Virtual microfluidics for digital quantification and single-cell sequencing
We have developed hydrogel-based virtual microfluidics as a simple and robust alternative to complex engineered microfluidic systems for the compartmentalization of nucleic acid amplification reactions. We applied in-gel digital multiple displacement amplification (dMDA) to purified DNA templates, c...
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| Format: | Article |
| Language: | en_US |
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Nature Publishing Group
2017
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| Online Access: | http://hdl.handle.net/1721.1/107124 https://orcid.org/0000-0002-6699-2634 https://orcid.org/0000-0001-8294-9364 https://orcid.org/0000-0001-7014-3830 |
| _version_ | 1826201158837862400 |
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| author | Xu, Liyi Brito, Ilana Lauren Alm, Eric J Blainey, Paul C |
| author2 | Massachusetts Institute of Technology. Department of Biological Engineering |
| author_facet | Massachusetts Institute of Technology. Department of Biological Engineering Xu, Liyi Brito, Ilana Lauren Alm, Eric J Blainey, Paul C |
| author_sort | Xu, Liyi |
| collection | MIT |
| description | We have developed hydrogel-based virtual microfluidics as a simple and robust alternative to complex engineered microfluidic systems for the compartmentalization of nucleic acid amplification reactions. We applied in-gel digital multiple displacement amplification (dMDA) to purified DNA templates, cultured bacterial cells and human microbiome samples in the virtual microfluidics system, and demonstrated whole-genome sequencing of single-cell MDA products with excellent coverage uniformity and markedly reduced chimerism compared with products of liquid MDA reactions. |
| first_indexed | 2024-09-23T11:47:09Z |
| format | Article |
| id | mit-1721.1/107124 |
| institution | Massachusetts Institute of Technology |
| language | en_US |
| last_indexed | 2024-09-23T11:47:09Z |
| publishDate | 2017 |
| publisher | Nature Publishing Group |
| record_format | dspace |
| spelling | mit-1721.1/1071242022-10-01T06:02:23Z Virtual microfluidics for digital quantification and single-cell sequencing Xu, Liyi Brito, Ilana Lauren Alm, Eric J Blainey, Paul C Massachusetts Institute of Technology. Department of Biological Engineering Xu, Liyi Brito, Ilana Lauren Alm, Eric J Blainey, Paul C We have developed hydrogel-based virtual microfluidics as a simple and robust alternative to complex engineered microfluidic systems for the compartmentalization of nucleic acid amplification reactions. We applied in-gel digital multiple displacement amplification (dMDA) to purified DNA templates, cultured bacterial cells and human microbiome samples in the virtual microfluidics system, and demonstrated whole-genome sequencing of single-cell MDA products with excellent coverage uniformity and markedly reduced chimerism compared with products of liquid MDA reactions. Broad Institute of MIT and Harvard (Lawrence Summers Fellowship) Burroughs Wellcome Fund (Career Award) Massachusetts Institute of Technology. Center for Microbiome Informatics and Therapeutics National Human Genome Research Institute (U.S.) (Broad Institute of MIT and Harvard. Grant U54HG003067) Massachusetts Institute of Technology. Center for Environmental Health Sciences Fiji. Ministry of Health 2017-02-23T18:21:59Z 2017-02-23T18:21:59Z 2016-08 2016-02 Article http://purl.org/eprint/type/JournalArticle 1548-7091 1548-7105 http://hdl.handle.net/1721.1/107124 Xu, Liyi et al. “Virtual Microfluidics for Digital Quantification and Single-Cell Sequencing.” Nature Methods 13.9 (2016): 759–762. https://orcid.org/0000-0002-6699-2634 https://orcid.org/0000-0001-8294-9364 https://orcid.org/0000-0001-7014-3830 en_US http://dx.doi.org/10.1038/nmeth.3955 Nature Methods Article is made available in accordance with the publisher's policy and may be subject to US copyright law. Please refer to the publisher's site for terms of use. application/pdf Nature Publishing Group PMC |
| spellingShingle | Xu, Liyi Brito, Ilana Lauren Alm, Eric J Blainey, Paul C Virtual microfluidics for digital quantification and single-cell sequencing |
| title | Virtual microfluidics for digital quantification and single-cell sequencing |
| title_full | Virtual microfluidics for digital quantification and single-cell sequencing |
| title_fullStr | Virtual microfluidics for digital quantification and single-cell sequencing |
| title_full_unstemmed | Virtual microfluidics for digital quantification and single-cell sequencing |
| title_short | Virtual microfluidics for digital quantification and single-cell sequencing |
| title_sort | virtual microfluidics for digital quantification and single cell sequencing |
| url | http://hdl.handle.net/1721.1/107124 https://orcid.org/0000-0002-6699-2634 https://orcid.org/0000-0001-8294-9364 https://orcid.org/0000-0001-7014-3830 |
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