Comment[ArrayExpressAccession]	E-GEOD-51429
MAGE-TAB Version	1.1											
Public Release Date	2013-10-19
Investigation Title	A microRNA-based primary tumor site classification of liver core biopsies											
Comment[Submitted Name]	A microRNA-based primary tumor site classification of liver core biopsies
Experiment Description	To develop a classifier based on microRNAs for primary tumor site identification of liver core biopsies and to explore the influence of surrounding normal liver tissue on classification. Tissue samples from 333 patients, corresponding to one of the following ten assay classes, were obtained from archives of the pathology department, Copenhagen University Hospital, Rigshospitalet, Denmark: Lung cancer, breast cancer, gastric/cardia cancer, colorectal cancer, bladder cancer, pancreatic cancer, hepatocellular carcinoma, cholangiocarcinoma, squamous cell cancers of different origin, and normal liver tissue											
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	Perell	Perell	Vincent	Vainer	Petersen	Federspiel	Møller	Madsen	Hansen	Friis-Hansen	Nielsen	Daugaard
Person First Name	Katharina	Katharina	Martin	Ben	Bodil	Birgitte	Anne	Mette	Niels	Lennart	Finn	Gedske
Person Mid Initials	Anne				L		K		R		C	
Person Email	katharina.anne.perell@regionh.dk											
Person Affiliation	Copenhagen University Hospital											
Person Address	Dep. of Oncology, Copenhagen University Hospital, Blegdamsvej, Copenhagen, Denmark											
Person Roles	submitter											
Protocol Name	P-GSE51429-1	P-GSE51429-5	P-GSE51429-6	P-GSE51429-2	P-GSE51429-3	P-GSE51429-4	P-GSE51429-7					
Protocol Description	Data were normalized by centering and scaling the individual samples to mean 0 and variance 1 ID_REF =  VALUE = normalized	see manufacturer's website	n/a	n/a	n/a	Total RNA was extracted from FFPE tissue using a combination of ReCover All Total Nucleic Acid Isolation Kit (Ambion, Austin, Tx) and RNAqueous Micro Kit (Ambion).	n/a					
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	TUMOR.PERCENTAGE	CLASS										
Experimental Factor Type	tumor.percentage	class										
Publication Title	Modeling tissue contamination to improve molecular identification of the primary tumor site of metastases.											
Publication Author List	Vincent M, Perell K, Nielsen FC, Daugaard G, Hansen NR											
PubMed ID	24463184											
Publication DOI	10.1093/bioinformatics/btu044											
Comment[SecondaryAccession]	GSE51429											
Comment[GEOReleaseDate]	2013-10-19											
Comment[ArrayExpressSubmissionDate]	2013-10-18											
Comment[GEOLastUpdateDate]	2014-03-24											
Comment[AEExperimentType]	transcription profiling by RT-PCR											
Comment[AdditionalFile:Data1]	GSE51429_non-normalized.txt											
SDRF File	E-GEOD-51429.sdrf.txt