Crispr: Methods and Protocols (Hardcover, 2015)

1. Investigating CRISPR RNA Biogenesis and Function using RNA-seq Nadja Heidrich, Gaurav Dugar, Jorg Vogel, and Cynthia M. Sharma 2. In vitro Co-reconstitution of Cas Protein Complexes Andre Plagens and Lennart Randau 3. Analysis of CRISPR pre-crRNA Cleavage Erin L. Garside and Andrew M. MacMillan 4. Annotation and Classification of CRISPR-Cas Systems Kira S. Makarova and Eugene V. Koonin 5. Computational Detection of CRISPR/crRNA Targets Ambarish Biswas, Peter C. Fineran, and Chris M. Brown 6. High-throughput CRISPR typing of Mycobacterium tuberculosis Complex and Salmonella enterica Serotype Typhimurium Christophe Sola, Edgar Abadia, Simon Le Hello, and Francois-Xavier Weill 7. Spacer-based Macroarrays for CRISPR Genotyping Igor Mokrousov and Nalin Rastogi 8. Analysis of crRNA using Liquid Chromatography Electrospray Ionisation Mass Spectrometry (LC ESI MS) Sakharam P. Waghmare, Alison O. Nwokeoji, and Mark J. Dickman 9. Rapid Multiplex Creation of Escherichia coli Strains Capable of Interfering with Phage Infection through CRISPR Alexandra Strotskaia, Ekaterina Semenova, Ekaterina Savitskaya, and Konstantin Severinov 10. Exploring CRISPR Interference by Transformation with Plasmid Mixtures: Identification Of Target Interference Motifs in Escherichia coli Cristobal Almendros and Francisco J.M. Mojica 11. Electrophoretic Mobility Shift Assay of DNA and CRISPR-Cas Ribonucleoprotein Complexes Tim Kunne, Edze R. Westra , and Stan J.J. Brouns 12. Expression and Purification of the CMR (Type III-B) Complex in Sulfolobus solfataricus Jing Zhang and Malcolm F White 13. Procedures for Generating CRISPR Mutants With Novel Spacers Acquired from Viruses Or Plasmids Marie-Eve Dupuis, Rodolphe Barrangou, and Sylvain Moineau 14. Archaeal Viruses of the Sulfolobales: Isolation, Infection, and CRISPR Spacer Acquisition Susanne Erdmann and Roger A. Garrett 15. Using the CRISPR-Cas system to Positively Select Mutants In Genes Essential for its Function Ido Yosef, Moran G. Goren, Rotem Edgar, and Udi Qimron 16. Analysis of Nuclease Activity of Cas1 Proteins Against Complex DNA Substrates Natalia Beloglazova, Sofia Lemak, Robert Flick, and Alexander F. Yakunin 17. Characterizing Metal-Dependent Nucleases of CRISPR-Cas prokaryotic Adaptive Immunity Systems Ki H. Nam, Matthew P. DeLisa , and Ailong Ke 18. Cas3 Nuclease-Helicase Activity Assays Tomas Sinkunas, Giedrius Gasiunas, and Virginijus Siksnys 19. Chemical and Enzymatic Footprint Analyses of R-loop Formation by Cascade-crRNA Complex Umit Pul 20. Creation and Analysis of a Virome: Using CRISPR Spacers Michelle Davison and Devaki Bhaya 21. Targeted Mutagenesis in Zebrafish using CRISPR RNA-guided Nucleases Woong Y Hwang, Yanfang Fu, Deepak Reyon, Andrew PW Gonzales, J Keith Joung, and Jing-Ruey Joanna Yeh 22. Precise Genome Editing of Drosophila with CRISPR RNA-guided Cas9 Scott J. Gratz, Melissa M. Harrison, Jill Wildonger, and Kate M. O'Connor-Giles 23. Targeted Transcriptional Repression in Bacteria using CRISPR Interference (CRISPRi) John S. Hawkins, Spencer Wong, Jason M. Peters, Ricardo Almeida, and Lei S. Qi