Comment[ArrayExpressAccession]	E-GEOD-56112
MAGE-TAB Version	1.1					
Public Release Date	2014-04-30
Investigation Title	Expression Array analysis of MTAP in HT080 cells					
Comment[Submitted Name]	Expression Array analysis of MTAP in HT080 cells
Experiment Description	Methylthioadenosine Phosphorylase (MTAP) is a tumor suppressor gene that encodes an enzyme responsible for the catabolism of the polyamine byproduct 5′deoxy-5′-methylthioadenosine (MTA).  To elucidate the mechanism by which MTAP inhibits tumor formation, we have created isogenic MTAP+ and MTAP- HT1080 fibrosarcoma cells. In this experiment we have performed expression array analysis on MTAP-, MTAP+, and MTAP+ cells treated with the MTAP inhibitor MT-DADMe-ImmA. Three biological replicates of each sample were grown and analyzed.  M- is MTAP-. M+ is MTAP+, and M+I is MTAP treated with inhibitor (48 hours).					
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	kruger	Kruger	Tan	Slifker	Li	
Person First Name	warren	Warren	Baiqing	Michael	Yue-Sheng	
Person Email	warren.kruger@fccc.edu					
Person Affiliation	Fox Chase Cancer Center					
Person Address	Fox Chase Cancer Center, 333 Cottman Ave., Philadelphia, PA, USA					
Person Roles	submitter					
Protocol Name	P-GSE56112-1	P-GSE56112-4	P-GSE56112-5	P-GSE56112-2	P-GSE56112-3	P-GSE56112-6
Protocol Description	The data were normalized with RMA. 6 additional arrays were included in the normalization, but these do not appear here. The data were filtered by including only probesets for which (1) at least three samples had expression intensities > 100, and (2) a valid Entrez identifier existed for the probeset (using Bioconductor annotations at the time of analysis). Probesets not passing the filters are given null values. ID_REF =  VALUE = log (base 2) RMA normalized expression intensities	Ten μg of total RNA were reverse transcribed to cDNA by using One-Cycle cDNA Synthesis kit (Affymetrix, Santa Clara, CA). Biotin-labeled cRNA synthesis was then carried out using the Affymetrix In Vitro Transcription Labeling Kit.	The biotinylated cRNA samples were cleaned up, fragmented, and then hybridized to human GeneChip (Human Genome U133 plus 2.0, Affymetrix) in Affymetrix GeneChip Hybridization Oven 640 according to manufacturer’s protocols. The washing procedures were carried out automatically in Affymetrix GeneChip Fluidics Station 450 .	Cells were grown in DMEM to 80% confluency. The MT-DADMe-ImmA Inhibitor was added 48 hours before harvesting at a concentration of 10 micromolar.	RNA was isolated using the RNeasy Mini Kit (Qiagen, Valencia, CA) according to manufacturer's instruction.	The processed GeneChip was scanned with Affymetrix GeneChip Scanner 3000 7G.
Protocol Type	normalization data transformation protocol	labelling protocol	hybridization protocol	growth protocol	nucleic acid extraction protocol	array scanning protocol
Experimental Factor Name	TREATMENT	MTAP				
Experimental Factor Type	treatment	mtap				
Comment[SecondaryAccession]	GSE56112					
Comment[GEOReleaseDate]	2014-04-30					
Comment[ArrayExpressSubmissionDate]	2014-03-21					
Comment[GEOLastUpdateDate]	2014-04-30					
Comment[AEExperimentType]	transcription profiling by array					
SDRF File	E-GEOD-56112.sdrf.txt