Comment[ArrayExpressAccession]	E-GEOD-41145
MAGE-TAB Version	1.1						
Public Release Date	2013-04-24
Investigation Title	Pseudonocardia dioxanivorans strain CB1190 during growth with H2/bicarbonate or pyruvate						
Comment[Submitted Name]	Pseudonocardia dioxanivorans strain CB1190 during growth with H2/bicarbonate or pyruvate
Experiment Description	Analysis of gene expression in Pseudonocardia dioxanivorans strain CB1190 during growth with H2/bicarbonate or pyruvate Two treatments, based on carbon/energy source used for growth: pyruvate and H2/bicarbonate. Triplicate microarrays (biological replicates) were prepared for each treatment. Pyruvate was used as the reference treatment for subsequent analysis. Gene expression changes were compared pair-wise: H2/bicarbonate vs. pyruvate						
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	Grostern	Grostern	Alvarez-Cohen				
Person First Name	Ariel	Ariel	Lisa				
Person Email	ariel.grostern@berkeley.edu						
Person Affiliation	UC Berkeley						
Person Address	Civil & Environmental Engineering, UC Berkeley, 209 O'Brien Hall, Berkeley, CA, USA						
Person Roles	submitter						
Protocol Name	P-GSE41145-1	P-GSE41145-5	P-GSE41145-6	P-GSE41145-2	P-GSE41145-3	P-GSE41145-4	P-GSE41145-7
Protocol Description	Primary data was generated with RMAExpress 1.05. Quantile normalization with background adjustment was performed across all arrays, and the PLM summarization method was used. ID_REF =  VALUE = log2 RMA	cDNA was obtained from 3.5 ug of RNA following the Affymetrix protocol for RT. RNA template was degraded with NaOH treatment. cDNA was fragmented with DNaseI, and fragmented cDNA while terminally labeled with biotin.	Hybridization followed the procedure of the Affymetrix protocol for Modified FlexMidi_euk2v3 for P. aeruginosa Array.	Cells were harvested by filtration and scraped from the filter into vials that were frozen at -80C.	Cells were grown in AMS medium amended with pyruvate (31 mM) or bicarbonate (36 mM) and H2 (10% in headspace).	Nucleic acids were obtained following cell lysis with heating and bead-beating in the presence of SDS and phenol. Phenol/chloroform extraction, followed by column-based purification, was performed. Nucleic acids were treated with DNaseI and RNA was finally purified by RNeasy purification.	Chips were scanned using an Affymetrix GeneChip Scanner 3000 scanner.
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						
Experimental Factor Type	treatment						
Comment[SecondaryAccession]	GSE41145						
Comment[GEOReleaseDate]	2013-04-24						
Comment[ArrayExpressSubmissionDate]	2012-09-25						
Comment[GEOLastUpdateDate]	2013-04-25						
Comment[AEExperimentType]	transcription profiling by array						
SDRF File	E-GEOD-41145.sdrf.txt