Investigation Title	Transcription profiling of heat shocked Methanococcus jannaschii]	
Comment[Submitted Name]	Experiment:Temp_shock	
Experimental Design	growth_condition_design	transcription profiling by array	
Experimental Design Term Source REF	mo	EFO	
Comment[ArrayExpressReleaseDate]		
Comment[AEMIAMESCORE]	2	
Comment[ArrayExpressAccession]	E-TIGR-18	
Comment[MAGETAB TimeStamp_Version]	2010-08-13 14:59:33 Last Changed Rev: 13058	
Experimental Factor Name	ExperimentalFactor:cold-shock	
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Person Last Name	Clark	El-Sayed	Boonyaratanakornkit	White	Simpson	
Person First Name	Douglas	Najib	Boonchai	Joseph	Annie	
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Person Email	clark@cchem.berkeley.edu	nelsayed@tigr.org	cornkid@berkeley.edu	jwhite@tigr.org	asimpson@tigr.org	
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Person Affiliation	Clark Lab	The Institute for Genomic Research	Clark Lab	The Institute for Genomic Research	The Institute for Genomic Research	
Person Roles	investigator	submitter	biomaterial_provider	data_coder	submitter	
Person Roles Term Source REF	mo	mo		mo	mo	
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Experiment Description	These experiments were designed to study the effect of heat shock and cold shock on expression profiles of a hyperthermophilic archaeon after a twenty-minute temperature shock. When cells entered the middle of the exponential growth phase at the optimal growth temperature of 85 C, they were transferred from an 85 C water bath to a 95 C water bath or a 65 C water bath. Two biological replicates were obtained under both heat shock and cold shock conditions. For each biological replicate, we performed a total of six technical replicates consisting of three pairs of flip-dye experiments. As for the reference sample, a pooled population of cDNA from three biological replicates consisting of cells growing in the mid-exponential phase at 85 C was used. All hybridizations were performed against this reference	
Protocol Name	tigr.org:mad:Protocol_MJ-RNA-Isolation	tigr.org:mad:Protocol_SOP M007.2	tigr.org:mad:Protocol_SOP M008.5	
Protocol Type	nucleic_acid_extraction	labeling	hybridization	
Protocol Description	Title: MJ-RNA-Isolation. Description: Growth conditions and RNA preparation  Methanococcus jannaschii was obtained from the Oregon Collection of  Methanogens and cultivated in 125-ml clear serum bottles (Wheaton)  containing 30 ml of media as described previously (Miller et al., Appl  Environ Microbiol 1988) with Na2S as the reducing agent. Bottles were  inoculated with 3 ml of inoculum and pressurized to 30 psi with a  4:1 v/v mixture of H2 and CO2 substrate, then placed in a reciprocal  shaking water bath (Precision Scientific Model 25) at 200 oscillations  per min and 85 C. Growth was followed by measuring optical density at  660 nm (Tsao et al., Biotech Bioeng 1994). After reaching mid-exponential  phase in ca. 3 h (OD660 ~ 0.20), the bottles were transferred to another  water bath and shaken at 200 oscillations per min at either 65 C or 95 C.  In both cases, bottles reached temperature equilibrium within 3 min. After  20 min, cells were harvested and RNA was extracted.  Samples were withdrawn from serum bottles (20 ml) and passed through a  0.45 µm nitrocellulose filter (Millipore) to collect cells. This filter  was placed in cold phenol with 1% SDS and 0.1 M sodium acetate and  homogenized using a beadbeater (BioSpec Products, Inc.) for 5 min at the  highest setting. The aqueous layer was removed and re-extracted with cold  phenol. Total RNA was then precipitated overnight at -20 C with 3M sodium  acetate and isopropanol. Precipitated RNA was re-suspended and treated  with DNase (Invitrogen), and each sample was purified on RNeasy columns  (Qiagen). 	Title: SOP M007.2. Description:  	Title: SOP M008.5. Description:  	
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SDRF File	E-TIGR-18.sdrf.txt	
Term Source Name	The MGED Ontology	ArrayExpress	mo	EFO	
Term Source File	http://mged.sourceforge.net/ontologies/MGEDontology.php	http://www.ebi.ac.uk/arrayexpress	http://mged.sourceforge.net/ontologies/MGEDontology.php	http://www.ebi.ac.uk/efo/	
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