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Wound healing process after TBI in zebrafish: time course (zebrafish)

ABSTRACT: The interaction between neurogenesis and angiogenesis after traumatic brain injury is a complex and dynamic process. To resolve this, we chose the zebrafish model organism for studying brain wound healing via systems biology approach. Transcriptome microarray data and histological analysis of injured fish were sampled at different time points during recovery process. Time-course microarray data following wound healing of zebrafish were obtained. From this set of data, we constructed two intracellular protein–protein interaction (PPI) networks for the traumatic brain injury healing mechanism.

ORGANISM(S): Danio rerio

PROVIDER: GSE56375 | GEO | 2014/09/30

SECONDARY ACCESSION(S): PRJNA243077

REPOSITORIES: GEO

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Wound healing process after TBI in zebrafish: time course (zebrafish)

Project description:The interaction between neurogenesis and angiogenesis after traumatic brain injury is a complex and dynamic process. To resolve this, we chose the zebrafish model organism for studying brain wound healing via systems biology approach. Transcriptome microarray data and histological analysis of injured fish were sampled at different time points during recovery process. Time-course microarray data following wound healing of zebrafish were obtained. From this set of data, we constructed two intracellular proteinM-bM-^@M-^Sprotein interaction (PPI) networks for the traumatic brain injury healing mechanism. Each fish in each group was injured by a 1.5 mm, 27G needle tip from day 0 to 28, respectively. These injured fish were collected at 0, 0.25, 1, 3, 6, 10, 15, 21, 28 dpi (day post injury). 0.625M-NM-<g of Cy3 cRNA for C. albicans array and 1.65 M-NM-<g of Cy3 cRNA for zebrafish array was fragmented to an average size of about 50-100 nucleotides by incubation with fragmentation buffer at 60M-BM-0C for 30 minutes. Each time point contain two biological repeats.

2014-09-30 | E-GEOD-56375 | biostudies-arrayexpress

Wound healing process after ventricular resection in zebrafish: time course (zebrafish)

Project description:The mechanism of cardiomyocyte prliferation and migration after ventricular resection is a complex and dynamic process. To resolve this, we chose the zebrafish model organism for studying post-injury heart regeneration and wound healing progress via systems biology approach. Transcriptome microarray data and histological analysis of injured fish were sampled at different time points during recovery process. Time-course microarray data following wound healing of zebrafish were obatined. From this set of data, we constructed two intracellular protein–protein interaction (PPI) networks to provide insights into the ventricular resection wound healing mechanism.

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Etiology matters - Comparing Genomic DNA Methylation Patterns in Three Rat Models of Acquired Epilepsy (TBI – MBD-seq)

Project description:Explore DNA methylation in traumatic brain injury model of epilepsy and its relationship to gene expression. Examination of methylation changes in stimulated rats compared to sham operated animals in traumatic brain injury model of epilepsy.

2016-09-06 | E-GEOD-75119 | biostudies-arrayexpress

Etiology matters - Comparing Genomic DNA Methylation Patterns in Three Rat Models of Acquired Epilepsy (TBI â mRNA-seq)

Project description:Explore DNA methylation in traumatic brain injury model of epilepsy and its relationship to gene expression. Examination of expression changes in stimulated rats compared to sham operated animals in traumatic brain injury model of epilepsy.

2016-09-06 | E-GEOD-75120 | biostudies-arrayexpress

Etiology matters - Comparing Genomic DNA Methylation Patterns in Three Rat Models of Acquired Epilepsy (TBI – mRNA-seq)

Project description:Explore DNA methylation in traumatic brain injury model of epilepsy and its relationship to gene expression.

2016-09-06 | GSE75120 | GEO

Etiology matters - Comparing Genomic DNA Methylation Patterns in Three Rat Models of Acquired Epilepsy (TBI – MBD-seq)

Project description:Explore DNA methylation in traumatic brain injury model of epilepsy and its relationship to gene expression.

2016-09-06 | GSE75119 | GEO

Single-nucleus profiling of adult mice subventricular zone after blast-TBI

Project description:To elucidate molecular features of the cells of Sub-ventricular Zone (SVZ), their progeny at each differentiation stage, and surrounding cells in SVZ under blast wave-induced changes, cells were profiled from matched SVZ of 3 mice that had received blast injury and 3 controls（The controls sequencing profile can be assessed in GEO at GSM5938054）.Cell type specific gene expression responding to (blast-related traumatic brain injury, bTBI) were revealed, some of which were closely associated with pathogenesis post-injury. Furthermore, the diverse cell to cell interaction networks uncovered an array of cellular processes under bTBI. Our gene expression atlas provides extensive resources for future researches regarding bTBI induced pathogenesis, its therapeutic interventions or diagnostic tests.

2022-06-28 | GSE207078 | GEO

Activation of innate immune pathways after brain injury promotes scar formation and impairs tissue recovery

Project description:Scar formation is a major hindrance to central nervous system regeneration upon traumatic injury. Glial cells are key players during the wound healing process, and their reaction to injury determines the extent of tissue restoration. Here, we used the regenerative potential of the zebrafish telencephalon to identify specific molecular and cellular mechanisms regulating glial scar formation. We demonstrated that contact of the cerebrospinal fluid with the brain parenchyma after injury activates toll-like receptor 2 (Tlr2) and the chemokine receptor 3 (Cxcr3) innate immunity pathways leading to initiation of a glial scar. These pathways were critical for scarring even after ablation of microglia and infiltrating monocytes. Our data support a specific role for the injury-induced Tlr1/2 and Cxcr3 signaling pathways in controlling proliferation of the oligodendrocyte progenitors and therefore exacerbated glial reactivity, contributing to scar formation. Interference with the Tlr1/2 and Cxcr3 pathways after injury alleviated glial scar formation and improved tissue restoration.

2022-01-18 | GSE98217 | GEO

Analysis of gene expression in zebrafish cornea during wound healing

Project description:The cornea, transparent and outermost structure of camera-type eyes, is prone to environmental challenges, but has remarkable wound healing capabilities which enables to preserve vision. The manner in which cell plasticity impacts wound healing remains to be determined. In this study, we report rapid wound closure after zebrafish corneal epithelium abrasion. Furthermore, by investigating the cellular and molecular events taking place during corneal epithelial closure, we show the induction of a bilateral response to a unilateral wound. Our transcriptomic results, together with our TGF-beta receptor inhibition experiments, demonstrate conclusively the crucial role of TGF-beta signaling in corneal wound healing. Finally, our results on Pax6 expression and bilateral wound healing, demonstrate the decisive impact of epithelial cell plasticity on the pace of healing. Altogether, our study describes terminally differentiated cell competencies in the healing of an injured cornea. These findings will enhance the translation of research on cell plasticity to organ regeneration.

2022-01-20 | GSE193784 | GEO

Comprehensive analysis of circRNA expression profiles in rat cerebral cortex after moderate traumatic brain injury

Project description:Background: Traumatic brain injury is a medical event of global concern, and a growing body of research suggests that circular RNA can play very important roles in traumatic brain injury. To explore the functions of more novel and valuable circular RNA in traumatic brain injury response, a moderate traumatic brain injury in rat was established and a comprehensive analysis of circular RNA expression profiles in rat cerebral cortex was done. Results: As a result, 301 up-regulated and 284 down-regulated circular RNAs were obtained in moderate traumatic brain injury rats, the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analysis were performed based on the circular RNA’s host genes, and a circRNA-miRNA interaction network based on differentially expressed circular RNAs was constructed. Also, four circular RNAs were validated by RT-qPCR and sanger sequencing. Conclusion: This study showed that differentially expressed circular RNAs existed between rat cerebral cortex after moderate traumatic brain injury and control. And this will provide valuable information for circular RNA research in the field of traumatic brain injury.

2022-01-15 | GSE193521 | GEO

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