GEO DataSets

(Submitter supplied) We applied single-cell RNA sequencing to investigate inter-species differences in germ cell development between chicken and zebra finch (Taeniopygia castanotis, formerly Taeniopygia guttata castanotis), a Neoaves songbird species and a common model of vocal learning.

Organism:

Taeniopygia guttata; Gallus gallus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL23499 GPL31898

4 Samples

Download data: MTX, TSV

(Submitter supplied) Many animals exhibit typical color patterns that have been linked to key adaptive functions, yet the developmental mechanisms establishing these crucial designs remain unclear. Here, we surveyed color distribution in the plumage across a large number of passerine finches. Despite extreme apparent pattern diversity, we identified a small set of conserved color regions whose combinatory association can explain all observed patterns. more...

Organism:

Taeniopygia guttata

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19155

21 Samples

Download data: TXT

(Submitter supplied) Sex in birds is genetically determined, molecular mechanism of which is not well-understood. Their Z sex chromosome (chrZ) lacks whole chromosome inactivation as known for mammalian chrX. To investigate the extent of chrZ dosage compensation and its role in somatic cell’s sex specification, we used a highly-quantitative method and analyzed transcriptional activities of male and female fibroblasts from seven birds. more...

Organism:

Gallus gallus; Anas platyrhynchos; Meleagris gallopavo; Coturnix japonica; Dromaius novaehollandiae; Pavo cristatus; Taeniopygia guttata

Type:

Expression profiling by high throughput sequencing

7 related Platforms

54 Samples

Download data: XLSX

(Submitter supplied) The identification of molecular specializations in cortical circuitry supporting complex behaviors, such as learned vocalizations, requires understanding the neuroanatomical context from which these circuits arise. In songbirds, the robust nucleus of the arcopallium (RA) provides the sole descending projection for fine motor control of vocalizations. Using single nuclei transcriptomics and spatial gene expression mapping in zebra finches, we were able to define cell types and molecular specializations that distinguish RA from adjacent regions involved in non-vocal motor and sensory processing. more...

Organism:

Taeniopygia guttata

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27119

2 Samples

Download data: RDS, TAR

(Submitter supplied) The aim of this experiment was to test whether the social setting changed neural transcriptomic responses to an endotoxin challenge in zebra finches

Organism:

Taeniopygia guttata

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27119

134 Samples

Download data: XLS

(Submitter supplied) In a rapidly warming world, exposure to high temperatures may impact fitness, but the gene regulatory mechanisms that link sublethal heat to sexually selected traits are not well understood, particularly in endothermic animals. Our experiment used zebra finches (Taeniopygia guttata), songbirds that experience extreme temperature fluctuations in their native Australia. We exposed captive males to an acute thermal challenge (43°C) compared with thermoneutral (35°C) and lower (27°C) temperatures. more...

Organism:

Taeniopygia guttata

Type:

Expression profiling by high throughput sequencing

Platform:

GPL22780

46 Samples

Download data: TSV

(Submitter supplied) Sexual dimorphisms in the brain give rise to sex differences in physiology and behavior, yet we have limited understanding of the transcriptomic changes underlying their development. We evaluated developmental transcriptome dynamics for one of the most extreme neuroanatomical sexual dimorphisms in vertebrates - the songbird robust nucleus of the arcopallium (RA). RA is the telencephalic motor output nucleus of the song system. more...

Organism:

Taeniopygia guttata

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27119

22 Samples

Download data: TSV

(Submitter supplied) 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. more...

Organism:

Taeniopygia guttata

Type:

Expression profiling by high throughput sequencing

Platform:

GPL31898

2 Samples

Download data: MTX, TSV

(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

(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

(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

(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

(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

(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

(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

(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

(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

(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:

Ploceus bicolor; Serinus canaria; Uraeginthus cyanocephalus; Taeniopygia guttata

Type:

Expression profiling by array

Platform:

GPL17605

155 Samples

Download data: CEL

(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:

Taeniopygia guttata; Chloebia gouldiae

Type:

Expression profiling by array

Platform:

GPL16788

6 Samples

Download data: CEL

(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