Comment[ArrayExpressAccession]	E-GEOD-43994
MAGE-TAB Version	1.1					
Public Release Date	2013-07-09
Investigation Title	Identification of genes involved in SHH subgroup medulloblastoma using murine whole-body Sleeping Beauty insertional mutagenesis					
Comment[Submitted Name]	Identification of genes involved in SHH subgroup medulloblastoma using murine whole-body Sleeping Beauty insertional mutagenesis
Experiment Description	Ptch+/- mice, which are predisposed to SHH subgroup medulloblastoma, were mutagenised using the Sleeping Beauty transposon to identify genes which increase the frequency of medulloblastoma formation. Gene expression in tumours was assessed both to investigate their relationship to human subgroup tumours, and to identify genes where expression was altered by mutagenesis. Total RNA isolated from tumours induced by SB mutagenesis were compared to normal cerebellum, tumours induced witout SB mutagenesis, and tumours from a distinct model of disease (GTML).					
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	Jackson	Jackson	Clifford	Williamson	Chesler	AlAfghani
Person First Name	Michael	Michael	Steven	Daniel	Louis	Hani
Person Mid Initials	Stewart	S	C			
Person Email	m.s.jackson@ncl.ac.uk					
Person Affiliation	Newcastle University					
Person Phone	+44 191 241 8677					
Person Address	Institute of Genetic Medicine, Newcastle University, Central Parkway, Newcastle upon Tyne, United Kingdom					
Person Roles	submitter					
Protocol Name	P-GSE43994-1	P-GSE43994-3	P-GSE43994-4	P-GSE43994-2	P-GSE43994-5	
Protocol Description	Standard Illumina processing followed by RMA quantile normalisation. ID_REF =  VALUE = log2 quantile normalized Detection Pval = 	Approximately 200ng of each RNA was amplified and Biotinylated using the Illumina TotalPrep RNA amplification kit (Applied Biosystems, Foster City, CA. USA), with the size distribution of cRNA being assessed using the Agilent Bioanalyser.	Approximately 750ng of each cRNA was hybridised using the standard Illumina hybridization protocol	RNA was extracted using the Qiagen RNeasy Lipid Tissue mini kit (Qiagen, Hilden, Germany) according to manufacturer's instructions.Quality control was performed using an Agilent 2100 Bioanalyser.	Standard Illumina scanning protocol	
Protocol Type	normalization data transformation protocol	labelling protocol	hybridization protocol	nucleic acid extraction protocol	array scanning protocol	
Experimental Factor Name	AGEWEEKS	INSERT IN NETWORK GENE	DISEASE STATE	STRAIN OR LINE	INSERT IN NFIA	GENOTYPE
Experimental Factor Type	ageweeks	insert in network gene	disease state	strain or line	insert in nfia	genotype
Comment[SecondaryAccession]	GSE43994					
Comment[GEOReleaseDate]	2013-07-09					
Comment[ArrayExpressSubmissionDate]	2013-02-01					
Comment[GEOLastUpdateDate]	2013-07-09					
Comment[AEExperimentType]	transcription profiling by array					
Comment[AdditionalFile:Data1]	GSE43994_non-normalized.txt					
SDRF File	E-GEOD-43994.sdrf.txt