Executing cell-specific cross-linking immunoprecipitation and sequencing (seCLIP) in C. elegans
Summary: The single-end enhanced cross-linking immunoprecipitation (seCLIP) method is well suited for efficient and unbiased transcriptome-wide interrogation of RNA-binding protein (RBP) interaction sites. Here, we provide a protocol for executing cell-specific seCLIP for any desired RBP in Caenorha...
| Main Authors: | , |
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| Format: | Article |
| Language: | English |
| Published: |
Elsevier
2023-03-01
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| Series: | STAR Protocols |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2666166722008395 |
| _version_ | 1797977770074046464 |
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| author | Stephen M. Blazie Yishi Jin |
| author_facet | Stephen M. Blazie Yishi Jin |
| author_sort | Stephen M. Blazie |
| collection | DOAJ |
| description | Summary: The single-end enhanced cross-linking immunoprecipitation (seCLIP) method is well suited for efficient and unbiased transcriptome-wide interrogation of RNA-binding protein (RBP) interaction sites. Here, we provide a protocol for executing cell-specific seCLIP for any desired RBP in Caenorhabditis elegans. We begin with steps and recommendations for transgene construction and Cas9-mediated chromosomal integration. We provide detailed procedures for isolation of RBP-associated RNA fragments, subsequent library preparation, and sequencing. We further discuss best practices for data analysis, interpretation of results, and troubleshooting.For complete details on the use and execution of this protocol, please refer to Blazie et al. (2021).1 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics. |
| first_indexed | 2024-04-11T05:12:17Z |
| format | Article |
| id | doaj.art-c77835d1cd9f41049871b74b72289f69 |
| institution | Directory Open Access Journal |
| issn | 2666-1667 |
| language | English |
| last_indexed | 2024-04-11T05:12:17Z |
| publishDate | 2023-03-01 |
| publisher | Elsevier |
| record_format | Article |
| series | STAR Protocols |
| spelling | doaj.art-c77835d1cd9f41049871b74b72289f692022-12-25T04:19:17ZengElsevierSTAR Protocols2666-16672023-03-0141101959Executing cell-specific cross-linking immunoprecipitation and sequencing (seCLIP) in C. elegansStephen M. Blazie0Yishi Jin1Department of Neurobiology, School of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Corresponding authorDepartment of Neurobiology, School of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Corresponding authorSummary: The single-end enhanced cross-linking immunoprecipitation (seCLIP) method is well suited for efficient and unbiased transcriptome-wide interrogation of RNA-binding protein (RBP) interaction sites. Here, we provide a protocol for executing cell-specific seCLIP for any desired RBP in Caenorhabditis elegans. We begin with steps and recommendations for transgene construction and Cas9-mediated chromosomal integration. We provide detailed procedures for isolation of RBP-associated RNA fragments, subsequent library preparation, and sequencing. We further discuss best practices for data analysis, interpretation of results, and troubleshooting.For complete details on the use and execution of this protocol, please refer to Blazie et al. (2021).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/S2666166722008395GeneticsGenomics |
| spellingShingle | Stephen M. Blazie Yishi Jin Executing cell-specific cross-linking immunoprecipitation and sequencing (seCLIP) in C. elegans STAR Protocols Genetics Genomics |
| title | Executing cell-specific cross-linking immunoprecipitation and sequencing (seCLIP) in C. elegans |
| title_full | Executing cell-specific cross-linking immunoprecipitation and sequencing (seCLIP) in C. elegans |
| title_fullStr | Executing cell-specific cross-linking immunoprecipitation and sequencing (seCLIP) in C. elegans |
| title_full_unstemmed | Executing cell-specific cross-linking immunoprecipitation and sequencing (seCLIP) in C. elegans |
| title_short | Executing cell-specific cross-linking immunoprecipitation and sequencing (seCLIP) in C. elegans |
| title_sort | executing cell specific cross linking immunoprecipitation and sequencing seclip in c elegans |
| topic | Genetics Genomics |
| url | http://www.sciencedirect.com/science/article/pii/S2666166722008395 |
| work_keys_str_mv | AT stephenmblazie executingcellspecificcrosslinkingimmunoprecipitationandsequencingseclipincelegans AT yishijin executingcellspecificcrosslinkingimmunoprecipitationandsequencingseclipincelegans |