Comment[ArrayExpressAccession]	E-MTAB-2532
Investigation Title	MoMaTEC1403
Comment[Submitted Name]	MoMaTEC1403
Experimental Design	disease_state_design
Experimental Factor Name	Histologic grade	FIGO stage	Histological subtype
Experimental Factor Type	clinical information	clinical information	clinical information
Experimental Factor Term Source REF
Person Last Name	Tangen1,2*	Krakstad1,2*	Halle1,2	Werner1,2	Oyan1,3	Kusonmano1,2,4	Petersen4	Kalland1,3	Akslen5,6	Trovik1,2	Hurtado7	Salvesen1,2
Person First Name	Ingvild	Camilla	Mari	Henrica	Anne	Kanthida	Kjell	Karl	Lars	Jone	Antoni	Helga
Person Mid Initials	L�berg		K.	M.J.	M.			Henning	A.			B.
Person Email	Ingvild.Tangen@k2.uib.no	Camilla.Krakstad@med.uib.no				kanthida.kusonmano@cbu.uib.no	Kjell.Petersen@cbu.uib.no					helga.salvesen@k2.uib.no
Person Phone
Person Address
Person Affiliation	1Center for Cancer Biomarkers, Department of Clinical Science, University of Bergen, 5020 Bergen, Norway 2Department of Gynecology and Obstetrics, Haukeland University Hospital, 5021 Bergen, Norway	1Center for Cancer Biomarkers, Department of Clinical Science, University of Bergen, 5020 Bergen, Norway 2Department of Gynecology and Obstetrics, Haukeland University Hospital, 5021 Bergen, Norway	1Center for Cancer Biomarkers, Department of Clinical Science, University of Bergen, 5020 Bergen, Norway 2Department of Gynecology and Obstetrics, Haukeland University Hospital, 5021 Bergen, Norway	1Center for Cancer Biomarkers, Department of Clinical Science, University of Bergen, 5020 Bergen, Norway 2Department of Gynecology and Obstetrics, Haukeland University Hospital, 5021 Bergen, Norway	1Center for Cancer Biomarkers, Department of Clinical Science, University of Bergen, 5020 Bergen, Norway 3Department of Microbiology, Haukeland University Hospital, 5021 Bergen, Norway	1Center for Cancer Biomarkers, Department of Clinical Science, University of Bergen, 5020 Bergen, Norway 2Department of Gynecology and Obstetrics, Haukeland University Hospital, 5021 Bergen, Norway 4Computational Biology Unit, University of Bergen, 5020 Bergen, Norway	4Computational Biology Unit, University of Bergen, 5020 Bergen, Norway	1Center for Cancer Biomarkers, Department of Clinical Science, University of Bergen, 5020 Bergen, Norway 3Department of Microbiology, Haukeland University Hospital, 5021 Bergen, Norway	5Center for Cancer Biomarkers, Department of Clinical Medicine, University of Bergen, 5020 Bergen, Norway 6Department of Pathology, Haukeland University Hospital, 5021 Bergen, Norway	1Center for Cancer Biomarkers, Department of Clinical Science, University of Bergen, 5020 Bergen, Norway 2Department of Gynecology and Obstetrics, Haukeland University Hospital, 5021 Bergen, Norway 3Department of Microbiology, Haukeland University Hospital, 5021 Bergen, Norway 4Computational Biology Unit, University of Bergen, 5020 Bergen, Norway  5Center for Cancer Biomarkers, Department of Clinical Medicine, University of Bergen, 5020 Bergen, Norway 6Department of Pathology, Haukeland University Hospital, 5021 Bergen, Norway 7Breast Cancer Research group, Centre for Molecular Medicine Norway, University of Oslo, 0318 Oslo, Norway	7Breast Cancer Research group, Centre for Molecular Medicine Norway, University of Oslo, 0318 Oslo, Norway 	1Center for Cancer Biomarkers, Department of Clinical Science, University of Bergen, 5020 Bergen, Norway 2Department of Gynecology and Obstetrics, Haukeland University Hospital, 5021 Bergen, Norway
Person Roles	investigator	investigator	investigator	investigator	investigator	submitter	investigator	investigator	investigator	investigator	investigator	investigator
Person Roles Term Source REF	MO	MO	MO	MO	MO	MO	MO	MO	MO	MO	MO	MO
Quality Control Type	biological_replicates
Quality Control Term Source REF	MO
Replicate Type	biological_replicates
Replicate Term Source REF	MO
Date of Experiment	2014-08-05
Public Release Date	2014-04-25
PubMed ID	24849812
Experiment Description	Aim for investigation of expression patterns of endometrial cancers
Protocol Name	P-TABM-3454	P-TABM-3446	P-MTAB-25634	P-MTAB-38926	P-MTAB-38927	P-TABM-3455
Protocol Type	LABELING	EXTRACTION	SAMPLING	EXTRACTION	DATA_PROCESSING	HYBRIDIZATION
Protocol Description	This protocol describes Agilent's recommended procedures for the preparation and labeling of complex biological targets for Agilent 60-mer oligonucleotide microarray-based one-color gene expression analysis.	RNA was extracted from the samples using Trizol (Invitrogen) before further purification using the RNeasy MiniElute Cleanup Kit (Qiagen), both according to the manufacturer's protocols.	The tissue was collected from surgery, put on liquid nitrogen, and kept at -80C. To prepare tissue for RNA extraction, the tissue was then sliced out approximately 35 ug (see file for protocol details).	QIAGEN RNeasy Mini kit (250) 4th edition April 2006, is used. See official protocol text - procedure for animal tissues, the step 3d is the utilized.	The data was analyzed in J-Express 2012 software (http://jexpress.bioinfo.no). Median spot signal (gMedianSignal) was used as intensity measure. Replicated arrays for same sample were combined using bi-weight method. Expression data were normalized using quantile normalization and then log2 transformed.	This protocol describes Agilent's recommended procedures for hybridization, washing, scanning, and feature extraction of Agilent 60-mer oligonucleotide microarrays for microarray-based one-color gene expression analysis.
Protocol Parameters
Protocol Term Source REF	BASE	BASE	BASE	BASE	BASE	BASE
Term Source Name	ArrayExpress	MO	BASE
Term Source File	http://www.ebi.ac.uk/arrayexpress/	http://mged.sourceforge.net/ontologies/MGEDontology.php	mandelpil.ii.uib.no
Term Source Version
Comment[AEExperimentType]	transcription profiling by array
SDRF File	E-MTAB-2532.sdrf.txt
Publication Author List	Tangen IL, Krakstad C, Halle MK, Werner HM, Oyan AM, Kusonmano K, Petersen K, Kalland KH, Akslen LA, Trovik J, Hurtado A, Salvesen HB.
Publication Title	Switch in FOXA1 Status Associates with Endometrial Cancer Progression.
Publication DOI	10.1371/journal.pone.0098069