1. GSE10391 Deb et al, Plos One, 2009 A Novel In Vitro Multiple-Stress Dormancy Model for Mycobacterium tuberculosis Generates a Lipid-Loaded, Drug-Tolerant, Dormant Pathogen M. tuberculosis H37Rv grown for 9 days under multiple stress in reduced Dubos medium (10%, pH5.0) without glycerol starting from OD600=0.2. M. tuberculosis H37Rv grown for 3 days under multiple stress in reduced Dubos medium (10%, pH5.0) without glycerol starting from OD600=0.2. M. tuberculosis H37Rv grown for 18 days in reduced Dubos medium (10%, pH7.0) without glycerol starting from OD600=0.2. M. tuberculosis H37Rv grown for 3 days in reduced Dubos medium (10%, pH7.0) without glycerol starting from OD600=0.2. M. tuberculosis H37Rv grown for 9 days in reduced Dubos medium (10%, pH7.0) without glycerol starting from OD600=0.2. M. tuberculosis H37Rv grown for 18 days under multiple stress in reduced Dubos medium (10%, pH5.0) without glycerol starting from OD600=0.2. 2. GSE10897 Shiloh et al, Cell host and microbe, 2008 Mycobacterium tuberculosis Senses Host-Derived Carbon Monoxide during Macrophage Infection MTB_CO-200-ppm MTB_CO-20-ppm MTB-WT-NO MTB-deltadosST-compdosT-NO MTB-deltadosS-NO MTB-deltadosST-compdosT-CO MTB-deltadosR-compdosR-CO MTB_CO-2000-ppm MTB-deltadosST-CO MTB-deltadosR-CO MTB-deltadosT-NO MTB-deltadosS-compdosS-NO MTB-deltadosR-NO MTB-WT-CO MTB-deltadosST-NO MTB-deltadosS-CO 3. GSE6209 Fontan et al, Infection and Immunity, 2008 Global Transcriptional Profile of Mycobacterium tuberculosis during THP-1 Human Macrophage Infection H37Rv 24hrs after infection in macrophage vs. H37Rv grown in 7H9 media biological H37Rv 4hrs after infection in macrophage vs. H37Rv grown in 7H9 media biological 4. GSE8664 Manganelli et al, Molecular Microbiology, 2001 The Mycobacterium tuberculosis ECF sigma factor sE:role in global gene expression and survival in macrophages Exposed to 0.05% SDS sigE mutant Exposed to 0.05% SDS H37Rv (wild type) Comparison between H37Rv (wild type) and sigE mutant 5. GSE8732 Rodriguez et al, Infection and Immunity, 2002 ideR, an Essential Gene in Mycobacterium tuberculosis: Role of IdeR in Iron-Dependent Gene Expression, Iron Metabolism, and Oxidative Response Comparison between iron-sufficient (50 uM FeCl3) and iron-deficient (2 uM FeCl3) grew conditions Comparison between ST52 and ST22. Growth conditions iron-sufficient (50 uM FeCl3) Comparison between ST22 and H37Rv. Growth conditions iron-sufficient (50 uM FeCl3) 6. GSE8827 Rohde et al, Cell host and Microbe, 2007 Mycobacterium tuberculosis Invasion of Macrophages: Linking Bacterial Gene Expression to Environmental Cues Mtb response to pH 5.5 (6 replicates) Mtb response to pH 6.5 (6 replicates) Phagosomal induced Mtb genes affected by Concanamycin A inhibition of phagosome acidification Effect of macrophage contact (phagocytosis inhibited with cytochalasin D) on Mtb gene expression M. tuberculosis CDC1551 2hr phagosome expression profile M. tuberculosis CDC1551 24hr phagosome expression profile 7. GSE8839 Voskuil et al, Journal of Exp. Med, 2003 Inhibition of Respiration by Nitric Oxide Induces aMycobacterium tuberculosis Dormancy Program Strain 1254 treated with 0.2% Oxygen by 2 hours + 0.01mM diethylenetriamine/nitric oxide by 40 minutes Strain 1254 treated with 0.2% Oxygen by 2 hours + 0.005mM diethylenetriamine/nitric oxide by 40 minutes Strain 1254 treated with 0.2% Oxygen by 2 hours + 0.001mM diethylenetriamine/nitric oxide by 40 minutes Strain 1254 treated with 0.5mM Potassium cyanide by 1 hour Strain 1254 treated with 0.5mM diethylenetriamine/nitric oxide by 2 hours Strain 1254 in 7H9 medium shaked at 90 rpm + 0.001mM diethylenetriamine/nitric oxide treatment by 40 minutes Strain 1254 treated with 0.5mM diethylenetriamine/nitric oxide by 5 minutes Strain 1254 treated with 0.5mM Potassium cyanide by 1 hour + 0.2% Oxygen by 2 hours Strain 1254 treated with 0.05mM diethylenetriamine/nitric oxide by 40 minutes H37Rv and RvdosR mutant grew under respiration limited environment Strain 1254 treated with 0.2% Oxygen by 2 hours Strain 1254 treated with 0.5mM diethylenetriamine/nitric oxide by 24 hours + 0.05mM DNO by 40 minutes Strain H37Rv grew under respiration limited environment Strain H37Rv. Growth curve 0 days (Control) Strain 1254 treated with 0.5mM Potassium cyanide by 1 hour + 0.05mM diethylenetriamine/nitric oxide by 40 minutes Strain 1254 treated with 0.5mM diethylenetriamine/nitric oxide by 40 minutes Strain 1254 in 7H9 medium shaked at 90 rpm + 0.005mM diethylenetriamine/nitric oxide treatment by 40 minutes Strain 1254 in 7H9 medium shaked at 90 rpm + 0.01mM diethylenetriamine/nitric oxide treatment by 40 minutes Strain 1254 treated with 0.5mM diethylenetriamine/nitric oxide by 8 hours Strain 1254 in 7H9 medium shaked at 90 rpm Strain 1254 treated with 0.5mM diethylenetriamine/nitric oxide by 20 minutes H37Rv and RvdosR mutant treated with0.05mM diethylenetriamine/nitric oxide by 40 minutes Strain 1254 treated with 0.5mM diethylenetriamine/nitric oxide by 24 hours Strain 1254 treated with 1.0mM diethylenetriamine/nitric oxide by 40 minutes Strain 1254 treated with 5.0mM diethylenetriamine/nitric oxide by 40 minutes RvdosR mutant plus DosR and RvdosR mutant grew under respiration limited environment Strain H37Rv treated with 0.05mM diethylenetriamine/nitric oxide by 40 minutes Strain CDC1551 treated with 0.05mM diethylenetriamine/nitric oxide by 40 minutes Strain 1254 in 7H9 medium shaked at 90 rpm + 0.05mM diethylenetriamine/nitric oxide treatment by 40 minutes Strain 1254 treated with 0.2% Oxygen by 2 hours + 0.05mM diethylenetriamine/nitric oxide by 40 minutes Strain 1254 treated with 0.5mM diethylenetriamine/nitric oxide by 16 hours Strain 1254 treated with 0.005mM diethylenetriamine/nitric oxide by 40 minutes Strain 1254 treated with 0.5mM diethylenetriamine/nitric oxide by 1 hour RvdosR mutant plus DosR and RvdosR mutant treated with 0.05mM diethylenetriamine/nitric oxide by 40 minutes 8. GSE9776 Williams et al, J bac, 2007 Mycobacterium tuberculosis SigF Regulates Genes Encoding Cell Wall-Associated Proteins and Directly Regulates the Transcriptional Regulatory Gene phoY1 Nutrient starved 2 hour 1ug/ml INH treated Log phase 2 hour 1ug/ml INH treated KatG knockout Log phase 2 hour 1ug/ml INH treated Log phase 6 hour 1ug/ml INH treated STANFORD DATASETS 9. Gao4 Gao et al, Tuberculosis, 2004 Comparative expression studies of a complex phenotype: cord formation in Mycobacterium tuberculosis H37Rv-7H9 Roll H37Rv-7H9 Shake H37Rv-Dubos H37Rv-Sauton's H37Rv-Youman 10. Lee Lee JH, et al. (2008_2) J Bacteriol 190(2):699-707 Roles of SigB and SigF in the Mycobacterium tuberculosis sigma factor network. [1] Lee JH, et al. (2008_3) J Bacteriol 190(3):1128-33 Role of stress response sigma factor SigG in Mycobacterium tuberculosis.[1] Ctrl-sigB-overexp-12h Control_Vs_sigG_Knockout 11. Mang2 Manganelli R, et al. (2002) Mol Microbiol 45(2):365-74 Role of the extracytoplasmic-function sigma factor sigma(H) in Mycobacterium tuberculosis global gene expression H37Rvdiamide-1h H37Rv-sigma-H-null-mutant-diamide-1h H37Rv-vs-H37-sigma-H-null-mutant 12. Morris5 Morris RP, et al. (2005) Proc Natl Acad Sci U S A 102(34):12200-5 Ancestral antibiotic resistance in Mycobacterium tuberculosis H37Rv-whiB7-null-ethanol-vs.-1.0-ug/ml-Tetracyclin-for-15-min H37Rv-whiB7-null-ethanol-vs.-1.0-ug/ml-Tetracyclin-for-2-hr H37Rv-whiB7-null-ethanol-vs.-1.0-ug/ml-Tetracyclin-for-24-hr H37Rv-whiB7-null-vs.-H37Rv-whiB7-null-with-whiB7-over-expression H37Rv-wild-type-vs.-H37Rv-whiB7-null H37Rv-wild-type-vs.-H37Rv-whiB7-null-with-whiB7-over-expression MTB1254-control-vs.-0.5-ug/ml-Streptomycin-for-15-min MTB1254-control-vs.-1.0-ug/ml-Erythromycin-for-2-hr-(ref) MTB1254-control-vs.-1.0-ug/ml-Erythromycin-for-24-hr-(ref) MTB1254-control-vs.-1.0-ug/ml-Streptomycin-for-15-min MTB1254-control-vs.-1.0-ug/ml-Streptomycin-for-2-hr-(ref) MTB1254-control-vs.-1.0-ug/ml-Streptomycin-for-24-hr-(ref) MTB1254-control-vs.-100-ug/ml-Streptomycin-for-15-min MTB1254-control-vs.-25-ug/ml-Streptomycin-for-15-min MTB1254-control-vs.-5.0-ug/ml-Streptomycin-for-15-min MTB1254-ethanol-vs.-0.5-ug/ml-Erythromycin-for-15-min MTB1254-ethanol-vs.-0.5-ug/ml-Erythromycin-for-30-min MTB1254-ethanol-vs.-0.5-ug/ml-Tetracyclin-for-15-min MTB1254-ethanol-vs.-0.5-ug/ml-Tetracyclin-for-30-min MTB1254-ethanol-vs.-1.0-ug/ml-Erythromycin-for-15-min MTB1254-ethanol-vs.-1.0-ug/ml-Erythromycin-for-30-min MTB1254-ethanol-vs.-1.0-ug/ml-Tetracyclin-for-15-min MTB1254-ethanol-vs.-1.0-ug/ml-Tetracyclin-for-2-hr MTB1254-ethanol-vs.-1.0-ug/ml-Tetracyclin-for-24-hr MTB1254-ethanol-vs.-1.0-ug/ml-Tetracyclin-for-30-min MTB1254-ethanol-vs.-100-ug/ml-Erythromycin-for-15-min MTB1254-ethanol-vs.-100-ug/ml-Erythromycin-for-30-min MTB1254-ethanol-vs.-100-ug/ml-Tetracyclin-for-15-min MTB1254-ethanol-vs.-100-ug/ml-Tetracyclin-for-30-min MTB1254-ethanol-vs.-25-ug/ml-Erythromycin-for-15-min MTB1254-ethanol-vs.-25-ug/ml-Erythromycin-for-30-min MTB1254-ethanol-vs.-25-ug/ml-Tetracyclin-for-15-min MTB1254-ethanol-vs.-25-ug/ml-Tetracyclin-for-30-min MTB1254-ethanol-vs.-5.0-ug/ml-Erythromycin-for-15-min MTB1254-ethanol-vs.-5.0-ug/ml-Erythromycin-for-30-min MTB1254-ethanol-vs.-5.0-ug/ml-Tetracyclin-for-15-min MTB1254-ethanol-vs.-5.0-ug/ml-Tetracyclin-for-30-min 13. Pang7 Pang X, et al. (2007) Microbiology 153(Pt 4):1229-42 Evidence for complex interactions of stress-associated regulons in an mprAB deletion mutant of Mycobacterium tuberculosis H37Rv-SDS-treated-vs.-H37Rv-delta-mprAB-mutant-SDS-treated H37Rv-delta-mprAB-mutant-vs.-H37Rv-delta-mprAB-mutant-SDS-treated H37Rv-vs.-H37Rv-SDS-treated H37Rv-vs.-H37Rv-delta-mprAB-mutant 14. Park3 Park HD, et al. (2003) Mol Microbiol 48(3):833-43 Rv3133c/dosR is a transcription factor that mediates the hypoxic response of Mycobacterium tuberculosis H37-Rv3133c/DosR-mutant-2hr H37Rv-hypoxia-2hr 15. Rus8 Rustad TR, et al. (2008) PLoS ONE 3(1):e1502 The enduring hypoxic response of Mycobacterium tuberculosis H37Rv-hypoxia-1-day H37Rv-hypoxia-12hr H37Rv-hypoxia-4-day H37Rv-hypoxia-4hr H37Rv-hypoxia-7-day H37Rv-hypoxia-8hr H37dosR-mutant-hypoxia-1-day H37dosR-mutant-hypoxia-12hr H37dosR-mutant-hypoxia-4-day H37dosR-mutant-hypoxia-4hr H37dosR-mutant-hypoxia-7-day H37dosR-mutant-hypoxia-8hr 16. Vos4 Voskuil MI, et al. (2004) Tuberculosis (Edinb) 84(3-4):218-27 Mycobacterium tuberculosis gene expression during adaptation to stationary phase and low-oxygen dormancy H37Rv-Day0 H37Rv-Day0vslowOxygenDay4 H37Rv-Day14 H37Rv-Day24 H37Rv-Day6 H37Rv-Day60 H37Rv-Day8 NRP-Day10 NRP-Day12 NRP-Day14 NRP-Day20 NRP-Day30 NRP-Day6 NRP-Day8 NRP-Day80