Ontology highlight
ABSTRACT:
PROVIDER: PRJNA641783 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12088354_1.fastq.gz | Fastqsanger.gz | |||
| SRR12088354_2.fastq.gz | Fastqsanger.gz | |||
| SRR12088355_1.fastq.gz | Fastqsanger.gz | |||
| SRR12088355_2.fastq.gz | Fastqsanger.gz | |||
| SRR12088356_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 24 |
Similar Datasets
Project description:Stroke remains a major global health challenge due to its high mortality and significant socioeconomic burden. Despite advances in clinical management, effective diagnostic tools and therapeutic strategies remain limited. This study aimed to identify and expand the repertoire of biomarkers of damage and repair that could serve as potential diagnostic and prognostic tools across post-stroke phases. Twenty-three male wild-type mice were assigned to control pre-stroke, 24-hour acute, and 35-day chronic post-stroke groups. Cerebral ischemic injury was induced via a 30-minute middle cerebral artery occlusion Koizumi method. Magnetic resonance imaging and neurological scoring were used to assess lesion size and functional deficit acutely, as well as structural and functional changes during the chronic phase. Proteomic profiling of the ipsilateral and contralateral cortices was performed using by data-independent acquisition (DIA)-based MS method. Seventy-four proteins showed significant alterations and were classified into four temporal expression clusters: acutely and chronically upregulated, acutely upregulated and chronically downregulated, acutely downregulated and chronically upregulated, and acutely and chronically downregulated. Gene ontology analysis identified 47 affected biological processes, including synaptic signaling, immune response, cell-cell communication, cytoskeletal organization, and proliferation. Several proteins not previously associated with stroke pathophysiology were identified, including 10 from the ipsilateral cortex (Dbi, Cpne3, Dnm2, Eef1a1, Taldo1, Pgls, Gnb5, Phf24, Ctsz, Capg) and 3 from the contralateral cortex (Agpat3, Cacng8, Endod). These findings provide novel molecular insights into post-stroke energy metabolism, neuroinflammation, and cellular remodeling, highlighting potential targets for further intervention.
2026-01-19 | PXD067155 | Pride
Project description:The blood-brain barier (BBB) function is impaired in several neurological diseases such as stroke. To better study the BBB dysfunction in stroke and to identify novel therapeutic targets, a detailed analysis of the neurovascular unit (NVU) cells that together regulate the BBB function is needed. To this end, we isolated the NVU cells EC, PC, AC, MG post stroke in mice using our newly developed SGD (Spitzer, Guérit, Devraj) method from the same starting material followed by RNA sequencing. Cells were isolated from both healthy appearing contralateral hemisphere and ipsilateral stroke hemisphere post tMCAO (1h occlusion, 23h repurfusion) using the SGD method. Each sample comprised 6 biological replicates with each replicate pooled from 3-4 male C57BL6 adult mouse brains either from contralateral or ipsilateral hemisphere post stroke. Only mice with neurological scores (mNSS) of atleast 8 were included for the NVU cell isolation. Our data showed regulation of several genes post stroke in each of the cell types analyzed with novel candidates that were co-regulated in the NVU cell types. As the blood-brain barrier (BBB) is co-regulated by several NVU cell types, we propose targeting the candidates co-regulated in multiple NVU cell-ytpes for novel and effective therapeutic options in stroke.
2022-07-20 | GSE163752 | GEO
Project description:Genome wide DNA methylation profiling of primary breast cancer tumors and their axillary metastasis and/or ipsilateral breast recurrence and/or contralateral breast recurrence. The Illumina Infinium 27k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 27,000 CpGs. Samples included 20 primary breast tumors and their matched axillary metastasis, 17 primary breast tumors and their matched ipsilateral breast recurrence, and 11 primary breast tumors and their matched contralateral breast recurrence.
2013-12-24 | GSE44870 | GEO
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.
2012-12-01 | GSE36010 | GEO
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:miRNA microarray profiling of primary cortical neurons exposed to 4h oxygen and glucose deprivation (OGD) in vitro. RNA samples collected at 8h post-OGD terminaion. miRNAs were also profiled in mice exposed to 3- vessel occlusion model of stroke. RNA samples collected from contralateral (control) and ipsilateral (infarct) sides of the brain following 24h of reperfusion.
2013-11-21 | GSE51586 | GEO
Project description:The goal of this study was to evaluate changes in metabolic homeostasis during the first 12 weeks of recovery in a distal middle cerebral artery occlusion mouse model of stroke. To achieve this goal, we compared the brain metabolomes of ipsilateral and contralateral hemispheres from aged male mice up to 12 weeks after stroke to that of age-matched naïve and sham mice. There were 707 biochemicals detected in each sample by liquid chromatography-mass spectroscopy (LC-MS). Mitochondrial fatty acid β-oxidation, indicated by acyl carnitine levels, was increased in stroked tissue at 1 day and 4 weeks following stroke. Glucose and several glycolytic intermediates were elevated in the ipsilateral hemisphere for 12 weeks compared to the aged naïve controls, but pyruvate was decreased. Additionally, itaconate, a glycolysis inhibitor associated with activation of anti-inflammatory mechanisms in myeloid cells, was higher in the same comparisons. Spatial transcriptomics and RNA in situ hybridization localized these alterations to microglia within the area of axonal degeneration. These results indicate that chronic metabolic differences exist between stroked and control brains, including alterations in fatty acid metabolism and glycolysis within microglia in areas of degenerating white matter for at least 12 weeks after stroke.
2022-10-06 | MTBLS5543 | MetaboLights
Project description:Genome wide DNA methylation profiling of primary breast cancer tumors and their axillary metastasis and/or ipsilateral breast recurrence and/or contralateral breast recurrence. The Illumina Infinium 27k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 27,000 CpGs. Samples included 20 primary breast tumors and their matched axillary metastasis, 17 primary breast tumors and their matched ipsilateral breast recurrence, and 11 primary breast tumors and their matched contralateral breast recurrence. Bisulphite converted DNA from the 96 samples were hybridised to the Illumina Infinium 27k Human Methylation Beadchip v1.2 contributed by Institut Curie - Fabien Reyal
2013-12-24 | E-GEOD-44870 | biostudies-arrayexpress
Project description:Many extracellular matrix (ECM) changes occur in the brain after traumatic brain injury. This work sought to understand the dynamics of ECM modifications after TBI by comparing RNA transcription between ipsilateral and contralateral brain regions. Mice underwent controlled cortical impact (with a 2mm depth) using a pneumatic impactor. Seven days later, brain tissue was harvested from the site of injury and from the corresponding contralateral cortex. Microarrays were used to measure gene expression to compare these tissues.
2024-08-30 | GSE242025 | GEO
Project description:Netherton syndrome (NS) is a rare skin disease caused by loss-of-function mutations in the serine peptidase inhibitor Kazal type 5 (SPINK5) gene. Disease severity and the lack of efficacious treatments call for a better understanding of NS mechanisms. Here we describe a viable, Spink5 conditional knock-out (cKO) mouse model, allowing to study NS progression. Using comparative transcriptomics and proteomics, we determine a disease molecular profile conserved in mouse models and NS patients. Spink5 cKO mice and NS patients share skin barrier and inflammation signatures defined by up-regulation of proteases, IL-17, IL-36, IL-20 family cytokines. Furthermore, we show that systemic inflammation in Spink5 cKO mice is associated with thymic atrophy and is driven by innate immunity and IL-17/IL-22 signaling. By comparing skin transcriptomes and proteomes, we uncovered several putative substrates of tissue kallikrein-related proteases (KLKs), demonstrating that KLKs can proteolytically regulate IL-36 pro-inflammatory cytokines. Our study thus provides a conserved molecular framework for NS disease, adding new insights into its mechanisms and therapeutic targets.
2023-02-02 | MSV000091184 | MassIVE