High-throughput functional analysis of regulatory variants using a massively parallel reporter assay
Summary: Association studies describe genetic associations between noncoding variants and disease susceptibility; however, they do not provide functional insight into the underlying molecular mechanisms of these variants. We present a protocol to assay the regulatory potential of thousands of noncod...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2023-12-01
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| Series: | STAR Protocols |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2666166723006986 |
| _version_ | 1797582956333629440 |
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| author | Kate Delfosse Chiara Gerhardinger John L. Rinn Philipp G. Maass |
| author_facet | Kate Delfosse Chiara Gerhardinger John L. Rinn Philipp G. Maass |
| author_sort | Kate Delfosse |
| collection | DOAJ |
| description | Summary: Association studies describe genetic associations between noncoding variants and disease susceptibility; however, they do not provide functional insight into the underlying molecular mechanisms of these variants. We present a protocol to assay the regulatory potential of thousands of noncoding variants using massively parallel reporter assays. We describe steps for oligo design, generating a plasmid pool, and extracting tag-seq libraries from cells to quantify the tested sequences.For complete details on the use and execution of this protocol, please refer to Oliveros and Delfosse et al.1 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics. |
| first_indexed | 2024-03-10T23:29:58Z |
| format | Article |
| id | doaj.art-ab322862dc5f402780c466cbf5a25657 |
| institution | Directory Open Access Journal |
| issn | 2666-1667 |
| language | English |
| last_indexed | 2024-03-10T23:29:58Z |
| publishDate | 2023-12-01 |
| publisher | Elsevier |
| record_format | Article |
| series | STAR Protocols |
| spelling | doaj.art-ab322862dc5f402780c466cbf5a256572023-11-19T04:35:30ZengElsevierSTAR Protocols2666-16672023-12-0144102731High-throughput functional analysis of regulatory variants using a massively parallel reporter assayKate Delfosse0Chiara Gerhardinger1John L. Rinn2Philipp G. Maass3Genetics & Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, CanadaDepartment of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USABioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80303, USA; Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80303, USAGenetics & Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 3E1, Canada; Corresponding authorSummary: Association studies describe genetic associations between noncoding variants and disease susceptibility; however, they do not provide functional insight into the underlying molecular mechanisms of these variants. We present a protocol to assay the regulatory potential of thousands of noncoding variants using massively parallel reporter assays. We describe steps for oligo design, generating a plasmid pool, and extracting tag-seq libraries from cells to quantify the tested sequences.For complete details on the use and execution of this protocol, please refer to Oliveros and Delfosse et al.1 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.http://www.sciencedirect.com/science/article/pii/S2666166723006986GeneticsGenomicsHigh Throughput ScreeningGene ExpressionSystems biology |
| spellingShingle | Kate Delfosse Chiara Gerhardinger John L. Rinn Philipp G. Maass High-throughput functional analysis of regulatory variants using a massively parallel reporter assay STAR Protocols Genetics Genomics High Throughput Screening Gene Expression Systems biology |
| title | High-throughput functional analysis of regulatory variants using a massively parallel reporter assay |
| title_full | High-throughput functional analysis of regulatory variants using a massively parallel reporter assay |
| title_fullStr | High-throughput functional analysis of regulatory variants using a massively parallel reporter assay |
| title_full_unstemmed | High-throughput functional analysis of regulatory variants using a massively parallel reporter assay |
| title_short | High-throughput functional analysis of regulatory variants using a massively parallel reporter assay |
| title_sort | high throughput functional analysis of regulatory variants using a massively parallel reporter assay |
| topic | Genetics Genomics High Throughput Screening Gene Expression Systems biology |
| url | http://www.sciencedirect.com/science/article/pii/S2666166723006986 |
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