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Li S, Kendall J, Park S, Wang Z, Alexander J, Moffitt A, Ranade N, Danyko C, Gegenhuber B, Fischer S, Robinson BD, Lepor H, Tollkuhn J, Gillis J, Brouzes E, Krasnitz A, Levy D, Wigler M. Copolymerization of single-cell nucleic acids into balls of acrylamide gel. Genome Res 2019; 30:49-61. [PMID: 31727682 PMCID: PMC6961581 DOI: 10.1101/gr.253047.119] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 11/13/2019] [Indexed: 01/06/2023]
Abstract
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.
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Affiliation(s)
- Siran Li
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Jude Kendall
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Sarah Park
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Zihua Wang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Joan Alexander
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Andrea Moffitt
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Nissim Ranade
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Cassidy Danyko
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Bruno Gegenhuber
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Stephan Fischer
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Brian D Robinson
- Department of Pathology and Laboratory Medicine, Weill Medical College of Cornell University, New York, New York 10021, USA
| | - Herbert Lepor
- Department of Urology, New York University Langone Medical Center, New York, New York 10017, USA
| | - Jessica Tollkuhn
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Jesse Gillis
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Eric Brouzes
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, New York 11794, USA
| | - Alex Krasnitz
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Dan Levy
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Michael Wigler
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
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