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Ribosome Profiling: Methods and Protocols

Ribosome Profiling

Methods and Protocols
 
Kiadás sorszáma: 1st ed. 2021
Kiadó: Humana
Megjelenés dátuma:
Kötetek száma: 1 pieces, Book
 
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A termék adatai:
ISBN13:9781071611494
ISBN10:1071611496
Kötéstípus:Keménykötés
Terjedelem:348 oldal
Méret:254x178 mm
Súly:874 g
Nyelv:angol
Illusztrációk: 19 Illustrations, black & white; 53 Illustrations, color
298
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Rövid leírás:

This book provides a single-source reference on the current state of the ribosome profiling method by describing experimental protocols for the quantitative analysis of translation in a variety of model organisms. In addition, the volume presents a detailed overview of the existing software tools and includes detailed description of methods for statistical analysis, data processing, and visualization of ribosome profiling data. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. 

Authoritative and practical, Ribosome Profiling: Methods and Protocols aims to provide the type of standardized protocols that have previously been unavailable in an effort to bypass the major barriers to wide use of ribosome profiling-based approaches.

Hosszú leírás:
This book provides a single-source reference on the current state of the ribosome profiling method by describing experimental protocols for the quantitative analysis of translation in a variety of model organisms. In addition, the volume presents a detailed overview of the existing software tools and includes detailed description of methods for statistical analysis, data processing, and visualization of ribosome profiling data. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. 

Authoritative and practical, Ribosome Profiling: Methods and Protocols aims to provide the type of standardized protocols that have previously been unavailable in an effort to bypass the major barriers to wide use of ribosome profiling-based approaches.
Tartalomjegyzék:

Part I: Experimental Protocols



 



1. Monitoring Bacterial Translation Rates Genome-Wide



            Eugene Oh



 



2. Identification of Translation Start Sites in Bacterial Genomes



            Sezen Meydan, Dorota Klepacki, Alexander S. Mankin, and Nora Vázquez-Laslop



 



3. Genome-Wide Ribosome Profiling of the Plasmodium falciparum Intraerythrocytic Developmental Cycle



            Florence Caro and Joseph L. DeRisi



 



4. Performing Ribosome Profiling to Assess Translation in Vegetative and Meiotic Yeast Cells



            Emily Nicole Powers and Gloria Ann Brar



 



5. Quantitative Comparisons of Translation Activity by Ribosome Profiling with Internal Standards



            Yinuo J. Wang and Wendy V. Gilbert



 



6. Genome-Wide Analysis of Translation in Replicatively Aged Yeast



            Hanna Barlit, Manish K. Rai, Sara Shoushtari, Carine Beaupere, and Vyacheslav M. Labunskyy



 



7. Tissue-Specific Ribosome Profiling in Drosophila



            Xun Chen and Dion Dickman



 



8. Measuring Organ-Specific Translation Elongation Rate in Mice



            Maxim Gerashchenko and Vadim N. Gladyshev



 



9. Active Ribosome Profiling with RiboLace: From Bench to Data Analysis



            Massimiliano Clamer, Fabio Lauria, Toma Tebaldi, and Gabriella Viero



 



10. Poly-A Tailing and Adaptor Ligation Methods for Ribo-Seq Library Construction



            Jingfan Qiu and Shu-Bing Qian



 



11. Choice of Ribonucleases for Ribosome Profiling Experiments



            Maxim Gerashchenko



 



Part II: Bioinformatics and Statistical Analysis



 



12. Codon Resolution Analysis of Ribosome Profiling Data



            Alexander Bartholomäus and Zoya Ignatova



 



13. Assessing Ribosome Distribution Along Transcripts with Polarity Scores and Regression Slope Estimates



            Ilya E. Vorontsov, Artyom A. Egorov, Aleksandra S. Anisimova, Irina A. Eliseeva, Vsevolod J. Makeev, Vadim N. Gladyshev, Sergey E. Dmitriev, and Ivan V. Kulakovskiy



 



14. Unsupervised Bayesian Prediction of RNA Translation from Ribosome Profiling Data



            Etienne Boileau and Christoph Dieterich



 



15. uORF-seqr: A Machine Learning-Based Approach to the Identification of Upstream Open Reading Frames in Yeast



            Pieter Spealman, Armaghan Naik, and Joel McManus



 



16. Genome-Wide Analysis of Actively Translated Open Reading Frames Using RiboTaper/ORFquant



            Dermot Harnett, Eelco Meerdink, Lorenzo Calviello, Dominique Sydow, and Uwe Ohler