RNA-seq of peri-infarct cortex of the rat dMCAO model of ischemic stroke treated with AAV7-hMANF or AAV7-GFP
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ABSTRACT:
INSTRUMENT(S): NextSeq 500
ORGANISM(S): Rattus norvegicus
SUBMITTER: Kert Mätlik
PROVIDER: E-MTAB-6709 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:The study was designed in order to identify genes differentially expressed when glucocorticoid signaling is blocked by a glucocorticoid-receptor antagonist (RU486 â?? mifepristone) in the context of brain inflammation induced by bacterial lipopolysaccharide (LPS). LPS is only able to cause murine brain damage in our experimental conditions upon RU486 pre-treatment. Hence, the study may reveal potential candidate genes to mediate neuroprotection or neurotoxicity. Due to the factorial design of the experiment, RU486 main-effect could be dissociated from the effects resultant of RU486/inflammation interaction. In addition, brain dissection was conducted to verify the effects in the brain side ipsilateral or contralateral to the site of intracerebral LPS infusion. Experiment Overall Design: C57Bl/6 mice received an i.p. injection of vehicle (DMSO - 50 microliters) or RU486 (50 mg/kg) and were submitted to surgery 4 h later. The mice receiving intraparenchymal injections were anesthetized and the right caudate putamen was reached, using a small cannula at the coordinates 0.0 mm anteroposterior, -2.0 mm lateral, and -3.0 mm dorsoventral according to a mouse brain atlas. The animals received an infusion of sterile pyrogen-free saline (1 microliter) or LPS (from Eschericia coli; serotype O55:B5; Sigma L2880 - 2.5 micrograms) over 2 min by means of a microinjection 18 pump. Animals were killed 12 h after the intracerebral infusion. The mice were anesthetized under isofluorane and blood was drawn via cardiac puncture before head decapitation. Brains were removed rapidly from the skulls and placed in cold phosphate buffered saline (PBS) solution. A brain region limited at plane anteroposterior +1.5 to -1.5 and dorsoventral -4.0 was dissected, separated in ipsilateral side and quickly immersed in liquid nitrogen. The tissue was stored at -80 oC until RNA extraction was performed. A total of 37 chips (MOE430A â?? Affymetrix, Santa Clara, CA) were used for oligonucleotide array analysis [one chip per biological sample; 8 groups (contralateral dmso/saline, dmso/LPS, RU486/saline, RU486/LPS and ipsilateral dmso/saline, dmso/LPS, RU486/saline, RU486/LPS) with 4 â?? 6 biological replicates each]. Expression values from the CEL files generated from scanning were obtained using RMA algorithm, available at http://www.bioconductor.org. The expression values were also inspected with GeneSpring software (Silicon Genetics). Statistical analysis was performed considering a factorial linear model according to the methods implemented in Limma package (R project packages are available at http://www.cran.r-project.org).
2008-06-14 | E-GEOD-6509 | biostudies-arrayexpress
Project description:This program addresses the gene signature associated with brain (cortex) in the tMCAO rat model for stroke. The tMCAO stroke model profiling data was analyzed by identifying genes that were up- and down-regulated at selected p value and fold change in brain cortex of the Sprague Dawley rats following middle cerebral artery occlusion compared to the sham-operated controls.
2013-03-22 | E-GEOD-38037 | biostudies-arrayexpress
Project 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 n number is of 12. Microarray analysis of different areas of the rat brain (core, periinfarct and contralateral cortex) after 24h and 3days of permanent ischemia
2012-12-01 | E-GEOD-36010 | biostudies-arrayexpress
Project description:To reveal the comparative pharmacological mechanism of differential compounds and its combination, we used a custom cNDA microarray to screen gene expression on ischemia mouse hippocampus. Cerebral ischemia was induced in anesthetized mice by urethane (1.5g/kg, i.p) to 38-48g male or female mice by occlusion of the middle cerebral artery (MCA) for 15 minutes twice with microvascular clips, followed by reperfusion for 10 minutes after the first occlusion. Experimental animal were divided into groups: Sham-operated, vehicle (M3,ischemic mice 3 hour;12 hour;24 hour),Baicalin(BA) (5mg/ml), Jasminoidin(JA) (25mg/ml),Jasminoidin(H) (50mg/ml),Cholic acid(CA) (7mg/ml),Concha margaritifera(CM) (50mg/ml), Nimodipine (NI) (50mg/ml),and JA+BA, JA+CA, JA+BA+CA, JA+BA+CA+CM. The prescription of combination therapies was composed of the same ratio on every compound. Treated compound dosage according to 0.2ml physic liquor/100g mouse or rat body weight treated at 1.5h post operation given through tail vein. Sham-operated mice underwent identical procedures except therapy were vehicle (2ml/kg; 100% DMSO). Infarct Volume and Neurological Score were tested to display variation on comeout change. Hippocampus (subfields CA1-4 of Ammon's horn) were carefully dissected out from re-anesthetized mice under RNAase-free conditions, flash frozen and stored at -75 C. Total RNA of each sample was extracted with Trizol reagent (Invitrogen, procedure according to the instruction manual). Three animals per group were pooled and homogenized in denaturing solution with a Polytron. Three pooled per group and nine times repeted microarray experiments of each pooled were preformed. Each microarray contained 374 cDNA derived from cDNA library of mouse brain (Invitrogen, Cat.1065-025). Plasmid magnified using Invitrogen provided library. Design and synthesize Primer according the information provided by selected genes.Total gene segment is 416, two of them is control(lambda-A and pUC19). The criterion of qualified PCR extending is: the total gained volume of the purpose strap DNA is greater or equal to 7?g;the purpose strap DNA gained volume/total DNA gained volume is greater or equal to 80%.Finally, the DNA concentration is adjusted to 0.5 ?g/ ?l.After refinded PCR_for every gene, 2?l DNA solution was taken to proceeding electrophoresis on the electrophoresis condition of 2%Gel.Then fix quantify analysis according electrophoresis photo have taken.Choosing 5 PCR refined products sequencing from two direction after amplification.These 5 genes all chosen from UniGene sample which marked by ?,one of them is used Dalian ? as cyclostyle to amplification.The five sequence genes was certified as aimed gene segment by Blast(Completed in TaKaRa(Dalian))
2010-01-01 | E-TABM-612 | biostudies-arrayexpress
Project description:Ischemic stroke triggers severe focal hypoperfusion accompanied with deprivation of oxygen and glucose to the cerebral tissue, together with loss of ATP, depolorization of neurons, elevated extracellular potassium concentration, and subsequently leads to excitotoxicity as well as increased oxidative stress promoting microvascular injury, blood-brain-barrier deregulation, post-ischemic inflammation and eventually the consequential neurological deficit. Although reperfusion of ischemic brain tissue is critical for restoring normal function, it can paradoxically result in secondary damage, called ischemia/reperfusion (I/R) injury. Microarray analysis was performed on the right striatum and cortex (corresponded to infarct area) of post-I/R injured brain tissues of wild-type (WT-MCAO) using Illumina mouse Ref8 V2 genechips. Suture-induced middle cerebral artery occlusion was induced for 2h followed by reperfusion, with tissue extraction taking place 2h, 8h and 24h post-reperfusion (n=4 respectively). Sham controls were included in this study too (n=4 respectively).
2011-01-10 | E-GEOD-23160 | biostudies-arrayexpress
Project description:Analysis of changes in gene expression induced by a transient (90') middle cerebral artery occulsion, at several time points post stroke induction, with the effect of a treatment with the drug FK506 studied at a single time point.
2010-06-19 | E-MEXP-2222 | biostudies-arrayexpress
Project description:Glutathione peroxidase (Gpx) is a selenium-containing enzyme that catalyses the reduction of a variety of biological peroxides at the expense of reduced glutathione (GSH). Gpx1 is the most abundant isoform and its role has been implicated in neurodegenerative disorders such as ParkinsonM-bM-^@M-^Ys disease (PD), dementia with Lewy bodies tissue (DLB) (Power and Blumbergs, 2009) and traumatic brain injury (Tsuru-Aoyagi et al., 2009). Due to its high abundance, mutation of the Gpx1 allele would lower overall Gpx activity in the brain significantly. Gpx1 knockout (Gpx1-/-) mice do not show overt phenotypic differences, but all indications suggest that these mice are in a chronic M-bM-^@M-^\pro-oxidantM-bM-^@M-^] state (Cheng et al. 1999; de Haan et al. 2004). Indeed, a recent study from our laboratory illustrated that the absence of Gpx1 exacerbated stroke injury via increased ROS production and vascular permeability (Wong et al. 2008). Furthermore, Gpx1-/- mice demonstrated an increase in caspase-3 activation and greater infarct volume (Crack et al. 2001) Microarray analysis was performed on the right striatum and cortex(corresponded to infarct area) of post-I/R injured brain tissues of Gpx1 -/- brains using Illumina mouse Ref8 V2 genechips. Suture-induced middle cerebral artery occlusion was induced for 2h followed by reperfusion, with tissue extraction taking place 2h, 8h and 24h post-reperfusion (n=4 respectively). Sham controls were included in this study too (n=4 respectively).
2011-01-10 | E-GEOD-23162 | biostudies-arrayexpress
Project description:To investigate age-dependent transcriptomic changes between young or aged intracerebral hemorrhage mice, we established collagenase IV-induced intracerebral hemorrhage mice models. Intracerebral hemorrhage was induced by infusion of sterile collagenase IV in ipsilateral caudate putamen of brain. We then performed gene expression profiling analysis using data obtained from RNA-seq of brain perihematomal tissues from young or aged ICH mice 24 hours after intracerebral hemorrhage.
2022-04-29 | GSE200575 | GEO
Project description:Introduction The identification of proteins involved in brain ischemia might allow the discovery of new putative biomarkers or potential therapeutic target of one of the most important neurological disorders. MALDI Imaging-Mass-Spectrometry (IMS) is a powerful technique that allows the visualization of protein distribution along a tissue without labeling. Our aim is to study the distribution of proteins along mouse brain after an ischemic insult and to identify relevant proteins involved in brain ischemia. Materials and methods We occluded the middle cerebral artery (60min) of C57BL/6J mice (n=4) with 24h of reperfusion. Brain slices were analyzed by MALDI-TOF and mass spectra from infarct (IC) and contralateral (CL) regions were compared using ClinProTools. Relevant m/z were selected after PCA analysis and their ion distribution maps were analyzed by FlexImagin3.0. Protein identification was conducted on mouse brain homogenates through a bottom-up approach consisting on complementary fractionations based on tricine gels and RP-HPLC. The identifications were confirmed by immunohistochemistry. Results We identified 102 m/z with different abundances between IC and CL (p<0.05), from which 21 m/z were selected by PCA as more relevant. Thirteen of them were found increased in the infarct region and 4 m/z showed a discrimination higher than 90% between IC and CL. After bottom-up identification, immunohistochemistry analysis confirmed increased ATP5i and COX6C expressions, and decreased UMP-CMP kinase in IC compared to CL. Conclusions We identified for the first time by MALDI-IMS several m/z peaks with different abundances between IC and CL. These proteins involved in brain ischemia might represent potential diagnostic biomarkers or target molecules for neurological recovery.
2016-12-14 | PXD003644 | Pride
Project description:Genes upregulated in stroke infiltrating stem cells were compared against the parent non-infiltrated mouse stem cell line derived from immortomouseTM. Abstract Background and Purpose- Although the therapeutic potential of bone marrow-derived stem cells (SC) has been addressed in different experimental models of ischemic stroke, it is still unclear how SC induce neuroprotection following stroke. In this study, we describe a novel method for recovering SC infiltrating post-stroke brain tissue allowing the determination of genes which become persistently activated / or depressed (compared to their naïve counterparts) during SC-mediated neuroprotection. Methods- Ischemic stroke was induced in C57BL/6 mice by middle cerebral artery occlusion for 1 h, followed by reperfusion. SC were isolated from H-2Kb-tsA58 (immortomouseTM) mice, and were administered (i.v.) 24 h after reperfusion. At the onset of therapeutic improvement (14 days after ischemia), infarcted brain tissue was isolated and infarct-infiltratng SC cultured at 33°C. Microarray analysis and RT-PCR were performed to compare persistent differential gene expression between naïve and infiltrating SC populations. Results- Z-scoring revealed dramatic changes in extracellular genes of analyzed cells. Pair-wise analysis detected 80 extracellular factor genes that were up-regulated ( 2 fold, P<0.05, Benjamini-Hochberg correction) between naïve and infiltrated SC. Although several conventional neuroregenerative, nerve guidance and angiogenic factors (bFGF, bone morphogenetic protein, angiopoietins, neural growth factors were among the expressed genes detected we identified Cytokine receptor-like factor 1 (Crlf1), Fgf7, family with sequence similarity 19, member A5 (Fam19a5), Glypican 1 (Gpc1), Dickkopf homolog 2 (Dkk2), Endothelial cell-specific molecule 1, Osteopontin (OPN)35, Tissue factor pathway inhibitor 2, Masp3 mRNA for MBL-associated serine protease-3, Glial cell line derived neurotrophic factor (Gdnf), Bone morphogenetic protein 2 (Bmp2), Olfactomedin 1, Sushi-repeat-containing protein, X-linked 2 (Srpx2). Conclusions- SC infiltrating the post-i schemic brain assume a persistently altered pattern of expressed extracellular genes compared to naïve SC that contributes to neuroprotection, regeneration and angiogenesis in infarcts. Keywords: Gene activation / suppression study Comparison of persistent stem cell gene expression induced by stroke-infarct infiltration
2010-12-31 | E-GEOD-21393 | biostudies-arrayexpress