Mycobacteria Protocols

1. Whole Genome Sequencing for Comparative Genomics and De Novo Genome Assembly

Andrej Benjak, Claudia Sala, and Ruben C. Hartkoorn

2. Whole Transcriptome Sequencing for High-resolution Transcriptomic Analysis in Mycobacterium tuberculosis

Andrej Benjak, Claudia Sala, and Ruben C. Hartkoorn

3. RNA Sequencing for Transcript 5'-end Mapping in Mycobacteria

Scarlet S. Shell, Michael R. Chase, Thomas R. Ioerger, and Sarah M. Fortune

4. Fractionation and Analysis of Mycobacterial Proteins

Megan C. Lucas, Lisa M. Wolfe, Rachel M. Hazenfield, Jade Kurihara, Nicole A. Kruh-Garcia, John Belisle, and Karen M. Dobos

5. Lipid and Lipoarabinomannan Isolation and Characterization

Marie-Antoinette Lanéelle, Jérôme Nigou, and Mamadou Daffé

6. Metabolomics of Mycobacterium tuberculosis

Madhumitha Nandakumar, Gareth A. Prosser, Luis Pedro S. de Carvalho, and Kyu Rhee

7. Electroporation of Mycobacteria

Renan Goude, David M. Roberts, and Tanya Parish

8. Targeted Gene Knockout and Essentiality Testing by Homologous Recombination

Krishnamoorthy Gopinath, Digby F. Warner, and Valerie Mizrahi

9. Construction of Conditional Knockdown Mutants in Mycobacteria

Dirk Schnappinger, Kathryn M. O'Brien, and Sabine Ehrt

10. Mycobacterial Recombineering

Kenan C. Murphy, Kadamba Papavinasasundaram, and Christopher M. Sassetti

11. In vitro Models that Utilize Hypoxia to Induce Non-replicating Persistence in Mycobacteria

Charles D. Sohaskey and Martin I. Voskuil

12. Genetic Dissection of Mycobacterial Biofilms

Anil K Ojha, William R. Jacobs Jr., and Graham F. Hatfull

13. Measuring Efflux and Permeability in Mycobacteria

Liliana Rodrigues, Miguel Viveiros, and José A. Aínsa

14. Single-cell Analysis of Mycobacteria using Microfluidics and Time-lapse Microscopy

Neeraj Dhar and Giulia Manina

15. Antimicrobial Susceptibility Testing for Mycobacterium sp.

Delia Blanco-Ruano, David M. Roberts, Ruben Gonzalez-Del-Rio, Daniel Álvarez, Mª José Rebollo, Esther Pérez-Herrán, and Alfonso Mendoza

16. Determination of Compound Kill Kinetics Against Mycobacterium tuberculosis

Julie Early and Torey Alling

17. Microplate Alamar Blue Assay (MABA) and Low Oxygen Recovery Assay (LORA) for Mycobacterium tuberculosis

Sanghyun Cho, Hyung Sup Lee, and Scott Franzblau

18. A Multi-Stress Model for High Throughput Screening Against Non-replicating Mycobacterium tuberculosis

Ben Gold, Thulasi Warrier, and Carl Nathan

19. Isolation and Characterization of Compound-resistant Isolates of Mycobacterium tuberculosis

Theresa O'Malley and Eduard Melief

20. Macrophage Infection Models for Mycobacterium tuberculosis

Benjamin K. Johnson and Robert B. Abramovitch

21. Infection of Human Neutrophils to Study Virulence Properties of Mycobacterium tuberculosis

Tobias Dallenga, Björn Corleis, and Ulrich E. Schaible

22. Isolation of Bead-phagosomes to Study Virulence Function of M. tuberculosis Cell Wall Lipids

Anna Christina Geffken, Emmanuel C. Patin, and Ulrich E. Schaible

23. Live Imaging of Mycobacterium marinum Infection in Dictyostelium discoideum

Caroline Barisch, Ana T. López-Jiménez, and Thierry Soldati

24. Testing Chemical and Genetic Modulators in Mycobacterium tuberculosis Infected Cells using Phenotypic Assays

Vincent Delorme, Ok-Ryul Song, Alain Baulard, and Priscille Brodin