Identifying essential long non-coding RNAs in cancer using CRISPRi-based dropout screens
Summary: Long non-coding RNAs (lncRNAs) are emerging as key regulators in the initiation, growth, and progression of cancer. High-throughput CRISPR-based techniques systematically assess the function of genes or regulatory elements present in the human genome. Here, we present a protocol for identif...
| 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/S2666166723005555 |
| _version_ | 1797671391028314112 |
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| author | Oscar Bril Laura J. Schwarzmueller Leandro F. Moreno Louis Vermeulen Nicolas Léveillé |
| author_facet | Oscar Bril Laura J. Schwarzmueller Leandro F. Moreno Louis Vermeulen Nicolas Léveillé |
| author_sort | Oscar Bril |
| collection | DOAJ |
| description | Summary: Long non-coding RNAs (lncRNAs) are emerging as key regulators in the initiation, growth, and progression of cancer. High-throughput CRISPR-based techniques systematically assess the function of genes or regulatory elements present in the human genome. Here, we present a protocol for identifying essential lncRNAs in cancer using CRISPRi-based dropout screens. We describe steps to select target sites, design guide RNAs, and generate CRISPRi cell lines. We then detail the execution and analysis of CRISPRi-based dropout screens. : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics. |
| first_indexed | 2024-03-11T21:14:50Z |
| format | Article |
| id | doaj.art-514d7088e61f442ba09b7809077387ca |
| institution | Directory Open Access Journal |
| issn | 2666-1667 |
| language | English |
| last_indexed | 2024-03-11T21:14:50Z |
| publishDate | 2023-12-01 |
| publisher | Elsevier |
| record_format | Article |
| series | STAR Protocols |
| spelling | doaj.art-514d7088e61f442ba09b7809077387ca2023-09-29T04:45:08ZengElsevierSTAR Protocols2666-16672023-12-0144102588Identifying essential long non-coding RNAs in cancer using CRISPRi-based dropout screensOscar Bril0Laura J. Schwarzmueller1Leandro F. Moreno2Louis Vermeulen3Nicolas Léveillé4Center for Experimental and Molecular Medicine, Cancer Center Amsterdam and Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, Amsterdam 1105AZ, The Netherlands; Oncode Institute, Meibergdreef 9, Amsterdam 1105AZ, The NetherlandsCenter for Experimental and Molecular Medicine, Cancer Center Amsterdam and Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, Amsterdam 1105AZ, The Netherlands; Oncode Institute, Meibergdreef 9, Amsterdam 1105AZ, The NetherlandsCenter for Experimental and Molecular Medicine, Cancer Center Amsterdam and Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, Amsterdam 1105AZ, The Netherlands; Oncode Institute, Meibergdreef 9, Amsterdam 1105AZ, The NetherlandsCenter for Experimental and Molecular Medicine, Cancer Center Amsterdam and Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, Amsterdam 1105AZ, The Netherlands; Oncode Institute, Meibergdreef 9, Amsterdam 1105AZ, The NetherlandsCenter for Experimental and Molecular Medicine, Cancer Center Amsterdam and Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, Amsterdam 1105AZ, The Netherlands; Oncode Institute, Meibergdreef 9, Amsterdam 1105AZ, The Netherlands; Corresponding authorSummary: Long non-coding RNAs (lncRNAs) are emerging as key regulators in the initiation, growth, and progression of cancer. High-throughput CRISPR-based techniques systematically assess the function of genes or regulatory elements present in the human genome. Here, we present a protocol for identifying essential lncRNAs in cancer using CRISPRi-based dropout screens. We describe steps to select target sites, design guide RNAs, and generate CRISPRi cell lines. We then detail the execution and analysis of CRISPRi-based dropout screens. : 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/S2666166723005555BioinformaticsCell BiologyGenomicsMolecular BiologyCRISPR |
| spellingShingle | Oscar Bril Laura J. Schwarzmueller Leandro F. Moreno Louis Vermeulen Nicolas Léveillé Identifying essential long non-coding RNAs in cancer using CRISPRi-based dropout screens STAR Protocols Bioinformatics Cell Biology Genomics Molecular Biology CRISPR |
| title | Identifying essential long non-coding RNAs in cancer using CRISPRi-based dropout screens |
| title_full | Identifying essential long non-coding RNAs in cancer using CRISPRi-based dropout screens |
| title_fullStr | Identifying essential long non-coding RNAs in cancer using CRISPRi-based dropout screens |
| title_full_unstemmed | Identifying essential long non-coding RNAs in cancer using CRISPRi-based dropout screens |
| title_short | Identifying essential long non-coding RNAs in cancer using CRISPRi-based dropout screens |
| title_sort | identifying essential long non coding rnas in cancer using crispri based dropout screens |
| topic | Bioinformatics Cell Biology Genomics Molecular Biology CRISPR |
| url | http://www.sciencedirect.com/science/article/pii/S2666166723005555 |
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