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Yeast functional genomics : methods and protocols / edited by Frédéric Devaux. -- Second edition -- New York : Humana Press, 2022. – (58.17/M592/v.2477) |
Contents
Preface
Contributors
PART I TRANSCRIPTOMIC ANALYSES
1 Single-Cell RNA Sequencing in Yeast Using the 10x Genomics Chromium Device
2 Genome-Wide Profiling of Transcription Initiation with STRIPE-seq
3 A Modified Cross-Linking Analysis of cDNAs (CRAC) Protocol for Detecting RNA-Protein Interactions and Transcription at Single-Nucleotide Resolution
4 High-Resolution Deep Sequencing of Nascent Transcription in Yeast with BioGRO-seq
5 Direct Sequencing of RNA and RNA Modification Identification Using Nanopore
6 UNAGI: Yeast Transcriptome Reconstruction and Gene Discovery Using Nanopore Sequencing
7 Identification of Taxonomically Restricted Transcripts from Illumina RNA Sequencing Data
PART II DNA REPLICATION AND PROTEIN/DNA INTERACTIONS
8 FORK-seq: Single-Molecule Profiling of DNA Replication
9 CUT&RUN Profiling of the Budding Yeast Epigenome
10 ChIP-SICAP: A New Tool to Explore Gene-Regulatory Networks in Candida albicans and Other Yeasts
PART III TRANSLATION DYNAMICS, PROTEIN COMPLEXES, AND PROTEOMICS
11 Purification of Ribosome-Nascent-Chain Complex for Ribosome Profiling and Selective Ribosome Profiling
12 Single-Step Affinity Purification (ssAP) and Mass Spectrometry of Macromolecular Complexes in the Yeast S. cerevisiae
13 Composition and Dynamics of Protein Complexes Measured by Quantitative Mass Spectrometry of Affinity-Purified Samples
14 Deep Mutational Scanning of Protein-Protein Interactions Between Partners Expressed from Their Endogenous Loci In Vivo
15 Proteomic Mapping by APEX2-Catalyzed Proximity Labeling in Saccharomyces cerevisiae Semipermeabilized Cells
16 Quantitative Proteomics in Yeast: From bSLIM and Proteome Discoverer Outputs to Graphical Assessment of the Significance of Protein Quantification Scores
17 A Strong Cation Exchange Chromatography Protocol for Examining N-Terminal Proteoforms
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
19 High-Throughput Gene Mutagenesis Screening Using Base Editing
20 SAturated Transposon Analysis in Yeast (SATAY) for Deep Functional Mapping of Yeast Genomes
21 High-Throughput, High-Precision Colony Phenotyping with Pyphe
22 Bulk-Fitness Measurements Using Barcode Sequencing Analysis in Yeast
PART 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
24 Enabling Studies of Genome-Scale Regulatory Network Evolution in Large Phylogenies with MRTLE
25 Omics Analyses: How to Navigate Through a Constant Data Deluge
Index
