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BASIC: BCR assembly from single cells.

ABSTRACT:

Motivation

The B-cell receptor enables individual B cells to identify diverse antigens, including bacterial and viral proteins. While advances in RNA-sequencing (RNA-seq) have enabled high throughput profiling of transcript expression in single cells, the unique task of assembling the full-length heavy and light chain sequences from single cell RNA-seq (scRNA-seq) in B cells has been largely unstudied.

Results

We developed a new software tool, BASIC, which allows investigators to use scRNA-seq for assembling BCR sequences at single-cell resolution. To demonstrate the utility of our software, we subjected nearly 200 single human B cells to scRNA-seq, assembled the full-length heavy and the light chains, and experimentally confirmed these results by using single-cell primer-based nested PCRs and Sanger sequencing.

Availability and implementation

http://ttic.uchicago.edu/∼aakhan/BASIC

Contact

aakhan@ttic.edu

Supplementary information

Supplementary data are available at Bioinformatics online.

SUBMITTER: Canzar S

PROVIDER: S-EPMC5408917 | biostudies-literature | 2017 Feb

REPOSITORIES: biostudies-literature

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Publications

BASIC: BCR assembly from single cells.

Canzar Stefan S Neu Karlynn E KE Tang Qingming Q Wilson Patrick C PC Khan Aly A AA

Bioinformatics (Oxford, England) 20170201 3

<h4>Motivation</h4>The B-cell receptor enables individual B cells to identify diverse antigens, including bacterial and viral proteins. While advances in RNA-sequencing (RNA-seq) have enabled high throughput profiling of transcript expression in single cells, the unique task of assembling the full-length heavy and light chain sequences from single cell RNA-seq (scRNA-seq) in B cells has been largely unstudied.<h4>Results</h4>We developed a new software tool, BASIC, which allows investigators to ...[more]

PMID: 28172415

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