Cf42b662-f237-452b-8131-9c55dd6860c3 - samples
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ABSTRACT:
PROVIDER: EGAD00001004185 | EGA |
REPOSITORIES: EGA
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Project description:Purpose: Signaling pathways mediated by microRNAs (miRNAs) represent one of the mechanisms that regulate stroke progression and recovery. The goal of this study is to investigate miRNA expression signatures in freshly removed human stroke brain tissue. Methods: Human brain samples (5 stroke and 3 non-stroke samples) obtained at 48-72 hours after stroke onset during craniectomy and stroke-ectomy, were subjected to histopathological and immunofluorescence microscopy analyses. NGS sequencing was performed by Qiagen company and analyses were carried out using QIAseq miRNA Quantification workflow and RNA-seq Analysis tools within CLC Genomics Workbench (version 20.0.2). Reads were normalized for expression analysis using trimmed mean of M-values method (TMM). miRNA profiling was performed using the EdgeR in Bioconductor package. Whole transcriptome RNA-sequencing Analysis: The unmapped reads from the NGS miRNA analysis were extracted, deduplicated and mapped to the genome. Gene expressions were calculated by counting number of reads mapping to the annotated gene loci. Human miR-155 Targets RT2 Profiler PCR Array (Qiagen) was performed using 3 RNA samples per stroke and control groups. The PCR Array Data analysis was performed using an automated PCR Analysis Web Portal and GeneGlobe Data Analysis (Qiagen). Results: Human stroke brain tissue was characterized by classic ischemic changes, including significant neuronal and vascular damage, and prominent edema. The absence of monocytes and notable neutrophil infiltration indicated the early stage of leukocyte response to ischemia. miRNA NGS analysis detected 36 miRNAs with significantly aberrant expression in stroke tissue, as compared to non-stroke samples. Of these miRNAs, 19 were previously identified in stroke patient blood and CSF, while dysregulation of 16 miRNAs was newly detected in this study. Bioinformatics pathway enrichment analysis demonstrated a strong association of the identified miRNAs with stroke-related biological processes and signaling pathways Conclusions: Dysregulated miRNAs detected in our study could be regarded as potential candidates for biomarkers and/or targets for therapeutic intervention. The obtained data will serve for better understanding of the molecular basis of stroke and provide valuable information for the future functional studies in the experimental models of stroke.
2020-07-29 | GSE155257 | GEO
Project description:We investigated the functional recovery of in ischemic stroke by Photothrombotic stroke (PT) model. RNA-Seq of the peri-infarct cortex at 28 day after PT to clarify the potential mechanisms of pushen capsule against ischemic stroke. Pushen (drug approval number: Z20040074; batch number: 20082403; Suzhong pharma) was dissolved in the vehicle of ultrapure water, and it was administered by oral gavage at 24 hours after surgery continuously for 28 days. Mice in the Sham and Vehicle group were administered with a vehicle of ultrapure water equal to the Pushen group. By applying the cutoffs of P <0.05 and |log2 (fold change)|>1, 2369 differentially expressed genes (DEGs) were identified between sham vs PT, and 231 differentially expressed genes (DEGs) were identified between PT vs Pushen.
2023-06-05 | GSE207034 | GEO
Project description:Cerebellar vasospasm is a severe complication of aneurysmal subarachnoid hemorrhage (aSAH) occurring for 30% of aSAH patients. To date, no biomarker of vasospasm occurrence exists and thus all aSAH patients undergo a preventive and dangerous treatment. In this study, we explored the miRNome of aSAH patients to detect potential expression differences between the patients developing a vasospasm (VSP+) or not (VSP-). The shared data include raw and normalized count miRNA data in aneurysmal subarachnoid hemorrhage patients with or without vasospasm.
| EGAS00001003092 | EGA
Project description:blood miRNA expression in ischemic stroke compared to controls miRNA expression in blood cells from patients with ischemic stroke were compared to controls with vascular risk factors
2014-07-01 | E-GEOD-55937 | biostudies-arrayexpress
Project description:Background: Ischemic stroke is a disease with high rate of death and disability worldwide. This study investigated key circRNAs related to ischemic stroke. Methods: Three ischemic stroke patients and three healthy individuals were included in the current study to obtain the circRNA expression profiles by RNA sequencing. Through bioinformatic analysis, differentially expressed circRNAs (DEcircRNAs) were identified, and GO and pathway analyses for the host genes of DEcircRNAs were conducted. To further explore the functions of key circRNAs, a DEcircRNA-miRNA interaction network was constructed. Finally, the expression levels of selected circRNAs were validated with qRT-PCR. Results: A total of 736 DEcircRNAs were detected in ischemic stroke. Functional annotation of host genes of DEcircRNAs revealed several significantly enriched pathways, including Fc epsilon RI signaling pathway, B cell receptor signaling pathway, and T cell receptor signaling pathway. A circRNA-miRNA network, including 1544 circRNA-miRNA pairs, 456 circRNAs and 4 miRNAs, was obtained. The qRT-PCR results were largely in keeping with our RNA-seq data. Conclusion: The results of our study may help to elucidate the specific mechanism underlying ischemic stroke.
2021-06-24 | GSE178764 | GEO
Project description:We have used microarrays to investigate the changes in gene expression at various times after stroke. Our findings reported that gene expression screening can detect known and unknown transcriptional features of stroke. Brain samples were obtained from 9 patients who died from stroke, with the approval of the local Ethics Committee. The patients were aged between 51 and 86 years and had survived between 2-37 days following stroke. Tissue samples were taken from infarct and peri-infarcted zones while controls were obtained from the contralateral hemisphere. We established mRNA expression profiles of the damaged brain tissues between 2 to 6 days, 9 to 20 days, and 26 to 37 days after stroke. RNA from three stroke patients was pooled for each patient survival group.
2010-06-25 | E-GEOD-9391 | biostudies-arrayexpress
Project description:We collected 4 paired esophageal cancer (EC) tissues and adjacent normal tissues. Total RNA was extracted from the tissues. Then total RNA was processed and transfer RNA-derived small RNAs (tsRNAs) were profiled using tsRNA sequencing technique. Raw read counts were filtered to remove the tsRNAs that were expressed in low levels. We only kept the tsRNAs with a nonzero raw read count in all 4 EC tissues or all 4 adjacent normal tissues, and normalized the remaining tsRNAs with DESeq2 in the statistical program R (version 4.0.1). Differentially expressed tsRNAs were screened using following criterions: fold change was larger than 2 and adjusted P value was less than 0.05.
2022-07-10 | GSE207635 | GEO
Project description:We tested the hypothesis that circulating microRNAs (miRNAs) present in plasma might display a specific signature in patients with intracerebral hemorrhage (ICH). Global miRNA profiles were determined with the Agilent Human miRNA Microarray platform, 027233. ICH patients display a characteristic inflammation-related miRNA profile as compared to healthy controls. Plasma samples were collected from the following 6 subject groups: male ICH patients (n=8), female ICH patients (n=7), male healthy control (n=4), female healthy control (n=4), male ischemic stroke patients (n=8) and female ischemic stroke patients (n=8). Total RNAs isolated from 1 ml plasma were pooled for each group. A fixed volume of RNA sample was withdrawn from each pool and used for microarray detection.
2013-01-19 | E-GEOD-43618 | biostudies-arrayexpress
Project description:The whole genome DASL HT assay was used in combination with the HumanHT-12 v4 BeadChip for screening normal and tumour tissue in a retrospective 28 sample cohort of small bowel adenocarcinoma patients. Non-normalized and average normalized (background subtracted) data
2015-09-03 | GSE61465 | GEO
Project description:Serum were obtained from 4 groups, day0 and day28 neonates with CLD and non-CLD. Serum samples (250ul) from cord blood at birth and venous blood of neonates at 28 DAYS were transferred to sterile tubes containing 63 μl of ExoQuick precipitation solution (System Bioscience, Mountain View, CA, USA), and mixed. The mixtures were incubated for 30 min at 4℃, and centrifuged at 1500×g for 30 min. Then, the supernatants were removed, the pellets (extracellular vesicles) were diluted to 60 μl with phosphosaline buffer, and then thawed on dry ice for total RNA extraction with a miRvana isolation kit (Ambion). 3pM synthetic ath-miR159a was spiked into each sample to correct for technical differences. Using a human miRNA array, we identified 62 miRNAs that were universally expressed in CLD patients and non-CLD patients (Normalized Template).
2021-04-06 | GSE129400 | GEO