Yeast Functional Genomics: Methods and Protocols

ISBN-13: 9781493930784 / Angielski / Twarda / 2015 / 406 str.

Frederic Devaux

Opis

This volume provides acollection of protocols for the study of DNA-DNA contact maps, replication profiles, transcription rates, RNA secondary structures, protein-RNA interactions, ribosome profiling and quantitative proteomes and metabolomes. Written for the 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, Yeast Functional Genomics: Methods and Protocols aims to ensure successful results in the further study of this vital field."

Spis treści

1. Using RNA-seq for Analysis of Differential Gene Expression in Fungal Species

Can Wang, Markus S. Schröder, Stephen Hammel, and Geraldine Butler

 

2. Enhancing Structural Annotation of Yeast Genomes with RNA-Seq Data

Hugo Devillers, Nicolas Morin, and Cécile Neuvéglise

 

3. Pathogen Gene Expression Profiling During Infection Using a Nanostring Ncounter Platform

Wenjie Xu, Norma V. Solis, Scott G. Filler, and Aaron P. Mitchell

 

4. Comparative Transcriptomics in Yeasts

Dawn A. Thompson

 

5. Mapping the Transcriptome-Wide Landscape of RBP Binding sites using gPAR-CLIP-seq: Experimental Procedures

Ting Ha and John K. Kim

 

6. Mapping the Transcriptome-wide Landscape of RBP Binding Sites using gPAR-CLIP-seq: Bioinformatic Analysis

Mallory A. Freeberg and John K. Kim

 

7. Translation Analysis at the Genome Scale by Ribosome Profiling

Agnès Baudin-Baillieu, Isabelle Hatin, Rachel Legendre, and Olivier Namy

 

8. Biotin-Genomic Run-on (Bio-GRO): A High-Resolution Method for the Analysis of Nascent Transcription in Yeast

Antonio Jordán-Pla, Ana Miguel, Eva Serna, Vicent Pelechano, and José E. Pérez-Ortín

 

9. Genome-wide Probing of RNA Structures in Vitro Using Nucleases and Deep Sequencing

Yue Wan,  Kun Qu, Zhengqing Ouyang and Howard Y. Chang

 

10. Genome-wide Chromatin Immunoprecipitation in Candida albicans and other Yeasts

Matthew B. Lohse, Pisiwat Kongsomboonvech, Maria Madrigal, Aaron D. Hernday, and Clarissa J. Nobile

 

11. ChIPseq in Yeast Species: from Chromatin Immumoprecipitation to High-Throughput Sequencing and Bioinformatics Data Analyses

Gaëlle Lelandais, Corinne Blugeon, and Jawad Merhej

 

12. Systematic Determination of Transcription factor DNA-binding Specificities in Yeast

Lourdes Peña-Castillo and Gwenael Badis

 

13. Generation and Analysis of Chromosomal Contact Maps of Yeast Species

Axel Cournac, Martial Marbouty, Julien Mozziconacci, and Romain Koszul

 

14. A Versatile Procedure to Generate Genome-Wide Spatio-Temporal Program of Replication in Yeast Species

Nicolas Agier and Gilles Fischer

 

15. Single-Step Affinity Purification (ssAP) and Mass Spectrometry of Macromolecular Complexes in the Yeast S. cerevisiae

Christian Trahan, Lisbeth-Carolina Aguilar, and Marlene Oeffinger

 

16. Label-Free Quantitative Proteomics in Yeast

Thibaut Léger, Camille Garcia, Mathieu Videlier, and Jean-Michel Camadro

 17. Profiling of Yeast Lipids by Shotgun Lipidomics

Klose Christian and Tarasov Kirill

 

18. Identification of Links between Cellular Pathways by Genetic Interaction Mapping (GIM)

Christophe Malabat and Cosmin Saveanu

 

19. On The Mapping of Epistatic Genetic Interactions in Natural Isolates: Combining Classical Genetics and Genomics

Jing Hou and Joseph Schacherer

 

20. Experimental Evolution and Resequencing Analysis of Yeast

Celia Payen and Maitreya J. Dunham

 

21. Reconstruction and Analysis of the Evolution of Modular Transcriptional Regulatory Programs using Arboretum

Sara A. Knaack, Dawn A. Thompson, and Sushmita Roy

 

22. Predicting Gene and Genomic Regulation in Saccharomyces cerevisiae, using the YEASTRACT Database: A Step By Step Guided Analysis

Miguel C. Teixeira, Pedro T. Monteiro, and  Isabel Sá-Correia