Similar Datasets
Project description:Protein extraction of zebra finch testes and ovaries samples
2020-01-13 | PXD014692 | Pride
Project description:To investigate the cellular basis of parental species bias at birdsong, we performed single nuclei RNA-seq for six zebra finch and owl finch F1 hybrid juvenile birds.
2023-11-04 | GSE217341 | GEO
Project description:To investigate the cellular basis of parental species bias at birdsong, we performed single nuclei RNA-seq for six zebra finch and owl finch F1 hybrid juvenile birds.
2023-11-04 | GSE217340 | GEO
Project description:DNA methylation is tightly linked with gene expression regulation and has long been regarded a stable epigenetic mark in postmitotic cells. However, it recently became clear that postnatal brains appear to show stimulus-induced de novo CpG methylation or active demethylation related to neuronal plasticity. Due to striking homologies between the brains of birds and mammals, songbirds, especially the zebra finch, propose an attractive model for investigating the genome-wide DNA methylation profile and DNA methylation reconfiguration during brain development. In order to obtain a first genome-wide compendium of genes under putative DNA methylation control, we performed MethyCap-seq experiments on two recently cultured zebra finch cell lines, G266 and ZFTMA, also upon AZA-induced demethylation. First, the MethylCap-seq methodology in zebra finch was validated by comparison with RRBS generated data. Subsequently, quantitative analysis identified 30,700 significantly demethylated loci upon AZA-treatment. Further examination revealed enrichment of these regions in exons and promoters. To assess the influence of methylation on gene expression, RNA-seq experiments were performed. Comparison of the RNA-seq and MethylCap-seq results showed that at least 357 of the 3,457 AZA-upregulated genes are putatively regulated by methylation in the promoter region, for which a pathway analysis showed obvious enrichment for neurological networks. A subset of genes was validated using qPCR and CpG pyrosequencing. To our knowledge, this study provides the first genome-wide DNA methylation map of the zebra finch genome as well as a comprehensive set of genes of which transcription is under putative methylation control. MethylCap-seq and RNA-seq experiments were performed on DMSO- and AZA-treated zebra finch cell lines, i.e. G266 and ZFTMA. As a quality control, also an untreated ZFTMA sample was analyzed with MethylCap-seq and RRBS.
2015-12-10 | E-GEOD-61060 | biostudies-arrayexpress
Project description:We queried a songbird brain to discover behaviorally regulated transcriptional mechanisms relevant for speech behavior. About 10% of zebra finch genes showed regulation during singing, and most were brain-region specific. We propose that the brain-regional diversity of the singing-regulated gene networks is derived both from differential combinatorial binding of transcription factors and the epigenetic state of these genes before singing begins. To test this hypothesis, we measured H3K27ac two brain regions that participate in song production. The examination of H3K27ac in two brain regions of zebra finch in singing and silent conditions
2014-12-08 | E-GEOD-63936 | biostudies-arrayexpress
Project description:The zebra finch is one of the most commonly studied songbirds in biology, particularly in genomics, neuroscience and vocal communication. However, this species lacks a robust cell line for molecular biology research and reagent optimization. We generated a cell line from zebra finch embryonic fibroblasts using the SV40 large and small T antigens, designated CFS414. This cell line demonstrates an improvement over previous songbird cell lines through continuous and density-independent growth, allowing for indefinite culture and monoclonal line derivation. Cytogenetic, genomic, and transcriptomic profiling established the provenance of this cell line and identified the expression of genes relevant to ongoing songbird research. This single-cell RNA sequencing experiment provided information on the gene expression landscape of the cell line, informing on its cell type, transcriptomic stability, and value to researchers utilizing the zebra finch as a model organism.
2022-02-04 | GSE195934 | GEO
Project description:We have conducted a Cross-Species Microarray analysis by hybridizing genomic DNA from the common whitethroat (Sylivia communis) on a newly developed Affymetrix costum array designed for the zebra finch (Taeniopygia guttata), the Lund-zf array. We have also quality tested the Lund-zf array by hybridizing zebra finch genomic DNA to the platform.
2007-09-30 | E-MEXP-1181 | biostudies-arrayexpress
Project description:We have performed a comparison of global patterns of gene expression between two bird species, the chicken and zebra finch, especially with regard to sex bias of autosomal vs. Z chromosome genes, dosage compensation and evolution of sex bias. Both species appear to lack a Z chromosome-wide mechanism of dosage compensation, because both have a similar pattern of significantly higher expression of Z genes in males relative to females. Unlike the chicken Z chromosome, which has female-specific expression of the non-coding RNA MHM (male hypermethylated), and acetylation of histone 4 lysine 16 (H4K16) near MHM, the zebra finch Z chromosome appears to lack the MHM sequence and acetylation of H4K16. The zebra finch also does not show the reduced male to female (M:F) ratio of gene expression near MHM similar to that found in the chicken. Although the M:F ratios of Z chromosome gene expression are similar across tissues and ages within each species, they differ between the two species. Z genes showing the greatest species difference in M:F ratio were concentrated near the MHM region of the chicken Z chromosome. The current study shows that the zebra finch differs from the chicken because it lacks a specialized region of greater dosage compensation along the Z chromosome, and shows dosage compensation for a different set of Z genes than the chicken. These patterns suggest that different avian taxa may have evolved specific compensatory mechanisms.
2010-02-11 | GSE20035 | GEO
Project description:DNA methylation is tightly linked with gene expression regulation and has long been regarded a stable epigenetic mark in postmitotic cells. However, it recently became clear that postnatal brains appear to show stimulus-induced de novo CpG methylation or active demethylation related to neuronal plasticity. Due to striking homologies between the brains of birds and mammals, songbirds, especially the zebra finch, propose an attractive model for investigating the genome-wide DNA methylation profile and DNA methylation reconfiguration during brain development. In order to obtain a first genome-wide compendium of genes under putative DNA methylation control, we performed MethyCap-seq experiments on two recently cultured zebra finch cell lines, G266 and ZFTMA, also upon AZA-induced demethylation. First, the MethylCap-seq methodology in zebra finch was validated by comparison with RRBS generated data. Subsequently, quantitative analysis identified 30,700 significantly demethylated loci upon AZA-treatment. Further examination revealed enrichment of these regions in exons and promoters. To assess the influence of methylation on gene expression, RNA-seq experiments were performed. Comparison of the RNA-seq and MethylCap-seq results showed that at least 357 of the 3,457 AZA-upregulated genes are putatively regulated by methylation in the promoter region, for which a pathway analysis showed obvious enrichment for neurological networks. A subset of genes was validated using qPCR and CpG pyrosequencing. To our knowledge, this study provides the first genome-wide DNA methylation map of the zebra finch genome as well as a comprehensive set of genes of which transcription is under putative methylation control.
2015-12-10 | GSE61060 | GEO
Project description:The goal of this research is to better understand the transcriptomic response in peripheral and neural tissue of zebra finch to lipopolysaccharide (LPS) challenge using RNASeq. The acute phase response (APR) is the initial reaction of the immune system to infection, and is triggered by pro-inflammatory cytokines or exposure to immunogens, such as bacterial LPS. The APR also inhibits reproduction and induces a number of physiological and behavioral symptoms, such as fever and sickness behavior. Through RNAseq, we can better understand the transcriptomic response of genes that are important for response to infection in a wild species such as the Zebra Finch. This has implications for disease surveillance programs that monitor the epidemiology of zoonotic diseases, like avian influenza and West Nile virus. We examine the transcriptomic response in Zebra Finch spleen and hypothalumus to lipopolysaccharide (LPS) challenge; however, unlike mammals, with the exception of the camel, avian species have red blood cells that contain a nucleus, and will have gene regulation depending on the physiological needs of the organism. Therefore, we also took the opportunity to investigate the transcriptomic response of nucleated red blood cells to lipopolysaccharide (LPS) challenge.
2019-07-17 | GSE121348 | GEO