End-to-end pipeline for differential analysis of pausing in ribosome profiling data
Summary: Ribosome profiling is a powerful technique which maps the distribution of ribosomes along mRNAs to analyze translation genome-wide. Ribosome density can be affected by multiple factors, such as changes to translation initiation or elongation rates. We describe the application of a metric fo...
| Main Authors: | , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Elsevier
2022-09-01
|
| Series: | STAR Protocols |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2666166722004853 |
| _version_ | 1811284170078420992 |
|---|---|
| author | Keegan Flanagan Wanxin Li Ethan J. Greenblatt Khanh Dao Duc |
| author_facet | Keegan Flanagan Wanxin Li Ethan J. Greenblatt Khanh Dao Duc |
| author_sort | Keegan Flanagan |
| collection | DOAJ |
| description | Summary: Ribosome profiling is a powerful technique which maps the distribution of ribosomes along mRNAs to analyze translation genome-wide. Ribosome density can be affected by multiple factors, such as changes to translation initiation or elongation rates. We describe the application of a metric for identifying genes rate-limited by these rates by analyzing the relative distribution of ribosome footprints along transcripts. This protocol also details two sample analyses comparing gene translation efficiencies and the distribution of ribosome densities on downloadable datasets.For complete details on the use and execution of this protocol, please refer to Flanagan et al. (2022). : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics. |
| first_indexed | 2024-04-13T02:24:40Z |
| format | Article |
| id | doaj.art-7557e064d6eb45c8a9410f9e25758220 |
| institution | Directory Open Access Journal |
| issn | 2666-1667 |
| language | English |
| last_indexed | 2024-04-13T02:24:40Z |
| publishDate | 2022-09-01 |
| publisher | Elsevier |
| record_format | Article |
| series | STAR Protocols |
| spelling | doaj.art-7557e064d6eb45c8a9410f9e257582202022-12-22T03:06:49ZengElsevierSTAR Protocols2666-16672022-09-0133101605End-to-end pipeline for differential analysis of pausing in ribosome profiling dataKeegan Flanagan0Wanxin Li1Ethan J. Greenblatt2Khanh Dao Duc3Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada; Department of Mathematics, University of British Columbia, Vancouver, BC, CanadaSchool of Computer Science, University of Waterloo, Waterloo, ON, Canada; Department of Computer Science, University of British Columbia, Vancouver, BC, CanadaDepartment of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada; Corresponding authorDepartment of Mathematics, University of British Columbia, Vancouver, BC, Canada; Department of Computer Science, University of British Columbia, Vancouver, BC, Canada; Corresponding authorSummary: Ribosome profiling is a powerful technique which maps the distribution of ribosomes along mRNAs to analyze translation genome-wide. Ribosome density can be affected by multiple factors, such as changes to translation initiation or elongation rates. We describe the application of a metric for identifying genes rate-limited by these rates by analyzing the relative distribution of ribosome footprints along transcripts. This protocol also details two sample analyses comparing gene translation efficiencies and the distribution of ribosome densities on downloadable datasets.For complete details on the use and execution of this protocol, please refer to Flanagan et al. (2022). : 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/S2666166722004853BioinformaticsSequence analysisGenomics |
| spellingShingle | Keegan Flanagan Wanxin Li Ethan J. Greenblatt Khanh Dao Duc End-to-end pipeline for differential analysis of pausing in ribosome profiling data STAR Protocols Bioinformatics Sequence analysis Genomics |
| title | End-to-end pipeline for differential analysis of pausing in ribosome profiling data |
| title_full | End-to-end pipeline for differential analysis of pausing in ribosome profiling data |
| title_fullStr | End-to-end pipeline for differential analysis of pausing in ribosome profiling data |
| title_full_unstemmed | End-to-end pipeline for differential analysis of pausing in ribosome profiling data |
| title_short | End-to-end pipeline for differential analysis of pausing in ribosome profiling data |
| title_sort | end to end pipeline for differential analysis of pausing in ribosome profiling data |
| topic | Bioinformatics Sequence analysis Genomics |
| url | http://www.sciencedirect.com/science/article/pii/S2666166722004853 |
| work_keys_str_mv | AT keeganflanagan endtoendpipelinefordifferentialanalysisofpausinginribosomeprofilingdata AT wanxinli endtoendpipelinefordifferentialanalysisofpausinginribosomeprofilingdata AT ethanjgreenblatt endtoendpipelinefordifferentialanalysisofpausinginribosomeprofilingdata AT khanhdaoduc endtoendpipelinefordifferentialanalysisofpausinginribosomeprofilingdata |