ONTOLOGY SOURCE REFERENCE
Term Source Name	"ArrayExpress"	"EFO"	"NCBITaxon"	"CHEBI"	"BTO"	"PATO"	
Term Source File	"http://www.ebi.ac.uk/arrayexpress/"	"http://www.ebi.ac.uk/efo/efo.owl"	"http://bioportal.bioontology.org/ontologies/47845"	"http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=CHEBI"	"http://bioportal.bioontology.org/ontologies/50688"	"http://bioportal.bioontology.org/ontologies/50280"	
Term Source Version	""	""	"47845"	"Jun 2010"	"50688"	"50280"	
Term Source Description	""	""	"National Center for Biotechnology Information (NCBI) Organismal Classification"	"Chemical Entities of Biological Interest"	"BRENDA Tissue and Enzyme Source Ontology"	"Phenotypic Quality Ontology"	
INVESTIGATION
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INVESTIGATION PUBLICATIONS
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STUDY
Study Identifier	"E-GEOD-36010"
Study Title	"Expression profiling of rat cerebral cortex after surgical induction of ischemia/infarction; the NSAID meloxicam was used during surgical prep. [original title: mRNA profiles after experimental ischemia]"
Study Description	"To analyze gene expression we isolated total mRNA from the core, periinfarct and contralateral cortex of 60 Sprague-Dawley rats after 24 hours or 3 days of permanent middle cerebral artery occlusion (pMCAo). Also ipsilateral and contralateral cortex was obtained from sham-operated and healthy animals. A total of 44 microarrays were performed with RNA pooled from 3 independent animals. For each experimental condition the total number is 12 [rats]. Microarray analysis of different areas of the rat brain (core, periinfarct and contralateral cortex) after 24h and 3 days of permanent ischemia."
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Study Public Release Date	"2012-12-01"
Study File Name	"s_E-GEOD-36010_study_samples.txt"
STUDY DESIGN DESCRIPTORS
Study Design Type	"transcription profiling by array"
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STUDY PUBLICATIONS
Study PubMed ID	"23284893"
Study Publication DOI	"10.1371/journal.pone.0052121"
Study Publication Author List	"Ramos-Cejudo J, Gutiérrez-Fernández M, Rodríguez-Frutos B, Expósito Alcaide M, Sánchez-Cabo F, Dopazo A, Díez-Tejedor E."
Study Publication Title	"Spatial and temporal gene expression differences in core and periinfarct areas in experimental stroke: a microarray analysis."
Study Publication Status	"Published"
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STUDY FACTORS
Study Factor Name	"treatment"	"brain region"	"rat"	"time"
Study Factor Type	"treatment"	"brain region"	"rat"	"time"
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STUDY ASSAYS
Study Assay File Name	"a_E-GEOD-36010_GeneChip_assay.txt"
Study Assay Measurement Type	"transcription profiling"
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Study Assay Technology Type	"DNA microarray"
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STUDY PROTOCOLS
Study Protocol Name	"P-GSE36010-3"	"P-GSE36010-2"	"P-GSE36010-4"	"P-GSE36010-5"	"P-GSE36010-6"	"P-GSE36010-7"	"P-GSE36010-8"	"P-GSE36010-1"	"healthy_rats"	"surgical_prep"	"three_vessel_occlusion"
Study Protocol Type	"grow"	"specified_biomaterial_action"	"nucleic_acid_extraction"	"labeling"	"hybridization"	"image_acquisition"	"feature_extraction"	"bioassay_data_transformation"	"specified_biomaterial_action"	"specified_biomaterial_action"	"specified_biomaterial_action"
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Study Protocol Description	"All experiments were designed to minimize suffering in compliance with our medical school’s Ethical Committee for the Care and Use of Animals in Research (following EU directives 86/609/CEE and 2003/65/CE).  Rats were fed ad libitum in their home cages until sacrifice."	"Animals were anesthetized before surgery by ketamine (25 mg/kg), diazepam (2 mg/kg), and atropine (0.1 mg/kg) at a dose of 2.5 ml/kg by intraperitoneal injection. Analgesia was provided with subcutaneous meloxicam 2 mg/kg. A small craniotomy was made above the rhinal fissure over the branch of the right middle cerebral artery (MCA), which was permanently ligated just before its bifurcation between the frontal and parietal branches. Complete interruption of blood flow was confirmed. An identical protocol was applied to Sham-operated rats, which were subjected to exactly the same surgery protocol but without infarct. All rats were fed ad libitum in their home cages until sacrifice at 24h or 3days"	"Total RNA was extracted with TRIzol reagent (Invitrogen) and the miRNeasy mini kit (Qiagen),Integrity and quantity were checked with the Agilent Bio-Analyzer QC"	"miRNA Labeling Kit (Agilent Technologies) was used to label RNA. Basically, 100 ng of total RNA were dephosphorylated and Cyanine 3-pCp molecule was ligated to the 3' end of each RNA molecule by using T4 RNA ligase."	"1.65 micrograms of Cy3-labeled aRNA were hybridized for 17 hours at 65°C in an Agilent hybridization oven (G2545A, Agilent Technologies) set at 10 rpm in a final concentration of 1x GEx Hybridization Buffer HI-RPM (Agilent Technologies). Arrays were washed and dried out using a centrifuge according to the manufacturer's instructions (One-Color Microarray-Based Gene Expression Analysis, Agilent Technologies)"	"Arrays were scanned at 5mm resolution on an Agilent DNA Microarray Scanner (G2565BA, Agilent Technologies) using the default settings for 4x44k format one-color arrays."	"Images provided by the scanner were analyzed using Feature Extraction software v10.7.3.1 (Agilent Technologies). Notes : Entity List : Filtered on Flags [Detected, Compromised] Interpretation : All Samples Entities where at least 1 out of 1 conditions have CV >= 2.5 percent"	"ID_REF =  VALUE = VSN2 normalized signal intensities minus bad spots"	"Animals were sacrificed at t = 0.  No surgery was performed."	"Animals were anesthetized before surgery by ketamine (25 mg/kg), diazepam (2 mg/kg), and atropine (0.1 mg/kg) at a dose of 2.5 ml/kg by intraperitoneal injection. Analgesia was provided with subcutaneous meloxicam 2 mg/kg.  A small craniotomy was made above the rhinal fissure over the branch of the right middle cerebral artery (MCA).  At 24 or 72 hours post-surgery, the animals were sacrificed and cerebral cortex was collected."	"The right MCA was permanently ligated with a 9-0 suture just before its bifurcation between the frontal and parietal branches. Both common carotid arteries were transiently occluded for 60 min.  Complete interruption of blood flow was confirmed using an operating microscope and indirectly confirmed by the presence of an ischemic lesion in magnetic resonance imaging (MRI) and ADC maps of the brains."
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STUDY CONTACTS
Study Person Last Name	"Cejudo"	"Ramos-Cejudo"	"Gutiérrez-Fernández"	"Rodríguez-Frutos"	"Alcaide"	"Sánchez-Cabo"	"Dopazo"	"Díez-Tejedor"
Study Person First Name	"Jaime"	"Jaime"	"María"	"Berta"	"Mercedes"	"Fátima"	"Ana"	"Exuperio"
Study Person Mid Initials	"Ramos"	""	""	""	"E"	""	""	""
Study Person Email	"jaime.ramosc@gmail.com"	""	""	""	""	""	""	""
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Study Person Address	"Neuroscience, La Paz University Hospital, Paseo de la Castellana, 261, Madrid, Spain"	""	""	""	""	""	""	""
Study Person Affiliation	"La Paz University Hospital"	""	""	""	""	""	""	""
Study Person Roles	"submitter"	""	""	""	""	""	""	""
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