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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Genome response to tissue plasminogen activator in experimental ischemic stroke

ABSTRACT: To further delineate tPA functions in the blood, we examined the gene expression profiles induced by tPA in a rat model of ischemic stroke. Forty-two Sprague-Dawley rats were subjected to: 2 hours of middle cerebral artery occlusion (MCAO); a permanent-MCAO; or were used as controls. tPA was administered to half of the rats in each group at 3hours. Whole blood was drawn at 24 hours, and isolated RNA levels measured on Affymetrix Rat Genome 230 2.0 GeneChip microarrays to examine the entire RNA transcriptome. 42 samples, 7 groups in total ( 2 treatmented disease, 2 untreated disease, and 3 control groups), each group had 6 replicates

ORGANISM(S): Rattus norvegicus

SUBMITTER: Glen Jickling

PROVIDER: E-GEOD-21136 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Genome response to tissue plasminogen activator in experimental ischemic stroke

Project description:To further delineate tPA functions in the blood, we examined the gene expression profiles induced by tPA in a rat model of ischemic stroke. Forty-two Sprague-Dawley rats were subjected to: 2 hours of middle cerebral artery occlusion (MCAO); a permanent-MCAO; or were used as controls. tPA was administered to half of the rats in each group at 3hours. Whole blood was drawn at 24 hours, and isolated RNA levels measured on Affymetrix Rat Genome 230 2.0 GeneChip microarrays to examine the entire RNA transcriptome.

2014-03-29 | GSE21136 | GEO

Comparing Reference-Based RNA-Seq Mapping Methods for Non-Human Primate Data

Project description:We present a comparison of four reference-based mapping methods for mapping non-human primate data to a human reference sequence. We utilize TopHat2 and GSNAP for mapping to the human genome, and Bowtie2 and Stampy for mapping to the human genome and transcriptome for a total of six mapping approaches Comparison of reference-based mapping methods for 12 yellow baboons

2014-07-10 | E-GEOD-57485 | biostudies-arrayexpress

Altered modulation of WNT-Î²-catenin and PI3K/Akt pathways in IgA nephropathy

Project description:To uncover new molecular mechanisms involved in IgAN pathogenesis, we compared the genomic profiles of 12 IgAN patients with 8 healthy subjects, We included addiotional disease controls 3 FSGS(Focal Segmenal glomerulosclerosis) patients and 3 membrano proliferative glomerulonephritis type I (MPGN-I) controls in our study to evaluate if the WNT-Î²-catenin and PI3K/Akt pathways were specfic to IgAN. Gene expression profile comparison between 12IgAN patients and 8 Healthy Subjects. Gene Set Enrichment Analysis (GSEA) performed on the additional disease controls determined that the a priori defined set of genes and the pathways generated were specific to the IgAN

2010-06-08 | E-GEOD-14795 | biostudies-arrayexpress

RNA-seq of blood samples from bovines immunized with a multicomponent recombinant vaccine against cattle tick.

Project description:Tick infestations by Rhipicephalus microplus, the cattle tick, cause enormous losses to health and animal production. Ticks induce immune response in their hosts; therefore their immunobiological control is feasible. The available anti-tick vaccines display variable efficacy and short-lived, encouraging the search for new protective antigens. The identification of important genes in tick parasitism may indicate protective antigens useful to compose an anti-tick vaccine. We have developed and tested so far four recombinant salivary antigens as a multicomponent anti-tick vaccine in tick-susceptible bovines (Holstein breed). The challenge with R. microplus larvae displayed that tick infestation in vaccinated bovines was significantly reduced. In order to elucidate the molecular mechanisms trigged after immunisation and during infestation, RNA-seq data of peripheral blood from vaccinated and control animals were obtained in different periods of the immunisation trial. A total of 24 mRNA-seq Illumina libraries (single-end, 100 bp) were analysed to identify differential gene expression according to the experimental condition.

2019-12-15 | E-MTAB-8022 | biostudies-arrayexpress

Transcriptome profile of peripheral blood from pancreatic ductal adenocarcinoma patients

Project description:Analysis of expression profile of peripheral blood from pancreatic ductal adenocarcinoma patients RNA expression profile of peripheral blood from pancreatic ductal adenocarcinoma patients Total RNA was isolated from peripheral blood. 36 patients with unresectable PDAC were recruited. The diagnosis of PDAC was based on clinical evaluation and imaging studies, which were histologically confirmed by surgery or imaging-guided biopsy. 14 gender, age, and habits matched healthy controls were also included. A total of 1000 ng of total RNA was processed using Illumina TotalPrep RNA Amplification Kit. Hybridization of human samples was performed on Illumina Human-HT12 Version 4.

2015-11-04 | E-GEOD-74629 | biostudies-arrayexpress

Transcription profiling of human erythroleukemia K562 cells during TPA-induced megakaryocyte differentiation

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Transcription profiling of peripheral blood from stable and acute rejection pediatric kidney transplant patients.

Project description:Full title: Expression data from whole blood gene expression analysis of stable and acute rejection pediatric kidney transplant patients Tissues are often made up of multiple cell-types. Blood, for example, contains many different cell-types, each with its own functional attributes and molecular signature. In humans, because of its accessibility and immune functionality, blood cells have been used as a source for RNA-based biomarkers for many diseases. Yet, the proportions of any given cell-type in the blood can vary markedly, even between normal individuals. This results in a significant loss of sensitivity in gene expression studies of blood cells and great difficulty in identifying the cellular source of any perturbations. Ideally, one would like to perform differential expression analysis between patient groups for each of the cell-types within a tissue but this is impractical and prohibitively expensive. This dataset is the validation dataset used to test the csSAM gene expression deconvolution algorithm as reported in the accompanying paper. Whole blood gene expression measurements for 24 pediatric renal transplant patients were analyzed on human specific HGU133V2.0 (+) whole genome expression arrays. Blood drawn using PaxGene Blood RNA Tubes (PreAnalytiX, Qiagen).

2010-04-06 | E-GEOD-20300 | biostudies-arrayexpress

Expression profiles of human primary keratinocytes differentiated with TPA

Project description:Human primary keratinocytes were left untreated or treated for 48 hr with 12-O-tetradecanoylphorbol-13-acetate (TPA) and expression profiles were compared to find long ncRNAs expressed and differentially regulated upon differentiation. 4 replicates of minus TPA and 3 of plus TPA with dye-swap. Custom-made microarray from Agilent.

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Age and albumin D site-binding protein control tissue plasminogen activator levels: neurotoxic impact.

Project description:Recombinant tissue-type plasminogen activator (tPA) is the fibrinolytic drug of choice to treat stroke patients. However, a growing body of evidence indicates that besides its beneficial thrombolytic role, tPA can also have a deleterious effect on the ischaemic brain. Although ageing influences stroke incidence, complications and outcome, age-dependent relationships between endogenous tPA and stroke injuries have not been investigated yet. Here, we report that ageing is associated with a selective lowering of brain tPA expression in the murine brain. Moreover, our results show that albumin D site-binding protein (DBP) as a key age-associated regulator of the neuronal transcription of tPA. Additionally, inhibition of DBP-mediated tPA expression confers in vitro neuroprotection. Accordingly, reduced levels of tPA in old mice are associated with smaller excitotoxic/ischaemic injuries and protection of the permeability of the neurovascular unit during cerebral ischaemia. Likewise, we provide neuroradiological evidence indicating the existence of an inverse relationship between age and the volume of the ischaemic lesion in patients with acute ischaemic stroke. Together, these results indicate that the relationship among DBP, tPA and ageing play an important role in the outcome of cerebral ischaemia.

2009-08-24 | GSE9004 | GEO

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2014-01-01 | E-GEOD-44314 | biostudies-arrayexpress

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