Copolymerization of single-cell nucleic acids into balls of acrylamide gel

Li, S., Kendall, J., Park, S., Wang, Z., Alexander, J., Moffitt, A., Ranade, N., Danyko, C., Gegenhuber, B., Fischer, S., Robinson, B. D., Lepor, H., Tollkuhn, J., Gillis, J., Brouzes, E., Krasnitz, A., Levy, D., Wigler, M. (November 2019) Copolymerization of single-cell nucleic acids into balls of acrylamide gel. Genome Res, 30 (1). pp. 49-61. ISSN 1088-9051 (Public Dataset)

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URL: https://www.ncbi.nlm.nih.gov/pubmed/31727682

DOI: 10.1101/gr.253047.119

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.

Item Type:	Paper
Subjects:	bioinformatics bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification diseases & disorders bioinformatics > genomics and proteomics > genetics & nucleic acid processing bioinformatics > genomics and proteomics Investigative techniques and equipment diseases & disorders > neoplasms organism description > animal Investigative techniques and equipment > assays organism description > animal > mammal organism description > animal > mammal > rodent > mouse organs, tissues, organelles, cell types and functions > cell types and functions > cell types > neurons organs, tissues, organelles, cell types and functions > cell types and functions > cell types > neurons organs, tissues, organelles, cell types and functions > cell types and functions > cell types > neurons bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > Nucleic Acids organism description > animal > mammal > rodent Investigative techniques and equipment > assays > Single cell sequencing
CSHL Authors:	Wigler, Michael H. Levy, Dan Krasnitz, Alexander Gillis, Jesse Tollkuhn, Jessica Kendall, Jude T. Wang, Zihua Alexander, Joan Moffitt, Andrea B Danyko, Cassidy Gegenhuber, Bruno Fischer, Stephan Li, Siran Park, Sarah Ranade, Nissim
Communities:	CSHL Cancer Center Program > Cancer Genetics and Genomics Program CSHL Cancer Center Program > Gene Regulation and Inheritance Program CSHL Cancer Center Shared Resources CSHL labs > Gillis Lab CSHL labs > Krasnitz lab CSHL labs > Levy lab CSHL labs > Tollkuhn lab CSHL labs > Wigler lab School of Biological Sciences > Publications
Depositing User:	Adrian Gomez
Date:	14 November 2019
Date Deposited:	22 Jan 2020 19:12
Last Modified:	02 Feb 2024 16:51
PMCID:	PMC6961581
Related URLs:	Publisher
Dataset ID:	SRA: PRJNA566441
URI:	https://repository.cshl.edu/id/eprint/38918

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