Title: PRJNA638224 - BCR repertoire sequencing from COVID-19 patients
Type Dataset Jacob D Galson (2020): PRJNA638224 - BCR repertoire sequencing from COVID-19 patients. Zenodo. Dataset. https://zenodo.org/record/3899008
Links
- Item record in Zenodo
- Digital object URL
Summary
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 improvingMore information
- DOI: 10.5281/zenodo.3899008
- Language: en
Subjects
- COVID-19, B cell repertoire, Antibody, SARS-CoV-2
Dates
- Publication date: 2020
- Issued: June 09, 2020
Rights
- https://creativecommons.org/licenses/by/4.0/legalcode Creative Commons Attribution 4.0 International
- info:eu-repo/semantics/openAccess Open Access
Format
electronic resource
Relateditems
| Description | Item type | Relationship | Uri |
|---|---|---|---|
| IsCitedBy | https://doi.org/10.1101/2020.05.20.106294 | ||
| IsVersionOf | https://doi.org/10.5281/zenodo.3886394 | ||
| IsPartOf | https://zenodo.org/communities/airr | ||
| IsPartOf | https://zenodo.org/communities/covid-19 | ||
| IsPartOf | https://zenodo.org/communities/zenodo |