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 deillegalscription 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.
Monitoring Bacterial Translation Rates Genome-Wide.- Identification of Translation Start Sites in Bacterial Genomes.- Genome-Wide Ribosome Profiling of the Plasmodium falciparum Intraerythrocytic Developmental Cycle.- Performing Ribosome Profiling to Assess Translation in Vegetative and Meiotic Yeast Cells.- Quantitative Comparisons of Translation Activity by Ribosome Profiling with Internal Standards.- Genome-Wide Analysis of Translation in Replicatively Aged Yeast.- Tissue-Specific Ribosome Profiling in Drosophila.- Measuring Organ-Specific Translation Elongation Rate in Mice.- Active Ribosome Profiling with RiboLace: From Bench to Data Analysis.- Poly-A Tailing and Adaptor Ligation Methods for Ribo-Seq Library Construction.- Choice of Ribonucleases for Ribosome Profiling Experiments.- Codon Resolution Analysis of Ribosome Profiling Data.- Assessing Ribosome Distribution Along Tranillegalscripts with Polarity Scores and Regression Slope Estimates.- Unsupervised Bayesian Predictionof RNA Translation from Ribosome Profiling Data.- uORF-seqr: A Machine Learning-Based Approach to the Identification of Upstream Open Reading Frames in Yeast.- Genome-Wide Analysis of Actively Translated Open Reading Frames Using RiboTaper/ORFquant.
Inhaltsverzeichnis
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 Tranillegalscripts 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
Klappentext
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 deillegalscription 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.
Includes cutting-edge techniques
Provides step-by-step detail essential for reproducible results
Contains key implementation advice from the experts
