Comment[ArrayExpressAccession]	E-GEOD-53371
MAGE-TAB Version	1.1				
Public Release Date	2013-12-17
Investigation Title	Neuroblastoma: MYCN normal vs. MYCN amplified				
Comment[Submitted Name]	Neuroblastoma: MYCN normal vs. MYCN amplified
Experiment Description	To evaluate the expression of genes associated with MYCN in NB, 10 tumors with MYCN amplification and 10 with normal MYCN copy number were subjected to oligonucleotide microarray using Agilent oligo microarray chips. Two-condition experiment, MYCN normal vs. MYCN amplified 10 NB patient tissues for each group.				
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	Wu	Hsu	Wu		
Person First Name	Pei-Yi	Wen-Ming	Pei-Yi		
Person Email	d96b41003@ntu.edu.tw				
Person Affiliation	National Taiwan University				
Person Address	National Taiwan University, 1 Roosevelt Rd., Sec. 4, Taipei, Taiwan				
Person Roles	submitter				
Protocol Name	P-GSE53371-1	P-GSE53371-3	P-GSE53371-4	P-GSE53371-2	P-GSE53371-5
Protocol Description	Scanned images were analyzed using Feature extraction 8.1 software (Agilent Technologies), image analysis and normalization software was used to quantify signal and background intensity for each feature, substantially normalizing the data by rank-consistency-filtering LOWESS method. ID_REF =  VALUE = normalized log10 ratio (Cy5/Cy3) representing test/reference	Total RNA (0.5 M-NM-<g) was amplified by a low RNA input fluor linear amp kit (Agilent Technologies, USA), and labeled with Cy3 or Cy5 (CyDye, PerkinElmer) during the in vitro transcription process. Tumor RNA was labeled by Cy5 and RNA from Universal Human Reference RNA was labeled by Cy3.	2 M-NM-<g of Cy-labeled cRNA was fragmented to an average size of approximately 50M-bM-^@M-^S100 nucleotides by incubation with a fragmentation buffer at 60M-0C for 30 min. Correspondingly fragmented labeled cRNA was then pooled and hybridized to Human 1A (version 2) oligo microarray (Agilent Technologies) at 60M-0C for 17 h.	Total RNA extracted using Trizol following manufacturer's instructions	After washing and drying by nitrogen gun blowing, microarrays were scanned with an Agilent microarray scanner (Agilent Technologies) at 535 nm for Cy3 and 625 nm for Cy5.
Protocol Type	normalization data transformation protocol	labelling protocol	hybridization protocol	nucleic acid extraction protocol	array scanning protocol
Experimental Factor Name	MYCN STATUS				
Experimental Factor Type	mycn status				
Comment[SecondaryAccession]	GSE53371				
Comment[GEOReleaseDate]	2013-12-17				
Comment[ArrayExpressSubmissionDate]	2013-12-16				
Comment[GEOLastUpdateDate]	2013-12-18				
Comment[AEExperimentType]	transcription profiling by array				
SDRF File	E-GEOD-53371.sdrf.txt