide sequence

germline_alignment         IMGT gapped germline sequence

v_call         IGHV gene segment(s) and allele

d_call         IGHD gene segment(s) and allele

j_call         IGHJ gene segment(s) and allele

c_call         Isotype subclass

junction         Junction nucleotide sequence

junction_aa         Junction amino acid sequence

duplicate_count         UMI count for the given unique sequence

consensus_count         Raw read count for the given unique sequence

Sequence metadata column description

sample_id         Unique identifier for each sequencing library

bioproject_accession         NCBI BioProject accession number

biosample_accession         NCBI BioSample accession number

sra_accession         NCBI SRA accession number

sex         Sex of patient

age         Age of patient at time of sampling

ethnicity         Ethnicity of patient

health_state         One of worsening, stable, or improving