ژنومیک عملکردی مخمر- روشها و پروتکل ها Yeast functional genomics _ methods and protocols

فهرست مطالب: s Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . v Contributors. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xi PART I TRANSCRIPTOMIC ANALYSES 1 Single-Cell RNA Sequencing in Yeast Using the 10 Genomics Chromium Device . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 Lieselotte Vermeersch, Abbas Jariani, Jana Helsen, Benjamin M. Heineike, and Kevin J. Verstrepen 2 Genome-Wide Profiling of Transcription Initiation with STRIPE-seq . . . . . . . . . 21 Robert A. Policastro and Gabriel E. Zentner 3 A Modified Cross-Linking Analysis of cDNAs (CRAC) Protocol for Detecting RNA–Protein Interactions and Transcription at Single-Nucleotide Resolution . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35 Drice Challal, Jessie Colin, Tommaso Villa, and Domenico Libri 4 High-Resolution Deep Sequencing of Nascent Transcription in Yeast with BioGRO-seq. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57 Antonio Jorda´n-Pla and Jose´ E. Pe´rez-Ortı´n 5 Direct Sequencing of RNA and RNA Modification Identification Using Nanopore . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71 Thidathip Wongsurawat, Piroon Jenjaroenpun, and Intawat Nookaew 6 UNAGI: Yeast Transcriptome Reconstruction and Gene Discovery Using Nanopore Sequencing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79 Mohamad Al kadi, Nicolas Jung, and Daisuke Okuzaki 7 Identification of Taxonomically Restricted Transcripts from Illumina RNA Sequencing Data. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 91 William R. Blevins PART II DNA REPLICATION AND PROTEIN/DNA INTERACTIONS 8 FORK-seq: Single-Molecule Profiling of DNA Replication. . . . . . . . . . . . . . . . . . . 107 Magali Hennion, Bertrand Theulot, Jean-Michel Arbona, Benjamin Audit, and Olivier Hyrien 9 CUT&RUN Profiling of the Budding Yeast Epigenome . . . . . . . . . . . . . . . . . . . . . 129 Sandipan Brahma and Steven Henikoff 10 ChIP-SICAP: A New Tool to Explore Gene-Regulatory Networks in Candida albicans and Other Yeasts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 149 Lasse van Wijlick, Ansh Goyal, Sophie Bachellier-Bassi, and Christophe d’Enfert viiPART III TRANSLATION DYNAMICS, PROTEIN COMPLEXES, AND PROTEOMICS 11 Purification of Ribosome-Nascent-Chain Complex for Ribosome Profiling and Selective Ribosome Profiling . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 179 Hagit Bar-Yosef, Johannes Venezian, Kevin Klann, and Ayala Shiber 12 Single-Step Affinity Purification (ssAP) and Mass Spectrometry of Macromolecular Complexes in the Yeast S. cerevisiae. . . . . . . . . . . . . . . . . . . . . . 195 Christian Trahan and Marlene Oeffinger 13 Composition and Dynamics of Protein Complexes Measured by Quantitative Mass Spectrometry of Affinity-Purified Samples . . . . . . . . . . . . . . 225 Abdelkader Namane and Cosmin Saveanu 14 Deep Mutational Scanning of Protein–Protein Interactions Between Partners Expressed from Their Endogenous Loci In Vivo . . . . . . . . . . . 237 Alexandre K. Dube´, Rohan Dandage, Soham Dibyachintan, Ugo Dionne, Philippe C. Despre´s, and Christian R. Landry 15 Proteomic Mapping by APEX2-Catalyzed Proximity Labeling in Saccharomyces cerevisiae Semipermeabilized Cells . . . . . . . . . . . . . . . . . . . . . . . . . 261 Birgit Singer-Kru¨ger and Ralf-Peter Jansen 16 Quantitative Proteomics in Yeast: From bSLIM and Proteome Discoverer Outputs to Graphical Assessment of the Significance of Protein Quantification Scores. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 275 Nicolas Se´ne´caut, Pierre Poulain, Laurent Lignie`res, Samuel Terrier, Ve´ronique Legros, Guillaume Chevreux, Gae ¨lle Lelandais, and Jean-Michel Camadro 17 A Strong Cation Exchange Chromatography Protocol for Examining N-Terminal Proteoforms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 293 Esperanza Ferna´ndez, Annelies Bogaert, Evy Timmerman, An Staes, Francis Impens, and Kris Gevaert PART IV GENOTYPIC SCREENS AND PHENOTYPIC PROFILING 18 RNA Interference (RNAi) as a Tool for High-Resolution Phenotypic Screening of the Pathogenic Yeast Candida glabrata. . . . . . . . . . . . . . . . . . . . . . . . 313 Andreas Tsouris, Joseph Schacherer, and Olena P. Ishchuk 19 High-Throughput Gene Mutagenesis Screening Using Base Editing . . . . . . . . . . 331 Philippe C. Despre´s, Alexandre K. Dube´, Nozomu Yachie, and Christian R. Landry 20 SAturated Transposon Analysis in Yeast (SATAY) for Deep Functional Mapping of Yeast Genomes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 349 Agne`s H. Michel and Benoıˆt Kornmann 21 High-Throughput, High-Precision Colony Phenotyping with Pyphe . . . . . . . . . . 381 Stephan Kamrad, Ju¨rg Bahler, and Markus Ralser € 22 Bulk-Fitness Measurements Using Barcode Sequencing Analysis in Yeast . . . . . . 399 Claire A. Chochinov and Alex N. Nguyen Ba viii ContentsPART V IN SILICO INTEGRATION OF FUNCTIONAL GENOMICS DATA 23 Prediction of Gene and Genomic Regulation in Candida Species, Using the PathoYeastract Database: A Comparative Genomics Approach . . . . . . 419 Pedro Pais, Jorge Oliveira, Romeu Viana, Ineˆs V. Costa, Isabel Sa´-Correia, Pedro T. Monteiro, and Miguel C. Teixeira 24 Enabling Studies of Genome-Scale Regulatory Network Evolution in Large Phylogenies with MRTLE . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 439 Shilu Zhang, Sara Knaack, and Sushmita Roy 25 Omics Analyses: How to Navigate Through a Constant Data Deluge . . . . . . . . . 457 Thomas Denecker and Gae ¨lle Lelandais Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 473   مشخصات فایل
عنوان (Title):	Yeast functional genomics _ methods and protocols
نام فایل (File name):	914-www.GeneProtocols.ir-Yeast functional genomics _ methods and protocols (2022).pdf
عنوان فارسی (Title in Persian):	ژنومیک عملکردی مخمر- روشها و پروتکل ها
ایجاد کننده:	Frédéric Devaux (editor)
زبان (Language):	انگلیسی English
سال انتشار:	2022
شابک ISBN:	9781071622575, 1071622579
نوع سند (Doc. type):	کتاب
فرمت (File extention):	PDF
حجم فایل (File size):	15.8 مگابایت
تعداد صفحات (Book length in pages):	467

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