CRISPR-SURF: discovering regulatory elements by deconvolution of CRISPR tiling screen data
Tiling screens that use CRISPR-Cas technologies provide a powerful approach for the mapping of regulatory elements to phenotypes of interest1–6. Here we present CRISPR screening uncharacterized region function (CRISPR-SURF), a deconvolution framework that can be used to identify functional regulator...
| Main Authors: | , , , , , , |
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| Other Authors: | |
| Format: | Article |
| Language: | English |
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Springer Science and Business Media LLC
2020
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| Online Access: | https://hdl.handle.net/1721.1/125387 |
| _version_ | 1811092238220918784 |
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| author | Hsu, Jonathan Y. Fulco, Charles P. Farouni, Rick Clement, Kendell Engreitz, Jesse Michael Lander, Eric Steven Pinello, Luca |
| author2 | Massachusetts Institute of Technology. Department of Biological Engineering |
| author_facet | Massachusetts Institute of Technology. Department of Biological Engineering Hsu, Jonathan Y. Fulco, Charles P. Farouni, Rick Clement, Kendell Engreitz, Jesse Michael Lander, Eric Steven Pinello, Luca |
| author_sort | Hsu, Jonathan Y. |
| collection | MIT |
| description | Tiling screens that use CRISPR-Cas technologies provide a powerful approach for the mapping of regulatory elements to phenotypes of interest1–6. Here we present CRISPR screening uncharacterized region function (CRISPR-SURF), a deconvolution framework that can be used to identify functional regulatory regions in the genome from data generated by CRISPR-Cas nuclease, CRISPR interference (CRISPRi), or CRISPR activation (CRISPRa) tiling screens. CRISPR-SURF can be run as a stand-alone command line utility (https://github.com/pinellolab/CRISPR-SURF) or as a web application (http://crisprsurf.pinellolab.org/) |
| first_indexed | 2024-09-23T15:15:16Z |
| format | Article |
| id | mit-1721.1/125387 |
| institution | Massachusetts Institute of Technology |
| language | English |
| last_indexed | 2024-09-23T15:15:16Z |
| publishDate | 2020 |
| publisher | Springer Science and Business Media LLC |
| record_format | dspace |
| spelling | mit-1721.1/1253872022-10-02T01:41:41Z CRISPR-SURF: discovering regulatory elements by deconvolution of CRISPR tiling screen data Hsu, Jonathan Y. Fulco, Charles P. Farouni, Rick Clement, Kendell Engreitz, Jesse Michael Lander, Eric Steven Pinello, Luca Massachusetts Institute of Technology. Department of Biological Engineering Massachusetts Institute of Technology. Department of Biology Tiling screens that use CRISPR-Cas technologies provide a powerful approach for the mapping of regulatory elements to phenotypes of interest1–6. Here we present CRISPR screening uncharacterized region function (CRISPR-SURF), a deconvolution framework that can be used to identify functional regulatory regions in the genome from data generated by CRISPR-Cas nuclease, CRISPR interference (CRISPRi), or CRISPR activation (CRISPRa) tiling screens. CRISPR-SURF can be run as a stand-alone command line utility (https://github.com/pinellolab/CRISPR-SURF) or as a web application (http://crisprsurf.pinellolab.org/) National Human Genome Research Institute (U.S.) (Career Development Award R00 HG008399) National Human Genome Research Institute (U.S.). Centers of Excellence in Genomic Science (Grant RM1HG009490) National Institutes of Health (U.S.) (Grant R35 GM118158) National Institutes of Health (U.S.) (Grant RM1 HG009490) National Human Genome Research Institute (U.S.) (Grant 1K99HG009917-01) 2020-05-21T19:12:31Z 2020-05-21T19:12:31Z 2018-12 2020-01-22T17:53:53Z Article http://purl.org/eprint/type/JournalArticle 1548-7091 https://hdl.handle.net/1721.1/125387 Hsu, Jonathan Y. et al. “CRISPR-SURF: discovering regulatory elements by deconvolution of CRISPR tiling screen data.” Nature methods 15 (2018): 992-993 © 2018 The Author(s) en 10.1038/S41592-018-0225-6 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 Springer Science and Business Media LLC PMC |
| spellingShingle | Hsu, Jonathan Y. Fulco, Charles P. Farouni, Rick Clement, Kendell Engreitz, Jesse Michael Lander, Eric Steven Pinello, Luca CRISPR-SURF: discovering regulatory elements by deconvolution of CRISPR tiling screen data |
| title | CRISPR-SURF: discovering regulatory elements by deconvolution of CRISPR tiling screen data |
| title_full | CRISPR-SURF: discovering regulatory elements by deconvolution of CRISPR tiling screen data |
| title_fullStr | CRISPR-SURF: discovering regulatory elements by deconvolution of CRISPR tiling screen data |
| title_full_unstemmed | CRISPR-SURF: discovering regulatory elements by deconvolution of CRISPR tiling screen data |
| title_short | CRISPR-SURF: discovering regulatory elements by deconvolution of CRISPR tiling screen data |
| title_sort | crispr surf discovering regulatory elements by deconvolution of crispr tiling screen data |
| url | https://hdl.handle.net/1721.1/125387 |
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