Investigation Title	Transcription profiling of human ovarian tumors (43) from untreated patients prior to surgery vs. chemotherapy treated prior to surgery	
Comment[Submitted Name]	Expression data from 43 Ovarian tumors	
Experimental Design	disease_state_design	co-expression_design	transcription profiling by array	
Experimental Design Term Source REF	mo	mo	EFO	
Comment[SecondaryAccession]	GDS2785	
Comment[SecondaryAccession]	GSE7463	
Comment[ArrayExpressReleaseDate]	2008-11-22	
Comment[AEMIAMESCORE]	5	
Comment[ArrayExpressAccession]	E-GEOD-7463	
Comment[MAGETAB TimeStamp_Version]	2010-08-07 19:50:26 Last Changed Rev: 13058	
Experimental Factor Name	DISEASESTAGE	DISEASESTATE	COMPOUND	
Experimental Factor Type	disease_stage	disease_state	compound	
Experimental Factor Term Source REF	
Person Last Name	Bowen	
Person First Name	Nathan	
Person Mid Initials	J.	
Person Email	nathan.bowen@biology.gatech.edu	
Person Phone	
Person Fax	
Person Address	Cancer Development and Evolution, Biology, Georgia Institute of Technology, 310 Ferst Drive, Atlanta, 30332, USA	
Person Affiliation	Georgia Institute of Technology	
Person Roles	submitter	
Person Roles Term Source REF		
Quality Control Type	
Quality Control Term Source REF	
Replicate Type	
Replicate Term Source REF	
Normalization Type	
Normalization Term Source REF	
Date of Experiment	
Public Release Date	2008-11-22	
PubMed ID	17505532	
Publication DOI	17505532	
Publication Author List	Moreno CS, Matyunina L, Dickerson EB, Schubert N, Bowen NJ, Logani S, Benigno BB, McDonald JF	
Publication Title	Evidence that p53-mediated cell-cycle-arrest inhibits chemotherapeutic treatment of ovarian carcinomas.	
Publication Status	journal_article	
Publication Status Term Source REF	The MGED Ontology	
Experiment Description	Gene expression profiles of malignant carcinomas surgically removed from ovarian cancer patients pre-treated with chemotherapy (neo-adjuvant) prior to surgery group into two distinct clusters. One group clusters with carcinomas from patients not pre-treated with chemotherapy prior to surgery (C-L) while the other clusters with non-malignant adenomas (A-L). Although the C-L cluster is preferentially associated with p53 loss-of-function (LOF) mutations, the C-L cluster cancer patients display a more favorable clinical response to chemotherapy as evidenced by enhanced long-term survivorships. Experiment Overall Design: A set of 43 ovarian tumors was obtained from the Ovarian Cancer Institute (Atlanta).  Tissue was collected at the time of surgery and preserved in RNAlater (Ambion, Austin, TX) within one minute of collection.  Labeled probe was hybridized to the Affymetrix HG-U95Av2 arrays.	
Protocol Name	P-G7463-1	P-G7463-2	P-G7463-4	P-G7463-3	P-AFFY-6	
Protocol Type	grow	specified_biomaterial_action	nucleic_acid_extraction	labeling	feature_extraction	
Protocol Description	A set of 43 ovarian tumors was obtained from the Ovarian Cancer Institute (Atlanta).  Tissue was collected at the time of surgery and preserved in RNAlater (Ambion, Austin, TX) within one minute of collection.	Tissue was collected at the time of surgery and preserved in RNAlater (Ambion, Austin, TX) within one minute of collection. Linear polyacrylamide (5 ul) was added to ~50 mg of tumor sample and homogenization was carried out on ice in 1.5 ml Trizol (Invitrogen, Carlsbad, CA) with a polytron homogenizer for 30 seconds.	RNA was isolated from crude homogenate according to the manufacturer’s protocols (Trizol) and further enriched using an RNEasy column (Qiagen, Valencia, CA).	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).	Title: Affymetrix CEL analysis. Description: 	
Protocol Parameters	
Protocol Hardware	
Protocol Software					MicroArraySuite 5.0	
Protocol Contact	
Protocol Term Source REF	
SDRF File	E-GEOD-7463.sdrf.txt	
Term Source Name	ncbitax		The MGED Ontology	ArrayExpress	NCI_thesaurus	mo	EFO	The MGED Ontology	
Term Source File	http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html		http://mged.sourceforge.net/ontologies/MGEDontology.php	http://www.ebi.ac.uk/arrayexpress	ncithesaurus.obo.alt	http://mged.sourceforge.net/ontologies/MGEDontology.php	http://www.ebi.ac.uk/efo/	http://mged.sourceforge.net/ontologies/MGEDontology.php	
Term Source Version