Essential Genes and Genomes Methods and Protocols

This book provides state-of-the-art information on gene essentiality screenings in a wide variety of organisms, i.e. screening for protein-coding genes and other genomic elements that are required by an organism to survive under specific conditions. With a focus on the two techniques that have revolutionized the field, the collection begins with chapters employing CRISPR/Cas9-based approaches followed by Tn-seq-based approaches, but later chapters also delve into other techniques for exploring essential genes, such as bioinformatics methods. Written for the highly successful 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. 

A Method to Map Gene Essentiality of Human Pluripotent Stem Cells by Genome-Scale CRISPR Screens with Inducible Cas9.- CRISPR/Cas9 Screening to Identify Conditionally Essential Genes in Human Cell Lines.- Target Identification of Small Molecules Using Large-Scale CRISPR-Cas Mutagenesis Scanning of Essential Genes.- Design and Generation of a CRISPR Interference System for Genetic Repression and Essential Gene Analysis in the Fungal Pathogen Candida albicans.- Identification of Essential Genes Using Sequential CRISPR and siRNA Screens.- A Simple Method that Combines CRISPR and AID to Quickly Generate Conditional Knockouts for Essential Genes in Various Vertebrate Cell Lines.- New Method for Genome-Scale Functional Genomics Study in Bacteria with Superior Performance: CRISPR Interference Screen.- A CRISPR-Based Method for Constructing Conditional Mutations of Essential Genes in Cyanobacteria.- A Method of Transposon Insertion Sequencing in Comprehensively Identifying Vibrio vulnificus Genes Required for Growth in Human Serum.- The Use of Tn-Seq and the FiTnEss Analysis to Define the Core Essential Genome of Pseudomonas aeruginosa.- Analysis of Escherichia coli K1 Virulence Genes by Transposon-Directed Sequencing.- Using Genome Scale Mutant Libraries to Identify Essential Genes.- Identification and Analysis of Essential Genes in Streptococcus mutans with Transposon Sequencing.- The Use of TnSeq to Identify Essential Alphaproteobacterial Genes Reveals Operational Variability in Conserved Developmental and Cell Cycle Systems.- A Proposed Framework to Identify Dispensable and Essential Functions in Bifidobacteria: Case Study of Bifidobacterium breve UCC2003 as a Prototype of Its Genus.- The Application of Transposon Insertion Sequencing in Identifying Essential Genes in B. fragilis.- Repressible Promoter System to Study Essential Genes in Mycobacteria.- A Single-Cell RNA-Seq-Based Approach for Genome-Wide Identification ofCell Essential Genes.- Identification of Essential Genes in Caenorhabditis elegans with Lethal Mutations Maintained by Genetic Balancers.- A Screening Method to Identify Essential Yeast Genes for Responses Towards Spermine.- An Effective Pre-Processing Method for High-Quality Pan-Genome Analysis of Bacillus subtilis and Escherichia coli.- Analysis of Gene Essentiality from TnSeq Data Using Transit.- Geptop 2.0: Accurately Select Essential Genes from the List of Protein-Coding Genes in Prokaryotic Genomes.