Title | Copolymerization of single-cell nucleic acids into balls of acrylamide gel. |
Publication Type | Journal Article |
Year of Publication | 2020 |
Authors | 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 |
Journal | Genome Res |
Volume | 30 |
Issue | 1 |
Pagination | 49-61 |
Date Published | 2020 01 |
ISSN | 1549-5469 |
Keywords | Acrylamide, DNA, DNA Contamination, DNA Copy Number Variations, Gene Dosage, Gene Expression Profiling, Gene Library, Humans, Neoplasms, Nucleic Acids, Oligonucleotide Array Sequence Analysis, Polymerization, RNA, Single-Cell Analysis |
Abstract | We show the use of 5'-Acrydite oligonucleotides to copolymerize single-cell DNA or RNA into balls of acrylamide el (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. |
DOI | 10.1101/gr.253047.119 |
Alternate Journal | Genome Res |
PubMed ID | 31727682 |
PubMed Central ID | PMC6961581 |
Grant List | R01 MH113005 / MH / NIMH NIH HHS / United States R01 CA181595 / CA / NCI NIH HHS / United States R01 LM012736 / LM / NLM NIH HHS / United States T32 CA148056 / CA / NCI NIH HHS / United States U01 MH105991 / MH / NIMH NIH HHS / United States T32 GM065094 / GM / NIGMS NIH HHS / United States P30 CA045508 / CA / NCI NIH HHS / United States R01 MH113628 / MH / NIMH NIH HHS / United States |
Related Faculty:
Brian Robinson, M.D.