Copolymerization of single-cell nucleic acids into balls of acrylamide gel
- Siran Li1,
- Jude Kendall1,
- Sarah Park1,
- Zihua Wang1,
- Joan Alexander1,
- Andrea Moffitt1,
- Nissim Ranade1,
- Cassidy Danyko1,
- Bruno Gegenhuber1,
- Stephan Fischer1,
- Brian D. Robinson2,
- Herbert Lepor3,
- Jessica Tollkuhn1,
- Jesse Gillis1,
- Eric Brouzes4,
- Alex Krasnitz1,
- Dan Levy1 and
- Michael Wigler1
- 1Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA;
- 2Department of Pathology and Laboratory Medicine, Weill Medical College of Cornell University, New York, New York 10021, USA;
- 3Department of Urology, New York University Langone Medical Center, New York, New York 10017, USA;
- 4Department of Biomedical Engineering, Stony Brook University, Stony Brook, New York 11794, USA
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.
Footnotes
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[Supplemental material is available for this article.]
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Article published online before print. Article, supplemental material, and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.253047.119.
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Freely available online through the Genome Research Open Access option.
- Received May 24, 2019.
- Accepted November 13, 2019.
This article, published in Genome Research, is available under a Creative Commons License (Attribution 4.0 International), as described at http://creativecommons.org/licenses/by/4.0/.
