Next generation sequence of RNA in hematoma basal ganglia tissue of ICH mice model
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ABSTRACT:
PROVIDER: PRJNA853171 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR19858318_1.fastq.gz | Fastqsanger.gz | |||
| SRR19858318_2.fastq.gz | Fastqsanger.gz | |||
| SRR19858319_1.fastq.gz | Fastqsanger.gz | |||
| SRR19858319_2.fastq.gz | Fastqsanger.gz | |||
| SRR19858320_1.fastq.gz | Fastqsanger.gz |
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Project description:Intracerebral hemorrhage (ICH) is a severe neurological disorder with no proven treatment. Our prior research identified a significant association with monocyte level and ICH mortality. To further advance our understanding, we sought to identify the gene expression changes after ICH using a swine model to test the hypothesis that ICH would result in changes in peripheral blood mononuclear cell (PBMC) gene expression. There were 182 significantly upregulated and 153 significantly down-regulated DEGs after ICH. Consistent with findings in humans, significant GO and KEGG pathways were those primarily related to inflammation, immune response, and response to infectious pathogens. There were five genes, all with increased expression post-ICH, that were repeatedly identified as significant DEGs in the statistically significant KEGG pathways: CD14 (cluster of differentiation 14), TLR4 (toll-like receptor-4), CXCL8 (CXC motif chemokine-8), IL-18 (interleukin-18), and CXCL2 (CXC motif chemokine-2). Conclusion: ICH induced changes in PBMC gene expression within 6 hours of onset. DEGs that were highly expressed in the significant biological pathways included those related to inflammation, the immune response, and, more specifically, monocyte activation. Further research is needed to determine if these changes affect outcomes and may represent new therapeutic targets.
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Project description:Similarities between speech and birdsong make songbirds advantageous for investigating the neurogenetics of learned vocal communication; a complex phenotype likely supported by ensembles of interacting genes in cortico-basal ganglia pathways of both species. To date, only FoxP2 has been identified as critical to both speech and birdsong. We performed weighted gene co-expression network analysis on microarray data from singing zebra finches to discover gene ensembles regulated during vocal behavior. We found ~2,000 singing- regulated genes comprising 3 co-expression groups unique to area X, the basal ganglia subregion dedicated to learned vocal-motor behavior. These contained known targets of human FOXP2 and potential avian targets. We validated novel biological pathways for vocalization. Our findings show that higher-order gene co-expression patterns, rather than expression levels, molecularly distinguish area X from the ventral striato-pallidum during singing. The previously unknown structure of singing-driven networks enables prioritization of molecular interactors that likely bear on human motor disorders, especially those affecting speech. Gene expression was measured in 2 basal ganglia sub-regions (area X & ventral striato-pallidum (VSP)) of 27 adult male zebra finches that sang different amounts of song over a 2hr period in the morning. 18 birds were allowed to sing freely, 9 birds were discouraged from singing by the presence of an investigator and those that sang fewer than 10 song motifs were considered “non-singers”.
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Project description:Similarities between speech and birdsong make songbirds advantageous for investigating the neurogenetics of learned vocal communication; a complex phenotype likely supported by ensembles of interacting genes in cortico-basal ganglia pathways of both species. To date, only FoxP2 has been identified as critical to both speech and birdsong. We performed weighted gene co-expression network analysis on microarray data from singing zebra finches to discover gene ensembles regulated during vocal behavior. We found ~2,000 singing- regulated genes comprising 3 co-expression groups unique to area X, the basal ganglia subregion dedicated to learned vocal-motor behavior. These contained known targets of human FOXP2 and potential avian targets. We validated novel biological pathways for vocalization. Our findings show that higher-order gene co-expression patterns, rather than expression levels, molecularly distinguish area X from the ventral striato-pallidum during singing. The previously unknown structure of singing-driven networks enables prioritization of molecular interactors that likely bear on human motor disorders, especially those affecting speech.
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