Comment[ArrayExpressAccession]	E-GEOD-41966
MAGE-TAB Version	1.1							
Public Release Date	2013-03-04
Investigation Title	Legionella pneumophila transcriptomic response to CuO nanoparticles							
Comment[Submitted Name]	Legionella pneumophila transcriptomic response to CuO nanoparticles
Experiment Description	Legionella pneumophila was exposed for 3h to 160 ug/ml of CuO nanoparticle. Untreated samples are used as the control condition. Two conditions: CuO (treated) and UN (untreated control. Three bioilogical repliucates. Genomic DNA is used as a reference channel. (Talaat, 2002, NAR).							
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	Faucher	Lu	Struewing	Buse	Kou	Shuman	Faucher	Ashbolt
Person First Name	Sebastien	Jingrang	Ian	Helen	Jiahui	Howard	Sebastien	Nicholas
Person Mid Initials				Y		A	P	J
Person Email	sebastien.faucher@gmail.com							
Person Affiliation	Columbia University Medical School							
Person Phone	212-305-1482							
Person Address	Microbiology and Immunology, Columbia University Medical School, 701 W 168th street, New York, NY, USA							
Person Roles	submitter							
Protocol Name	P-GSE41966-1	P-GSE41966-6	P-GSE41966-3	P-GSE41966-8	P-GSE41966-7	P-GSE41966-2	P-GSE41966-4	P-GSE41966-5
Protocol Description	ID_REF =  VALUE = log2 ratio of Ch2 over Ch1 (ie, log2 of cDNA/gDNA ratio). Values for both channel have been background subtracted and % total normalised.	Hybridization was performed as previously described (Hovel-Miner, G 2009. JB, 191:2461).	BYE broth, 37°C shaking.	The data was background subtracted and normalized by calculating the contribution of each spot to the total intensity and the ratio to gDNA was recorded. Excel and TigrMEV was used for processing.	Scanning and image acquisition was performed on a Scan Array Express (Perkin Elmer) using ScanArray 3.0 software as previously described (Hovel-Miner, G 2009. JB, 191:2461).	160 ug/ml CuO nanoparticles, 3h	RNA: TRIzol reagent, reverse-transcribed into cDNA. Genomic DNA: QIAamp kit.	RNA: 15 ug of Total RNA was labeled with amino-allyl dUTP during reverse transcriptase and subsequently coupled with the succinimidyl ester fluorescent dye AlexaFluor 546 as previously described (Hovel-Miner, G 2009. JB, 191:2461). Genomic DNA: 5 ug of genomic DNA was labeled with amino-allyl dUTP with klenow fragment and random hexamer as previously described (Porwollik, S. 2001. Mutat Res 483:1). Subsequently, the resulting DNA was coupled to the succinimidyl ester fluorescent dye AlexaFluor 647.
Protocol Type	bioassay_data_transformation	hybridization	grow	feature_extraction	image_aquisition	specified_biomaterial_action	nucleic_acid_extraction	labeling
Experimental Factor Name	COMPOUND							
Experimental Factor Type	compound							
Comment[SecondaryAccession]	GSE41966							
Comment[GEOReleaseDate]	2013-03-04							
Comment[ArrayExpressSubmissionDate]	2012-11-01							
Comment[GEOLastUpdateDate]	2013-03-06							
Comment[AEExperimentType]	transcription profiling by array							
SDRF File	E-GEOD-41966.sdrf.txt