Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1055589 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR27320138.fastq.gz | Fastqsanger.gz | |||
| SRR27320139.fastq.gz | Fastqsanger.gz | |||
| SRR27320140.fastq.gz | Fastqsanger.gz | |||
| SRR27320141.fastq.gz | Fastqsanger.gz | |||
| SRR27320142.fastq.gz | Fastqsanger.gz |
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Project description:The aim of this experiment was to test whether the social setting changed neural transcriptomic responses to an endotoxin challenge in zebra finches
2023-03-06 | GSE203528 | GEO
Project description:Telomeres are essential for chromosomal protection, yet their guanine-rich repeats are sensitive to oxidative damage. ROS-dependent oxidative stress accelerates telomere attrition in vitro, but telomere dysfunction under oxidative conditions in vivo remains unclear. We studied the effects of ROS-inducing agent methyl-mercury (MeHg) on telomere and genome dysfunction in zebra finches (Taeniopygia guttata). Using qPCR, we found that continuous exposure to sublethal MeHg (1.2 ppm in the diet) resulted in longer telomere length than controls by sexual maturity in red blood cells and several other tissues. These findings were accompanied by suppressed bone marrow transcriptomic pathways related to cilia formation and mitotic progression. Further analysis revealed oncogenic and pro-inflammatory signaling reminiscent of tumorigenesis. We also demonstrate that PCNA expression in the lung remains unchanged by MeHg, suggesting telomere maintenance independent of replication. Our results show that chronic sublethal MeHg exposure may lead to replicative immortality of telomeres rather than shortening.
2025-08-13 | GSE274961 | GEO
Project description:Human speech is one of the few examples of vocal learning among mammals, yet ~half of avian species exhibit this ability. Its genetic basis is unknown beyond a shared requirement for FoxP2 in both humans and zebra finches. Here we manipulated FoxP2 isoforms in Area X during a critical period for song development, delineating, for the first time, unique contributions of each to vocal learning. We used weighted gene coexpression network analysis of RNA-seq data to construct transcriptional profiles and found gene modules correlated to singing, learning, or vocal variability. The juvenile song modules were preserved adults, whereas the learning modules were not. The learning modules were preserved in the striatopallidum adjacent to Area X whereas the song modules were not. The confluence of learning and singing coexpression in juvenile, but not adult, Area X may underscore molecular processes that drive vocal learning in zebra finches and, by analogy, humans.
2018-01-25 | GSE96843 | GEO
Project description:Male zebra finches of a captive population in the University of Sheffield were artificially selected for long or short sperm based on their breeding values for three generations. We used Affymetrix microarrays to examine gene expression differences between testes of selection line male birds.
2017-07-17 | GSE96970 | GEO
Project description:A male zebra finch begins to learn to sing by memorizing a tutorM-bM-^@M-^Ys song during a sensitive period in juvenile development. Tutor song memorization requires molecular signaling within the auditory forebrain. Using microarray and in situ hybridizations, we tested whether the auditory forebrain at an age just before tutoring expresses a different set of genes compared with later life after song learning has ceased. Microarray analysis revealed differences in expression of thousands of genes in the male auditory forebrain at posthatch day 20 (P20) compared with adulthood. Furthermore, song playbacks had essentially no impact on gene expression in P20 auditory forebrain, but altered expression of hundreds of genes in adults. Most genes that were song-responsive in adults were expressed at constitutively high levels at P20. Using in situ hybridization with a representative sample of 44 probes, we confirmed these effects and found that birds at P20 and P45 were similar in their gene expression patterns. Additionally, eight of the probes showed maleM-bM-^@M-^Sfemale differences in expression. We conclude that the developing auditory forebrain is in a very different molecular state from the adult, despite its relatively mature gross morphology and electrophysiological responsiveness to song stimuli. Developmental gene expression changes may contribute to fine-tuning of cellular and molecular properties necessary for song learning. Post-hatch day 20 male zebra finches that had been raised in acoustic isolation with a foster female or adult male zebra finches were placed in a song playback chamber. The next day, birds heard either silence (control) or 30 minutes of novel song. All samples were hybridized against the universal SoNG RNA reference pool, 6 biological replicates per group in each of 4 groups.
2012-03-24 | E-GEOD-36657 | biostudies-arrayexpress
Project description:Vocal learning and neuronal replacement have been studied extensively in the songbird brain, but until recently, few molecular and genomic tools have been available for this work. Here we describe new molecular/genomic resources for songbird research. We made cDNA libraries from zebra finch (Taeniopygia guttata) brains at different developmental stages. A total of 11000 clones were sequenced from these libraries, representing 5870 unique gene transcripts. A web-based database has been established for sequence analysis and functional annotations. The cDNA libraries were not normalized. Sequence analysis revealed that a cDNA library made from brains at post-hatching day 30-50, when the song system goes through rapid development and birds learn to sing, shows the highest gene discovery rate. We grouped genes into functional categories according to the Gene Ontology classification and found that expression of the functional categories changed as the brain developed. We also identified five microRNAs whose sequences are highly conserved between zebra finch and other species. We printed cDNA microarrays and profiled gene expression in the HVC of both adult male zebra finches and canaries (Serinus canaria). Statistical Analysis of Microarrays (SAM) was used for data analysis. A subset of the differentially regulated genes was validated by in situ hybridization. The bioinformatic tools EASE and Ingenuity Pathway Analysis were used to identify over-represented functional groups and gene networks among the regulated genes. These resources provide songbird biologists with tools for genome annotation, comparative genomics, and microarray gene expression analysis. Keywords: HVC, songbird, cDNA microarray, gene expression
2006-12-06 | GSE6412 | GEO
Project description:Background: Vocal learning is a rare and complex behavioral trait that serves as a basis for the acquisition of human spoken language. In songbirds, vocal learning and production depend on a set of specialized brain nuclei known as the song system. Methodology/Principal Findings: Using high-throughput functional genomics we have identified, 200 novel molecular markers of adult zebra finch HVC Vocal, a key node of the song system. These markers clearly differentiate HVC from the general pallial region to which HVC belongs, and thus represent molecular specializations of this song nucleus. Bioinformatics analysis reveals that several major neuronal cell functions and specific biochemical pathways are the targets of transcriptional regulation in HVC, including: 1) cell-cell and cell-substrate interactions (e.g., cadherin/catenin-mediated adherens junctions, collagen-mediated focal adhesions, and semaphorin-neuropilin/plexin axon guidance pathways); 2) cell excitability (e.g., potassium channel subfamilies, cholinergic and serotonergic receptors, neuropeptides and neuropeptide receptors); 3) signal transduction (e.g., calcium regulatory proteins, regulators of G-protein-related signaling); 4) cell proliferation/death, migration and differentiation (e.g., TGF-beta/BMP and p53 pathways); and 5) regulation of gene expression (candidate retinoid and steroid targets, modulators of chromatin/nucleolar organization). The overall direction of regulation suggest that processes related to cell stability are enhanced, whereas proliferation, growth and plasticity are largely suppressed in adult HVC, consistent with the observation that song in this songbird species is mostly stable in adulthood. Conclusions/Significance: Our study represents one of the most comprehensive molecular genetic characterizations of a brain nucleus involved in a complex learned behavior in a vertebrate. The data indicate numerous targets for pharmacological and genetic manipulations of the song system, and provide novel insights into mechanisms that might play a role in the regulation of song behavior and/or vocal learning. Comparison of HVC and shelf regions from adult male zebra finches, 6 biological replicates per group. Each sample was hybridized against the SoNG universal reference RNA pool.
2012-03-15 | E-GEOD-36270 | biostudies-arrayexpress
Project description:<p>Recent studies have demonstrated that the cognitive abilities of songbirds are linked to gut microbiome beta diversity. To explore whether the gut microbiome influences vocalization, a cognitive trait, we examined how antibiotics impact metabolism, microbiome and singing behavior in adult male zebra finches. Using untargeted liquid chromatography-mass spectrometry and metagenomic sequencing, we observed significant changes in stool metabolites, microbiome composition and vocal behavior after 14 days of antibiotic treatment. Metabolomic analysis revealed disruptions in the alanine, aspartate and glutamate pathways post-treatment. Furthermore, an analysis of phyla in the gut microbiome demonstrated a decrease in Firmicutes and an increase in Bacteroidetes. Treated birds sang fewer female-directed (FD) songs and produced more introductory notes compared to controls, suggesting possible alterations in neural pathways tied to motivation and vocalization. Despite the decrease in their number, the spectral and temporal properties of FD songs remained stable. Our findings suggest that antibiotic-induced changes in the gut microbiome may influence complex social behaviors such as vocal communication in zebra finches.</p>
2025-06-25 | MTBLS12553 | MetaboLights