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Yeast Functional Genomics

Methods and Protocols

  • Includes cutting-edge methods and protocols

  • Provides step-by-step detail essential for reproducible results

  • Contains key notes and implementation advice from the experts

Part of the book series: Methods in Molecular Biology (MIMB, volume 2477)

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  • ISBN: 978-1-0716-2257-5
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  • Tax calculation will be finalised during checkout
Hardcover Book USD 219.99
Price excludes VAT (USA)

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Table of contents (25 protocols)

  1. Front Matter

    Pages i-xv
  2. Transcriptomic Analyses

    1. Front Matter

      Pages 1-1
    2. Single-Cell RNA Sequencing in Yeast Using the 10× Genomics Chromium Device

      • Lieselotte Vermeersch, Abbas Jariani, Jana Helsen, Benjamin M. Heineike, Kevin J. Verstrepen
      Pages 3-20Open Access
    3. Genome-Wide Profiling of Transcription Initiation with STRIPE-seq

      • Robert A. Policastro, Gabriel E. Zentner
      Pages 21-34
    4. High-Resolution Deep Sequencing of Nascent Transcription in Yeast with BioGRO-seq

      • Antonio Jordán-Pla, José E. Pérez-Ortín
      Pages 57-70
    5. Direct Sequencing of RNA and RNA Modification Identification Using Nanopore

      • Thidathip Wongsurawat, Piroon Jenjaroenpun, Intawat Nookaew
      Pages 71-77
    6. UNAGI: Yeast Transcriptome Reconstruction and Gene Discovery Using Nanopore Sequencing

      • Mohamad Al kadi, Nicolas Jung, Daisuke Okuzaki
      Pages 79-89
  3. DNA Replication and Protein/DNA Interactions

    1. Front Matter

      Pages 105-105
    2. FORK-seq: Single-Molecule Profiling of DNA Replication

      • Magali Hennion, Bertrand Theulot, Jean-Michel Arbona, Benjamin Audit, Olivier Hyrien
      Pages 107-128
    3. CUT&RUN Profiling of the Budding Yeast Epigenome

      • Sandipan Brahma, Steven Henikoff
      Pages 129-147Open Access
    4. ChIP-SICAP: A New Tool to Explore Gene-Regulatory Networks in Candida albicans and Other Yeasts

      • Lasse van Wijlick, Ansh Goyal, Sophie Bachellier-Bassi, Christophe d’Enfert
      Pages 149-175
  4. Translation Dynamics, Protein Complexes, and Proteomics

    1. Front Matter

      Pages 177-177
    2. Purification of Ribosome-Nascent-Chain Complex for Ribosome Profiling and Selective Ribosome Profiling

      • Hagit Bar-Yosef, Johannes Venezian, Kevin Klann, Ayala Shiber
      Pages 179-193
    3. Deep Mutational Scanning of Protein–Protein Interactions Between Partners Expressed from Their Endogenous Loci In Vivo

      • Alexandre K. Dubé, Rohan Dandage, Soham Dibyachintan, Ugo Dionne, Philippe C. Després, Christian R. Landry
      Pages 237-259
    4. Quantitative Proteomics in Yeast : From bSLIM and Proteome Discoverer Outputs to Graphical Assessment of the Significance of Protein Quantification Scores

      • Nicolas Sénécaut, Pierre Poulain, Laurent Lignières, Samuel Terrier, Véronique Legros, Guillaume Chevreux et al.
      Pages 275-292Open Access

About this book

This second edition volume discusses the latest techniques and protocols used in the field that were not covered in the previous edition. The chapters in this book are organized into five parts. Part One looks at transcriptomic analyses and Part Two covers DNA replication and protein/DNA interactions. Part Three discusses translation dynamics, protein complexes, and proteomics. Part Four looks at genotypic screens and phenotypic profiling, and Part Five explores in silico integration of functional genomics data. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary material and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.

Cutting edge and practical, Yeast Functional Genomics: Methods and Protocols, Second Edition is a valuable resource for all researchers interested in learning more about the evolving field of yeast.

Chapters 1, 9, 16, 20, 22, 24, and 25 are available open access under a Creative Commons Attribution 4.0 International License via link.springer.com. 

 

Keywords

  • RNA-RNA interactions
  • ChIP
  • mass spectrometry
  • COFRADIC
  • CRISPR-CAS.

Editors and Affiliations

  • Institut de Biologie Paris Seine, Sorbonne Université, Paris, France

    Frédéric Devaux

Bibliographic Information

  • Book Title: Yeast Functional Genomics

  • Book Subtitle: Methods and Protocols

  • Editors: Frédéric Devaux

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-0716-2257-5

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: The Editor(s) (if applicable) and The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature 2022

  • Hardcover ISBN: 978-1-0716-2256-8

  • eBook ISBN: 978-1-0716-2257-5

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 2

  • Number of Pages: XV, 474

  • Number of Illustrations: 8 b/w illustrations, 74 illustrations in colour

  • Topics: Microbiology

Buying options

eBook USD 169.00
Price excludes VAT (USA)
  • ISBN: 978-1-0716-2257-5
  • Instant PDF download
  • Readable on all devices
  • Own it forever
  • Exclusive offer for individuals only
  • Tax calculation will be finalised during checkout
Hardcover Book USD 219.99
Price excludes VAT (USA)