Investigation Title PilotStudy1 Experimental Design co-expression_design disease_state_design Experimental Factor Name DiseaseState Experimental Factor Type disease_state Experimental Factor Term Source REF Person Last Name Yilmaz Person First Name Saliha Person Mid Initials Person Email
[email protected] Person Phone Person Fax Person Address Person Affiliation Person Roles submitter Person Roles Term Source REF MGED Ontology Quality Control Type Quality Control Term Source REF Replicate Type Replicate Term Source REF Normalization Type Normalization Term Source REF Date of Experiment Public Release Date 2009-01-28 PubMed ID Publication DOI Publication Author List Publication Title Publication Status Publication Status Term Source REF Experiment Description As the EU IP @neurIST Project aims at integrating biomedical informatics technologies in the assessment of rupture risks and treatments of cerebral aneurysms in humans. Genetic involvement in the disease is known, mRNA biomarkers will be searched as possible risk factors in easy to assess PBMCs (peripheral blood cells). The aim of this pilot study is specifically to check the clinical samples going from the patientï¾ s bed side to the genomic analysis platform. Briefly, we hybridized biotin labelled cRNA from 2 controls (C1, C2), 1 patient bearing an intracranial aneurysm (I) and 1 patients bearing an intracranial aneurysm and subarachnoid haemorrhage (S). For each sample, one technical replicate was performed. Thus a total of 8 arrays was used. Protocol Name P-TABM-2344 P-TABM-2339 P-TABM-2341 P-TABM-2340 P-TABM-2343 Protocol Type specified_biomaterial_action nucleic_acid_extraction labeling hybridization feature_extraction Protocol Description 2.5 mL of blood was collected into two 2.5 mL PAXgeneï¾® Blood RNA tubes. After returning the tubes several times, to mix thoroughly the blood with the liquid present, PAXgene tubes were immediately stored at -20ï¾°C using wire rack supports. After thawing at room temperature overnight, total RNA was extracted from the approximately 2.5 ml of peripheral blood using Preanalytix Blood RNA Kit (Qiagen) following the manufacturerï¾'s protocol. The quality and integrity of the total RNA was evaluated on the 2100 Bioanalyzer (Agilent Technologies) and the concentration was measured using a NanoDrop spectrophotometer (NanoDrop Technologies) following the manufacturersï¾'s protocols. Total RNA (500 ng) was amplified using the MessageAmpTM II aRNA Kit according to the manual (Ambion Inc.) to obtain biotin-labeled cRNA. Biotinylated cRNA was hybridized to Sentrix humanRef-8 v2 WG-8 arrays Scanned on the BeadArray Reader, as described by Illumina, Inc. at www.illumina.com Protocol Parameters Protocol Hardware Protocol Software
Protocol Contact Protocol Term Source REF MGED Ontology MGED Ontology MGED Ontology MGED Ontology SDRF File E-TABM-421.sdrf.txt Term Source Name The NCBI Taxonomy nci_thesaurus The MGED Ontology ArrayExpress Term Source File http://www.ncbi.nlm.nih.gov/ ncithesaurus.obo.alt http://mged.sourceforge.net/ontologies/MGEDontology.php http://www.ebi.ac.uk/arrayexpress/ Term Source Version 1.1.3