BASIC: BCR assembly from single cells
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 …
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 …
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
Supplementary information
Supplementary data are available at Bioinformatics online.
Oxford University Press