BASIC: BCR assembly from single cells.
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.



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.



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



aakhan@ttic.edu



Supplementary data are available at Bioinformatics online.
Toyota Technological Institute at Chicago, Chicago, IL, USA
Stefan
S
Canzar
Committee on Immunology, The Knapp Center of Lupus and Immunology Research, The University of Chicago, Chicago, IL 60637, USA.
Karlynn E
KE
Neu
Toyota Technological Institute at Chicago, Chicago, IL, USA
Qingming
Q
Tang
Committee on Immunology, The Knapp Center of Lupus and Immunology Research, The University of Chicago, Chicago, IL 60637, USA.
Patrick C
PC
Wilson
Toyota Technological Institute at Chicago, Chicago, IL, USA
Aly A
AA
Khan
D020869:Gene Expression Profiling / Q000379:methods*; D005786:Gene Expression Regulation; D006801:Humans; D011947:Receptors, Antigen, B-Cell / Q000235:genetics*; D017423:Sequence Analysis, RNA / Q000379:methods*; D059010:Single-Cell Analysis / Q000379:methods*; D012984:Software
D011947:Receptors, Antigen, B-Cell