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Items: 1 to 20 of 1520

1.

Single-cell Next Generation Sequencing (scNGS) facilitates analysis of gonadal single cells transcriptomes and revealed germ cell heterogeneity

(Submitter supplied) The unraveling of heterogenous cell populations, — previously masked in bulk transcriptome measurements — are made possible through analysis of single-cell transcriptomics. The goals of this study are to examine single-cell NGS-derived gonadal cell transcriptome profiling and to evaluate heterogeneity of gonadal germ cells in avian species. We performed single-cell RNA sequencing using embryonic gonadal cells of HH stage 28 from male and female zebra finches. more...
Organism:
Taeniopygia guttata
Type:
Expression profiling by high throughput sequencing
Platform:
GPL30263
2 Samples
Download data: H5, MTX, TSV
Series
Accession:
GSE177478
ID:
200177478
2.

Functional Identification of Specialized Basal Ganglia Circuits that Regulate Vocal Motor Sequences

(Submitter supplied) Production of learned vocalizations requires precise selection and accurate sequencing of appropriate vocal-motor actions. The basal ganglia are essential for the selection and sequencing of motor actions, but the cellular specializations and circuit mechanisms governing accurate sequencing of vocalizations are unknown. Here, we use single-nucleus RNA sequencing and genetic manipulations to map basal ganglia cell types and circuits involved in the production of songbird vocal sequences. more...
Organism:
Taeniopygia guttata
Type:
Expression profiling by high throughput sequencing
Platform:
GPL27119
2 Samples
Download data: TXT
Series
Accession:
GSE136086
ID:
200136086
3.

DNA methylation regulates transcription factor specific neurodevelopmental but not sexually dimorphic gene expression dynamics in zebra finch telencephalon

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Taeniopygia guttata
Type:
Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing
Platform:
GPL22780
72 Samples
Download data: COV
Series
Accession:
GSE147974
ID:
200147974
4.

DNA methylation regulates transcription factor specific neurodevelopmental but not sexually dimorphic gene expression dynamics in zebra finch telencephalon [RRBS]

(Submitter supplied) Song learning in zebra finches is a prototypical example of a complex learned behavior, yet knowledge on the underlying molecular processes is limited. Therefore, we characterized transcriptomic (RNA sequencing) and epigenomic (RRBS, reduced representation bisulfite sequencing; immunofluorescence) dynamics in matched zebra finch telencephalon samples of both sexes from 1 day post hatching (1 dph) to adulthood, spanning the critical period for song learning (20 dph and 65 dph). more...
Organism:
Taeniopygia guttata
Type:
Methylation profiling by high throughput sequencing
Platform:
GPL22780
48 Samples
Download data: COV
Series
Accession:
GSE147973
ID:
200147973
5.

DNA methylation regulates transcription factor specific neurodevelopmental but not sexually dimorphic gene expression dynamics in zebra finch telencephalon [RNA-Seq]

(Submitter supplied) Song learning in zebra finches is a prototypical example of a complex learned behavior, yet knowledge on the underlying molecular processes is limited. Therefore, we characterized transcriptomic (RNA sequencing) and epigenomic (RRBS, reduced representation bisulfite sequencing; immunofluorescence) dynamics in matched zebra finch telencephalon samples of both sexes from 1 day post hatching (1 dph) to adulthood, spanning the critical period for song learning (20 dph and 65 dph). more...
Organism:
Taeniopygia guttata
Type:
Expression profiling by high throughput sequencing
Platform:
GPL22780
24 Samples
Download data: TXT
Series
Accession:
GSE147972
ID:
200147972
6.

Single-nuclei RNA sequencing of HVC and RA in zebra finches

(Submitter supplied) The evolution of the six-layered neocortex is often credited with an increased capacity for complex behaviors and cognition in humans and other mammals. However, birds, despite lacking a laminated neocortex, display complex and non-instinctual behaviors including vocal learning, tool use, and problem-solving1,2. The evolution of brain circuits and cell-types supporting advanced behavioral repertoires remains poorly understood. more...
Organism:
Taeniopygia guttata
Type:
Expression profiling by high throughput sequencing
Platform:
GPL27119
4 Samples
Download data: TXT
Series
Accession:
GSE153665
ID:
200153665
7.

Transcriptome profiling of the HVC of the young and adult zebra finch brain by RNA-Seq

(Submitter supplied) Abstract: Juvenile zebra finches learn to sing by imitating songs of adult males early in life. The development of the song control circuit and the song learning and maturation processes are highly intertwined, involving gene expression, neurogenesis, circuit formation, synaptic modification, and sensory-motor learning, which eventually lead to a mature song. To better understand the genetic mechanisms underlying these events, we used RNA-sequencing (RNA-Seq) to profile genome-wide transcriptomes in the HVC, a brain nucleus controlling song behavior, in juvenile and adult zebra finches. more...
Organism:
Taeniopygia guttata
Type:
Expression profiling by high throughput sequencing
Platform:
GPL27759
5 Samples
Download data: XLSX
Series
Accession:
GSE140470
ID:
200140470
8.

Time-lapse transcriptomic profiling of the brains of adult female canaries from the onset of testosterone-induced singing behavior

(Submitter supplied) In this data set, we compared the expression data of song nuclei HVC dissected from adult female canaries (S. canaria) implanted with 7-mm SilasticTM tubes filled with testosterone for 6 periods (1h, 3h, 8h, 3d, 7d, and 14d) with control birds (implanted with empty tube) to identify testosterone effects on gene expression.
Organism:
Taeniopygia guttata
Type:
Expression profiling by array
Platform:
GPL17605
39 Samples
Download data: CEL
Series
Accession:
GSE118522
ID:
200118522
9.

Transcriptomics of the Avian Immune Response in Hypothalamus, Spleen, and Red Blood Cells using RNA-seq

(Submitter supplied) 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. more...
Organism:
Taeniopygia guttata
Type:
Expression profiling by high throughput sequencing
Platform:
GPL22780
24 Samples
Download data: TXT
Series
Accession:
GSE121348
ID:
200121348
10.

Singing female songbirds: Female-specific gene networks in the song area HVC

(Submitter supplied) In this data set, we compared the expression data of song nuclei HVC, visual cortex entopallium, and the molecular layer of the cerebellum dissected from females and males of 3 songbird species (S. canaria, U. cyanocephalus, P. bicolor) to identify sex-specific stimulated gene expression. Testosterone-treated male and female canaries were also included in order to study whether testosterone effect on transcriptomes is sex-specific. more...
Organism:
Taeniopygia guttata; Ploceus bicolor; Serinus canaria; Uraeginthus cyanocephalus
Type:
Expression profiling by array
Platform:
GPL17605
155 Samples
Download data: CEL
Series
Accession:
GSE83674
ID:
200083674
11.

Expression data from feathers of the black/red morphs of the Gouldian finches

(Submitter supplied) Regenerating feathers of the Gouldian finches were collected from heads of moulting individuals from an Australian captive population. Affymetrix microarrays were used to examine gene expression differences between black and red morphs.
Organism:
Chloebia gouldiae; Taeniopygia guttata
Type:
Expression profiling by array
Platform:
GPL16788
6 Samples
Download data: CEL
Series
Accession:
GSE125295
ID:
200125295
12.

Genome-wide mRNA expression and methylation patterns of neural genes in response to prenatal hormones

(Submitter supplied) We explored the molecular mechanisms that mediate changes in neural gene expression (i.e., hypothalamus and nucleus taenia of the amygdala) and aggression in male and female zebra finches (Taeniopygia guttata) exposed to prenatal testosterone. We used egg injections of testosterone or the vehicle to mimic maternal hormones, which are transferred to offspring during prenatal development. Many researchers have postulated that prenatal maternal hormones can generate adaptive phenotypic plasticity; however, no study has determined the mechanism facilitating these long-term changes. more...
Organism:
Taeniopygia guttata
Type:
Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing
Platform:
GPL22780
48 Samples
Download data: DIFF, TSV
Series
Accession:
GSE100396
ID:
200100396
13.

Epigenetic signature of extended critical period learning

(Submitter supplied) We used a combination of ChIPseq, RNAseq, bioinformatic analysis, and molecular biology in the auditory forebrain, a brain area required for tutor song memorization to elucidate the role epigenetics plays in song learning. These  analyses revealed thousands of genes were differentially marked by PTMs under these two conditions, indicating greater transcription in the birds with extended learning.
Organism:
Taeniopygia guttata
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL22780
23 Samples
Download data: BED, BW
Series
Accession:
GSE91399
ID:
200091399
14.

Weighted gene coexpression analysis of RNA-seq data from 65d juvenile Area X and adjacent non-song ventral striatopallidum (VSP).

(Submitter supplied) 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. more...
Organism:
Taeniopygia guttata
Type:
Expression profiling by high throughput sequencing
Platform:
GPL23198
38 Samples
Download data: TSV
Series
Accession:
GSE96843
ID:
200096843
15.

Expression data from testes of zebra finch males artificially selected for long or short sperm

(Submitter supplied) 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.
Organism:
Taeniopygia guttata
Type:
Expression profiling by array
Platform:
GPL23222
69 Samples
Download data: CEL
Series
Accession:
GSE96970
ID:
200096970
16.

Expression data from Zebrafinch

(Submitter supplied) The quality of vocal learning is influenced by the tutoring from conspecifics. We used microarrays to detail the global programme of gene expression underlying differential tutoring condition during the development.
Organism:
Taeniopygia guttata
Type:
Expression profiling by array
Platform:
GPL16788
6 Samples
Download data: CEL
Series
Accession:
GSE45208
ID:
200045208
17.

Hormones, Genes, and Athleticism: Effect of Androgens on the Avian Muscular Transcriptome

(Submitter supplied) Male vertebrate social displays vary from physically simple to complex, with the latter involving exquisite motor command of the body and appendages. Studies of these displays have, in turn, provided substantial insight into neuromotor mechanisms. The neotropical golden-collared manakin (Manacus vitellinus) has been used previously as a model to investigate intricate motor skills because adult males of this species perform an acrobatic and androgen-dependent courtship display. more...
Organism:
Manacus vitellinus; Taeniopygia guttata
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL20980 GPL19155
24 Samples
Download data: TXT
Series
Accession:
GSE73660
ID:
200073660
18.

Validation of a genome-wide search for zebra finch epigenetically regulated genes using Zebra finch Exon Arrays

(Submitter supplied) 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. more...
Organism:
Taeniopygia guttata
Type:
Expression profiling by array
Platform:
GPL17605
25 Samples
Download data: CEL, TXT
Series
Accession:
GSE71344
ID:
200071344
19.

A genome-wide search for epigenetically regulated genes in zebra finch using MethylCap-seq and RNA-seq

(Submitter supplied) 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. more...
Organism:
Taeniopygia guttata
Type:
Methylation profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform:
GPL19155
10 Samples
Download data: BEDGRAPH, TXT
Series
Accession:
GSE61060
ID:
200061060
20.

Core and region enriched networks of behaviorally regulated genes: the singing epigenome

(Submitter supplied) 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. more...
Organism:
Taeniopygia guttata
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL19155
8 Samples
Download data: BW, TXT
Series
Accession:
GSE63936
ID:
200063936
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