Comment[ArrayExpressAccession] E-GEOD-45364 MAGE-TAB Version 1.1 Public Release Date 2014-03-01 Investigation Title MicroRNA expression profiles distinguish liposarcoma subtypes and implicate miR-145 and miR-451 as tumor suppressors Comment[Submitted Name] MicroRNA expression profiles distinguish liposarcoma subtypes and implicate miR-145 and miR-451 as tumor suppressors Experiment Description This SuperSeries is composed of the SubSeries listed below. Refer to individual Series 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 Wiemer Person First Name Erik Person Email e.wiemer@erasmusmc.nl Person Affiliation Erasmus University Medical Center Person Phone +31-10-7044357 Person Address Medical Oncology, Erasmus University Medical Center, Dr. Molewaterplein 50, Rotterdam, Netherlands Person Roles submitter Protocol Name P-GSE45364-1 P-GSE45364-4 P-GSE45364-5 P-GSE45364-2 P-GSE45364-3 P-GSE45364-6 Protocol Description After background subtraction, expression values were quantile normalized using R software, bad spots were deleted, and duplicate spots were averaged. For each expression value, the ratio to the geometric mean of the miRNA was log2 transformed. These values were used to determine differentially expressed miRNAs by using BRB-Array Tools. ID_REF = VALUE = Quantile-normalisation-signal intensity 1ug of total RNA was fluorescently labeled using the Createch Cy3 label kit (Createch) Labeled samples were hybridized (for 16 hours at 60M-0C) to locked nucleic acid (LNAM-bM-^DM-") modified oligonucleotide capture probes (Exiqon) spotted in duplicate on Nexterion E slides. The capture probe set (based on miRBase version 10, annotation version 13) contains 1344 probes of which 725 are capable of detecting human miRNAs. Slides were subsequently washed and scanned. (MicroRNA profiling was performed as previously described by Pothof et al. 2009) Fresh tissue samples were snap frozen in liquid nitrogen Total RNA was isolated from frozen tissues using RNAbee (Tel Test Inc.) according to the manufacturerM-bM-^@M-^Ys recommendations. Hybridized slides were scanned and median spot intensity was determined using ImaGene software (BioDiscovery Inc.). Protocol Type normalization data transformation protocol labelling protocol hybridization protocol sample treatment protocol nucleic acid extraction protocol array scanning protocol Experimental Factor Name LOCATION AGE SEX ORGANISM PART Experimental Factor Type location age sex organism part Comment[SecondaryAccession] GSE45364 Comment[GEOReleaseDate] 2014-03-01 Comment[ArrayExpressSubmissionDate] 2013-03-20 Comment[GEOLastUpdateDate] 2014-03-01 Comment[AEExperimentType] transcription profiling by array SDRF File E-GEOD-45364.sdrf.txt