Comment[ArrayExpressAccession]	E-GEOD-45029
MAGE-TAB Version	1.1								
Public Release Date	2013-04-22
Investigation Title	Doxycycline alters metabolism and proliferation of human cell lines								
Comment[Submitted Name]	Doxycycline alters metabolism and proliferation of human cell lines
Experiment Description	The tetracycline antibiotics are widely used in biomedical research as mediators of inducible gene expression systems. Despite many known effects of tetracyclines on mammalian cells -- including inhibition of the mitochondrial ribosome -- there have been few reports on potential off-target effects at concentrations commonly used in inducible systems. Here, we report that in human cell lines, commonly used concentrations of doxycycline change gene expression patterns and concomitantly shift metabolism towards a more glycolytic phenotype, evidenced by increased lactate secretion and reduced oxygen consumption. We also show that these concentrations are sufficient to slow proliferation and alter cell cycle progression in vitro. These findings suggest that researchers using doxycycline in inducible expression systems should design appropriate controls to account for potential confounding effects of the drug on cellular metabolism. Total RNA was extracted from MCF12A cells treated with either vehicle control or Dox at 1 ug/mL. The experiment was performed in biological triplicate. Microarray results were processed using the RMA method.								
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	Sullivan	Ahler	Sullivan	Cass	Braas	York	Bensinger	Graeber	Christofk
Person First Name	William	Ethan	William	Ashley	Daniel	Autumn	Steven	Thomas	Heather
Person Mid Initials			J			G	J	G	R
Person Email	wsullivan@mednet.ucla.edu								
Person Affiliation	University of California, Los Angeles								
Person Phone	(310) 206-0163								
Person Address	Molecular & Medical Pharmacology, University of California, Los Angeles, 650 Charles E Young Drive S, CHS 34-115, Los Angeles, California, USA								
Person Roles	submitter								
Protocol Name	P-GSE45029-1	P-GSE45029-5	P-GSE45029-6	P-GSE45029-2	P-GSE45029-3	P-GSE45029-4	P-GSE45029-7		
Protocol Description	Data was processed with R/Bioconductor via the RMA method. ID_REF =  VALUE = RMA signal (non-log-transformed)	Labeling was performed with the Ambion MessageAmp Premier kit (cat#: 4383452).	Labeled cRNA was mixed with hybridization mix according to the Affymetrix protocol and hybridized in an Affymetrix GeneChip hybridization oven 645 at 45C for 16 hours with rotation at 60 rpm.	Cells were treated with doxycycline (dissolved in water) at 1 μg/mL or with vehicle for 4 days. Media, with appropriate treatment, was refreshed after 2 days.	MCF12A breast epithelial cells were grown in 10 cm culture plates in DMEM/F12 supplemented with 5% horse serum, 1% penicillin/streptomycin, 10μg/mL insulin, 0.5 μg/mL hydrocortisone, 20 ng/mL EGF, and 10 μg/mL cholera toxin.	Total RNA was extracted using the Qiagen RNeasy kit using the manufacturer's guidelines.	Scanning was performed on an Affymetrix 7G scanner with target intensity 500.		
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]	GSE45029								
Comment[GEOReleaseDate]	2013-04-22								
Comment[ArrayExpressSubmissionDate]	2013-03-11								
Comment[GEOLastUpdateDate]	2013-04-24								
Comment[AEExperimentType]	transcription profiling by array								
SDRF File	E-GEOD-45029.sdrf.txt