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. (January 2020) 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: 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
Investigative techniques and equipment > assays > Single cell sequencing
CSHL Authors:
Communities: 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
CSHL Cancer Center Program > Cancer Genetics and Genomics Program
CSHL Cancer Center Program > Gene Regulation and Inheritance Program
Depositing User: Adrian Gomez
Date: January 2020
Date Deposited: 22 Jan 2020 19:12
Last Modified: 29 Oct 2020 19:02
Related URLs:
Dataset ID:
URI: https://repository.cshl.edu/id/eprint/38918

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