Comment[ArrayExpressAccession]	E-GEOD-46184
MAGE-TAB Version	1.1					
Public Release Date	2014-04-17
Investigation Title	Breast Cancer Gene Expression Data from Hamburg Series					
Comment[Submitted Name]	Breast Cancer Gene Expression Data from Hamburg Series
Experiment Description	Gene expression profiling of surgical biopsies from 74 breast cancer patients of different subtypes from Hamburg dataset. Fresh frozen pre-treatment surgical biopsy samples from breast cancer patients were analyzed on Affymetrix HGU133A.					
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	Karn	Karn	Müller			
Person First Name	Thomas	Thomas	Volkmar			
Person Email	t.karn@em.uni-frankfurt.de					
Person Affiliation	J.W.Goethe-University					
Person Address	J.W.Goethe-University, Theodor-Stern-Kai 7, Frankfurt, Germany					
Person Roles	submitter					
Protocol Name	P-GSE46184-1	P-GSE46184-4	P-GSE46184-5	P-GSE46184-2	P-GSE46184-3	P-GSE46184-6
Protocol Description	The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500. ID_REF =  VALUE = MAS5	Starting from 5 µg total RNA, labeled cRNA was prepared using the Roche Microarray cDNA Synthesis, Microarray RNA Target Synthesis (T7) and Microarray Target Purification Kit, according to the manufacturers instructions	Following fragmentation, 15 µg of cRNA were hybridized for 16 hr at 45°C on GeneChip HG-U133a Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.	samples were snap frozen and stored at -80°C	RNeasy kit, Qiagen. according to the manufacturer's instructions	GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
Protocol Type	normalization data transformation protocol	labelling protocol	hybridization protocol	sample treatment protocol	nucleic acid extraction protocol	array scanning protocol
Publication Title	Prognostic relevance of glycosylation-associated genes in breast cancer.					
Publication Author List	Milde-Langosch K, Karn T, Schmidt M, Zu Eulenburg C, Oliveira-Ferrer L, Wirtz RM, Schumacher U, Witzel I, Sch�tze D, M�ller V					
PubMed ID	24737166					
Publication DOI	10.1007/s10549-014-2949-z					
Comment[SecondaryAccession]	GSE46184					
Comment[GEOReleaseDate]	2014-04-17					
Comment[ArrayExpressSubmissionDate]	2013-04-18					
Comment[GEOLastUpdateDate]	2014-04-19					
Comment[AEExperimentType]	transcription profiling by array					
SDRF File	E-GEOD-46184.sdrf.txt