RT Journal
A1 Li, Siran
A1 Kendall, Jude
A1 Park, Sarah
A1 Wang, Zihua
A1 Alexander, Joan
A1 Moffitt, Andrea
A1 Ranade, Nissim
A1 Danyko, Cassidy
A1 Gegenhuber, Bruno
A1 Fischer, Stephan
A1 Robinson, Brian D.
A1 Lepor, Herbert
A1 Tollkuhn, Jessica
A1 Gillis, Jesse
A1 Brouzes, Eric
A1 Krasnitz, Alex
A1 Levy, Dan
A1 Wigler, Michael
T1 Copolymerization of single-cell nucleic acids into balls of acrylamide gel
JF Genome Research 
JO Genome Research 
YR 2020 
FD January 01 
VO 30 
IS 1 
SP 49 
OP 61 
DO 10.1101/gr.253047.119 
UL http://genome.cshlp.org/content/30/1/49.abstract 
AB We show the use of 5′-Acrydite oligonucleotides to copolymerize single-cell DNA or RNA into balls of acrylamide gel (BAGs). Combining this step with split-and-pool techniques for creating barcodes yields a method with advantages in cost and scalability, depth of coverage, ease of operation, minimal cross-contamination, and efficient use of samples. We perform DNA copy number profiling on mixtures of cell lines, nuclei from frozen prostate tumors, and biopsy washes. As applied to RNA, the method has high capture efficiency of transcripts and sufficient consistency to clearly distinguish the expression patterns of cell lines and individual nuclei from neurons dissected from the mouse brain. By using varietal tags (UMIs) to achieve sequence error correction, we show extremely low levels of cross-contamination by tracking source-specific SNVs. The method is readily modifiable, and we will discuss its adaptability and diverse applications.