Ribosome Profiling: Methods and Protocols

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