Comment[ArrayExpressAccession] E-GEOD-32089 MAGE-TAB Version 1.1 Public Release Date 2013-10-18 Investigation Title Gene Expression Profile for the identification of miR-126 targets Comment[Submitted Name] Gene Expression Profile for the identification of miR-126 targets Experiment Description "The analysis was designed to search for putative seed sequences for miR-126 in the 3M-bM-^@M-^YUTR of up-regulated genes. ECs were co-transfected with anti-miR-126 and a plasmid vector bearing the GFP-coding sequence and three complementary sites for miR-126 downstream. As a consequence of the presence of miR-126 binding sites the GFP expression was under the control of miR-126. Fluorescente cells were the cells transfected with anti-miR-126 oligo. MiR-126 target enrichment analysis was performed on the basis of the Miranda database, as provided by Diana miRGen. Significance was estimated on the basis of hyper geometric distribution p-values comparing the occurrence of miR targets in the signature with respect to the universe, defined as the genes expressed in HUVEC. Frequency of log 2 ratio between the subset of mir-126 targets and the genes which are not targets of miR-126 were plotted, highlighting enrichment of the target of miR in differentially regulated genes. " 3 x biological replicates of transiently trasfected cells with anti miR-126 oligo (LNA), and controls oligo. 2 biological replicates for GFP are included as technical controls. 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 Medico Sessa Primo Medico Isella Person First Name Enzo Roberto Luca Enzo Claudio Person Email enzo.medico@ircc.it Person Affiliation Institute for Cancer Research and Treatment, University of Torino Person Phone +39-011-9933234 Person Address Oncological Sciences, Institute for Cancer Research and Treatment, University of Torino, Strada Prov. 142, km 3,95, Candiolo, TO, Italy Person Roles submitter Protocol Name P-GSE32089-1 P-GSE32089-4 P-GSE32089-5 P-GSE32089-2 P-GSE32089-3 P-GSE32089-6 Protocol Description Data were normalized by Illumina's BeadStudio version 1.5.1.3 with ranbk invariant normalization ID_REF = VALUE = Data were summarized and rank-invariant normalized using the Illumina Beadstudio software (ver. 1.5.1.3). DETECTION = Five hundred ng of total RNA was reverse transcribed and amplified overnight with T7 RNA polymerase and labeled with biotin following the manufacturerM-bM-^@M-^Ys protocol. 0.85 microgram of biotin-labeled cRNA was hybridized to Illumina HumanRef8 V2 at 55 M-0C overnight. BeadChips were incubated with Cy3 streptavidin and washed according to the manufacturerM-bM-^@M-^Ys protocol. M199 containing 20% FBS RNA extraction was performed using Trizol plus RNA purification kit (Invitrogen). RNA qualitative and quantitative assessment was performed using the Bioanalyzer 2100 (Agilent Tecnologies). The hybridized BeadChips were scanned by Illumina BeadScan confocal scanner and analyzed by Illumina's BeadStudio version 1.5.1.3 Protocol Type normalization data transformation protocol labelling protocol hybridization protocol growth protocol nucleic acid extraction protocol array scanning protocol Experimental Factor Name TRANDUCER Experimental Factor Type tranducer Comment[SecondaryAccession] GSE32089 Comment[GEOReleaseDate] 2013-10-18 Comment[ArrayExpressSubmissionDate] 2011-09-13 Comment[GEOLastUpdateDate] 2013-10-19 Comment[AEExperimentType] transcription profiling by array Comment[AdditionalFile:Data1] GSE32089_non-normalized.txt SDRF File E-GEOD-32089.sdrf.txt