Comment[ArrayExpressAccession]	E-GEOD-41842
MAGE-TAB Version	1.1										
Public Release Date	2012-10-27
Investigation Title	Distinctive microRNA signature of medulloblastomas associated with the WNT signaling pathway										
Comment[Submitted Name]	Distinctive microRNA signature of medulloblastomas associated with the WNT signaling pathway
Experiment Description	Medulloblastoma is a malignant brain tumor that occurs predominantly in children. Current risk stratification based on the clinical parameters is inadequate for accurate prognostication. In order to get a better understanding of medulloblastoma biology, miRNA profiling of medulloblastomas was carried out in parallel with the expression profiling of protein- coding genes. miRNA profiling of medulloblastomas was carried out using Taqman Low Density Density Aarray v 1.0 having 365 human microRNAs. In parallel, genome--wide expression profiling of protein coding genes was carried out using Affymetrix gene 1.0 ST arrays. Both the profiling studies identified four molecular subtypes of medulloblastomas. Expression levels of select protein-coding genes and miRNAs could classify an independent set of medulloblastomas. Twelve of 31 medulloblastomas were found to overexpress genes belonging to the canonical WNT signaling pathway and carry a mutation in CTNNB1 gene. A number of miRNAs like miR-193a, miR-224/miR-452 cluster, miR-182/miR-183/miR-96 cluster, and miR-148a having potential tumor/metastasis suppressive activity were found to be overexpressed in the WNT signaling associated medulloblastomas. Exogenous expression of miR-193a and miR-224, two miRNAs that have the highest WNT pathway specific upregulation, was found to inhibit proliferation, increase radiation sensitivity and reduce anchorage-independent growth of medulloblastoma cells. Expression level of tumor/metastasis suppressive miRNAs in the WNT signaling associated medulloblastomas is likely to determine their response to treatment, and thus, these miRNAs would be important biomarkers for risk stratification within the WNT signaling associated medulloblastomas. A total of 19 human sporadic medulloblastomas were profiled using the Affymetrix Gene 1.0 ST array										
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	Shirsat	Gokhale	Kunder	Goel	Sarin	Moiyadi	Shenoy	Mamidipally	Noronha	Kannan	Shirsat
Person First Name	Neelam	A	R	A	R	A	A	C	S	S	N
Person Mid Initials	V										V
Person Email	nshirsat@actrec.gov.in										
Person Affiliation	Advanced Centre for Treatment, Research and Education in Cancer. Tata Memorial Centre										
Person Address	Shirsat Lab, Advanced Centre for Treatment, Research and Education in Cancer. Tata Memorial Centre, Kharghar, Sector 21, Navi Mumbai, Maharashtra, India										
Person Roles	submitter										
Protocol Name	P-GSE41842-1	P-GSE41842-5	P-GSE41842-4	P-GSE41842-2	P-GSE41842-3	P-GSE41842-6					
Protocol Description	ID_REF =  VALUE = log2 GCRMA normalised value	GeneChips were scanned using the Affymetrix GeneChip scanner 2500.	Following fragmentation, 2 ug cRNA was hybridized for 16 hr at 45M-0C on Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station	Total RNA was extracted from tumor tissues using the mirVANA kit ( Ambion, Austin, TX, USA) , as per the manufacturerM-bM-^@M-^Ys protocol after ensuring at least 80% tumor cell content.The RNA was further purified using RNeasy columns (Qiagen,Valencia, CA, USA), for removing genomic DNA contamination if at all . RNAs having more than 7.0 RIN value and no detectable genomic DNA contamination were used for the analysis.	100 ng total RNA was reverse transcribed, amplified, and labeled with biotin using the whole transcript sense target labeling kit as per the manufacturerM-bM-^@M-^Ys instructions (Affymetrix, Santa Clara, CA, USA).	Data normalization was done using GCRMA algorithm in the Bioconductor package (v 2.1) of the R statistical environment (http://www.bioconductor.org)					
Protocol Type	bioassay_data_transformation	image_aquisition	hybridization	nucleic_acid_extraction	labeling	feature_extraction					
Experimental Factor Name	MOLECULAR SUBGROUP	AGE YR	SEX								
Experimental Factor Type	molecular subgroup	age yr	sex								
Publication Title	Distinctive microRNA signature of medulloblastomas associated with the WNT signaling pathway.										
Publication Author List	Gokhale A, Kunder R, Goel A, Sarin R, Moiyadi A, Shenoy A, Mamidipally C, Noronha S, Kannan S, Shirsat NV										
PubMed ID	21358093										
Publication DOI	10.4103/0973-1482.77072										
Comment[SecondaryAccession]	GSE41842										
Comment[GEOReleaseDate]	2012-10-27										
Comment[ArrayExpressSubmissionDate]	2012-10-26										
Comment[GEOLastUpdateDate]	2012-11-02										
Comment[AEExperimentType]	transcription profiling by array										
SDRF File	E-GEOD-41842.sdrf.txt