Comment[ArrayExpressAccession]	E-GEOD-64065
MAGE-TAB Version	1.1						
Public Release Date	2014-12-12
Investigation Title	The Mycobacterium tuberculosis Clp Gene Regulator is Required for in vitro Reactivation from Hypoxia-induced Dormancy						
Comment[Submitted Name]	The Mycobacterium tuberculosis Clp Gene Regulator is Required for in vitro Reactivation from Hypoxia-induced Dormancy
Experiment Description	The isogenic Mtb:ΔRv2745c mutant is significantly more sensitive normoxia conditions after a period of hypoxia, relative to wild-type Mtb, implicating a role for ClgR in response to reactivation, in vivo. Both hypoxia and reaeration treatment led to dysregulation of the σH regulon in the isogenic mutant, Mtb:ΔRv2745c. Induction of clgR in Mtb did lead to Clp protease induction, indicating that clgR plays a role in differntially activating downstream genes in a condition dependent manner. Disruption of genes involved in the dosR regulon, the Enduring Hypoxia Response, lipid synthesis, and mycolic acid synthesis also occurred in the knock out, implicating clgR as a possible regulator of downstream signaling cascades that facilitate Mtb survival. There was also a differnetial response of genes that are known Clp protease targets, in addition to potential Clp protease targets that had similar induction patterns as known Clp protease targets. At different time points, following hypoxia (day 1, day 5, and day 7) and reaeration (1 hour, 4 hour, 6 hour, 12 hour, 24 hour, and 48 hour) treatments M. tuberculosis CDC1551 cultures, RNA was extracted and labeled with Cy5. RNA was also extracted from pre-hypoxia (t=0) time points and labeled with Cy3. These samples were cohybridized on M. tuberculosis CDC1551 whole genome microarrays using biological triplicate samples (i.e. samples derived from three distinct cultures and treatments) and thus three unique datasets were generated for each of the three time points for Mtb. Similar experiments were performed for an isogenic Rv2745c (clgR) mutant in Mtb CDC1551 which was generated by allelic exchange.						
Term Source Name	ArrayExpress	EFO
Term Source File	http://www.ebi.ac.uk/arrayexpress/	http://www.ebi.ac.uk/efo/efo.owl					
Person Last Name	Kaushal	McGillivray	Kaushal				
Person First Name	Deepak	Amanda	Deepak				
Person Email	dkaushal@tulane.edu						
Person Affiliation	Tulane National Primate Research Center						
Person Address	Bacteriology, Tulane National Primate Research Center, 18703 Three Rivers Rd, Covington, LA, USA						
Person Roles	submitter						
Protocol Name	P-GSE64065-1	P-GSE64065-5	P-GSE64065-6	P-GSE64065-2	P-GSE64065-3	P-GSE64065-4	P-GSE64065-7
Protocol Description	Data analysis was performed as described earlier (Mehra and Kaushal, PMCID: PMC2698404) ID_REF =  VALUE = Values are expression of M, i.e. a log2 ratio of treated sample at a particular time in a particular strain to the pre-treatment sample from the same strain, e.g Mtb treated with either hypoxia or reaeration relative to Mtb prior to hypoxia treatment	cDNA labeling was performed as described earlier (Mehra and Kaushal, PMCID: PMC2698404)	Hybridization to arrays was performed as described earlier (Mehra and Kaushal, PMCID: PMC2698404)	Bacterial cultures were treated with either hypoxia or reaeration	Mtb strains were cultured as described earlier (Mehra and Kaushal, PMCID: PMC2698404)	RNA was extracted as described earlier (Mehra and Kaushal, PMCID: PMC2698404)	Slides were scanned as described earlier (Mehra and Kaushal, PMCID: PMC2698404)
Protocol Type	normalization data transformation protocol	labelling protocol	hybridization protocol	sample treatment protocol	growth protocol	nucleic acid extraction protocol	array scanning protocol
Experimental Factor Name	treatment	time	genotype				
Experimental Factor Type	treatment	time	genotype				
Comment[SecondaryAccession]	GSE64065						
Comment[GEOReleaseDate]	2014-12-12						
Comment[ArrayExpressSubmissionDate]	2014-12-11						
Comment[GEOLastUpdateDate]	2014-12-12						
Comment[AEExperimentType]	transcription profiling by array						
SDRF File	E-GEOD-64065.sdrf.txt