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E-raamat: Yeast Functional Genomics: Methods and Protocols

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This volume provides a collection 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 Protocolsaims to ensure successful results in the further study of this vital field.

Preface v
Contributors ix
1 Using RNA-seq for Analysis of Differential Gene Expression in Fungal Species
1(40)
Can Wang
Markus S. Schroder
Stephen Hammel
Geraldine Butler
2 Enhancing Structural Annotation of Yeast Genomes with RNA-Seq Data
41(16)
Hugo Devillers
Nicolas Morin
Cecile Neuveglise
3 Pathogen Gene Expression Profiling During Infection Using a Nanostring nCounter Platform
57(10)
Wenjie Xu
Norma V. Solis
Scott G. Filler
Aaron P. Mitchell
4 Comparative Transcriptomics in Yeasts
67(10)
Dawn A. Thompson
5 Mapping the Transcriptome-Wide Landscape of RBP Binding Sites Using gPAR-CLIP-seq: Experimental Procedures
77(14)
Ting Han
John K. Kim
6 Mapping the Transcriptome-Wide Landscape of RBP Binding Sites Using gPAR-CLIP-seq: Bioinformatic Analysis
91(14)
Mallory A. Freeberg
John K. Kim
7 Translation Analysis at the Genome Scale by Ribosome Profiling
105(20)
Agnes Baudin-Baillieu
Isabelle Hatin
Rachel Legendre
Olivier Namy
8 Biotin-Genomic Run-On (Bio-GRO): A High-Resolution Method for the Analysis of Nascent Transcription in Yeast
125(16)
Antonio Jordan-Pla
Ana Miguel
Eva Serna
Vicent Pelechano
Jose E. Perez-Ortin
9 Genome-Wide Probing of RNA Structures In Vitro Using Nucleases and Deep Sequencing
141(20)
Yue Wan
Kun Qu
Zhengqing Ouyang
Howard Y. Chang
10 Genome-Wide Chromatin Immunoprecipitation in Candida albicans and Other Yeasts
161(24)
Matthew B. Lohse
Pisiwat Kongsomboonvech
Maria Madrigal
Aaron D. Hernday
Clarissa J. Nobile
11 ChIPseq in Yeast Species: From Chromatin Immunoprecipitation to High-Throughput Sequencing and Bioinformatics Data Analyses
185(18)
Gaelle Lelandais
Corinne Blugeon
Jawad Merhej
12 Systematic Determination of Transcription Factor DNA-Binding Specificities in Yeast
203(24)
Lourdes Pena-Castillo
Gwenael Badis
13 Generation and Analysis of Chromosomal Contact Maps of Yeast Species
227(20)
Axel Cournac
Martial Marbouty
Julien Mozziconacci
Romain Koszul
14 A Versatile Procedure to Generate Genome-Wide Spatiotemporal Program of Replication in Yeast Species
247(18)
Nicolas Agier
Gilles Fischer
15 Single-Step Affinity Purification (ssAP) and Mass Spectrometry of Macromolecular Complexes in the Yeast S. cerevisiae
265(24)
Christian Traban
Lisbeth-Carolina Aguilar
Marlene Oeffinger
16 Label-Free Quantitative Proteomics in Yeast
289(20)
Thibaut Leger
Camille Garcia
Mathieu Videlier
Jean-Michel Camadro
17 Profiling of Yeast Lipids by Shotgun Lipidomics
309(16)
Christian Klose
Kirill Tarasov
18 Identification of Links Between Cellular Pathways by Genetic Interaction Mapping (GIM)
325(20)
Christophe Malabat
Cosmin Saveanu
19 On the Mapping of Epistatic Genetic Interactions in Natural Isolates: Combining Classical Genetics and Genomics
345(16)
Jing Hou
Joseph Schacherer
20 Experimental Evolution and Resequencing Analysis of Yeast
361(14)
Celia Payen
Maitreya J. Dunham
21 Reconstruction and Analysis of the Evolution of Modular Transcriptional Regulatory Programs Using Arboretum
375(16)
Sara A. Knaack
Dawn A. Thompson
Sushmita Roy
22 Predicting Gene and Genomic Regulation in Saccharomyces cerevisiae, using the YEASTRACT Database: A Step-by-Step Guided Analysis
391(14)
Miguel C. Teixeira
Pedro T. Monteiro
Isabel Sa-Correia
Index 405
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