Essential genes and genomes : methods and protocols
Author(s)
Bibliographic Information
Essential genes and genomes : methods and protocols
（Methods in molecular biology / John M. Walker, series editor, 2377）（Springer protocols）
Humana Press, 2022 [i.e. 2021]
- : [hbk.]
Available at 1 libraries
Note
Includes bibliographical references and index
Description and Table of Contents
Description
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.
Comprehensive and authoritative, Essential Genes and Genomes: Methods and Protocols is an ideal guide for researchers attempting to strip genetics down to its fundamentals.
Table of Contents
1. A Method to Map Gene Essentiality of Human Pluripotent Stem Cells by Genome-Scale CRISPR Screens with Inducible Cas9
Barbara Mair, Michael Aregger, Amy H.Y. Tong, Katherine S.K. Chan, and Jason Moffat
2. CRISPR/Cas9 Screening to Identify Conditionally Essential Genes in Human Cell Lines
Kimberly S. Huggler, Nicholas J. Rossiter, Kyle M. Flickinger, and Jason R. Cantor
3. Target Identification of Small Molecules Using Large-Scale CRISPR-Cas Mutagenesis Scanning of Essential Genes
Bert Kwanten, Jasper Neggers, and Dirk Daelemans
4. Design and Generation of a CRISPR Interference System for Genetic Repression and Essential Gene Analysis in the Fungal Pathogen Candida albicans
Lauren Wensing and Rebecca S. Shapiro
5. Identification of Essential Genes Using Sequential CRISPR and siRNA Screens
Luke DeHart, Oliver P. Yockey, and Jesse Bakke
6. A Simple Method that Combines CRISPR and AID to Quickly Generate Conditional Knockouts for Essential Genes in Various Vertebrate Cell Lines
Kohei Nishimura and Tatsuo Fukagawa
7. New Method for Genome-Scale Functional Genomics Study in Bacteria with Superior Performance: CRISPR Interference Screen
Xihao Liao, Xin-Hui Xing, and Chong Zhang
8. A CRISPR-Based Method for Constructing Conditional Mutations of Essential Genes in Cyanobacteria
Ju-Yuan Zhang, Tian-Cai Niu, Gui-Ming Lin, and Cheng-Cai Zhang
9. A Method of Transposon Insertion Sequencing in Comprehensively Identifying Vibrio vulnificus Genes Required for Growth in Human Serum
Miguel Carda-Dieguez and Carmen Amaro
10. The Use of Tn-Seq and the FiTnEss Analysis to Define the Core Essential Genome of Pseudomonas aeruginosa
Bradley E. Poulsen, Anne E. Clatworthy, and Deborah T. Hung
11. Analysis of Escherichia coli K1 Virulence Genes by Transposon-Directed Sequencing
Alex J. McCarthy and Peter W. Taylor
12. Using Genome Scale Mutant Libraries to Identify Essential Genes
Kevin S. Myers, Piyush Lal, Daniel R. Noguera, and Timothy J. Donohue
13. Identification and Analysis of Essential Genes in Streptococcus mutans with Transposon Sequencing
Alejandro R. Walker and Robert C. Shields
14. The Use of TnSeq to Identify Essential Alphaproteobacterial Genes Reveals Operational Variability in Conserved Developmental and Cell Cycle Systems
Gayatri Sharma and Patrick D. Curtis
15. A Proposed Framework to Identify Dispensable and Essential Functions in Bifidobacteria: Case Study of Bifidobacterium breve UCC2003 as a Prototype of Its Genus
Lorena Ruiz, Francesca Bottacini, Lucie Semenec, Amy Cain, and Douwe van Sinderen
16. The Application of Transposon Insertion Sequencing in Identifying Essential Genes in B. fragilis
Yaligara Veeranagouda and Hannah M. Wexler
17. Repressible Promoter System to Study Essential Genes in Mycobacteria
Francesca Boldrin and Riccardo Manganelli
18. A Single-Cell RNA-Seq-Based Approach for Genome-Wide Identification of Cell Essential Genes
Yuqiu Lu and Shaolin Shi
19. Identification of Essential Genes in Caenorhabditis elegans with Lethal Mutations Maintained by Genetic Balancers
Shicheng Yu, Chaoran Zheng, and Jeffrey Shih-Chieh Chu
20. A Screening Method to Identify Essential Yeast Genes for Responses Towards Spermine
Mustapha Aouida and Dindial Ramotar
21. An Effective Pre-Processing Method for High-Quality Pan-Genome Analysis of Bacillus subtilis and Escherichia coli
Hao Wu, Zhi-Kai Yang, Tong Yang, Dan Wang, Hao Luo, and Feng Gao
22. Analysis of Gene Essentiality from TnSeq Data Using Transit
Thomas R. Ioerger
23. Geptop 2.0: Accurately Select Essential Genes from the List of Protein-Coding Genes in Prokaryotic Genomes
Qing-Feng Wen, Wen Wei, and Feng-Biao Guo
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