GEO DataSets

(Submitter supplied) Following laboratory and clinical findings implicating circadian biology in the pathogenesis of myopia (nearsightedness), we examined gene expression in two crucial tissues controlling post-natal refractive development, the retina and choroid. Inducing unilateral visual form deprivation myopia in young chicks, a widely studied and validated model, we isolated retinal and choroidal tissues every 4 hours over a single day from myopic and contralateral control eyes during a period time when myopia progresses rapidly.

Organism:

Gallus gallus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23499

144 Samples

Download data: TXT

(Submitter supplied) Developing tissues rely on the coordinated differentiation of stem cell populations in dynamically changing environments. The formation of the vertebrate neural tube is a well characterized example, where stem cells in the caudal epiblast differentiate to neural tissue while transitioning through a changing landscape of signals: rostro-caudally from Retinoic Acid (RA) to Wnt/FGF and dorsal-ventrally from sonic hedgehog to BMP. more...

Organism:

Gallus gallus

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL23499

8 Samples

Download data: JSON, MTX, TSV

(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:

Gallus gallus; Taeniopygia guttata

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL23499 GPL31898

4 Samples

Download data: MTX, TSV

(Submitter supplied) The oviduct plays an indispensable role in the formation of eggs, especially the magnum and uterus. The identification of oviduct development in different stages will help to target candidate genes and pathways in regulation of albumen and eggshell formation, as well as defense mechanism in oviduct and egg. To identify the function differences and the molecular defense mechanism of the oviduct and egg, we performed transcriptome sequencing analysis of the magnum and uterus in 120d and 300d old Lohmann layers, three birds in each group. more...

Organism:

Gallus gallus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23499

12 Samples

Download data: TXT

(Submitter supplied) Recent studies have demonstrated the complex coordination of pro-inflammatory signaling and reactive microglia/macrophage on the formation Müller glial-derived progenitor cells (MGPCs) intheretinas offish, birds and mice.We generated scRNA-seq libraries to identify transcriptional changes in Müller glia (MG) that result from the depletion of microglia from the chick retina. We found significant changes in different networks of genes in MG in normal and damaged retinas when the microglia are ablated. more...

Organism:

Gallus gallus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23499

4 Samples

Download data: MTX, TSV

(Submitter supplied) During embryonic development, tissues must possess precise material properties to ensure that cell-generated forces give rise to the stereotyped morphologies of developing organs. However, the question of how material properties are established and regulated during development remains understudied. Here, we aim to address these broader questions through the study of intestinal looping, a process by which the initially straight intestinal tube buckles into loops, permitting ordered packing within the body cavity. more...

Organism:

Gallus gallus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23499

9 Samples

Download data: TXT

(Submitter supplied) The formation of the vertebrate body is driven by the progressive and coordinated production of trunk tissues from pools of progenitors located in the posterior of the embryo. Aspects of this process are recapitulated by in vitro models based on pluripotent stem cells (PSCs). However, these models lack several tissue components normally found in the vertebrate trunk. Most strikingly, the notochord, a hallmark of chordates and the source of midline signals that pattern surrounding tissues, is absent from current models of human trunk formation. more...

Organism:

Gallus gallus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23499

4 Samples

Download data: CSV, H5AD, MTX

(Submitter supplied) We sequenced single cells with the 10x platform of chicken spleens from chickens genetically resistant and genetically susceptible to Marek's disease, with both infected individuals and uninfected controls from both lines

Organism:

Gallus gallus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23499

12 Samples

Download data: MTX, TSV

(Submitter supplied) Here, the m6A modification patterns in chicken liver at the acute stage of LPS-stimulated inflammation and at the normal state were explored via m6A and RNA sequencing and bioinformatics analysis. A total of 7815 m6A peaks distributed in 5066 genes were identified in the normal chicken liver, and were mostly located in the CDS, 3’UTR region and around the stop codon. At 2 h after the LPS intraperitoneal injection, the m6A modification pattern changed, and showed 1200 different m6A peaks. more...

Organism:

Gallus gallus

Type:

Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing

Platform:

GPL23499

8 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Gallus gallus

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platforms:

GPL22626 GPL19005 GPL23499

877 Samples

Download data: BROADPEAK, NARROWPEAK

(Submitter supplied) The vertebrate inner ear arises from a pool of progenitors with the potential to give rise to all the sense organs and cranial ganglia of the head1-6. Here we explore the molecular mechanisms that control ear specification from these progenitors. Using a multi-omics approach combined with loss-of-function experiments we identify a core transcriptional circuit that imparts ear identity, along with non-coding elements that integrate this information. more...

Organism:

Gallus gallus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23499

858 Samples

Download data: CSV, LOOM

(Submitter supplied) The vertebrate inner ear arises from a pool of progenitors with the potential to give rise to all the sense organs and cranial ganglia of the head1-6. Here we explore the molecular mechanisms that control ear specification from these progenitors. Using a multi-omics approach combined with loss-of-function experiments we identify a core transcriptional circuit that imparts ear identity, along with non-coding elements that integrate this information. more...

Organism:

Gallus gallus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23499

6 Samples

Download data: TSV

(Submitter supplied) The vertebrate inner ear arises from a pool of progenitors with the potential to give rise to all the sense organs and cranial ganglia of the head1-6. Here we explore the molecular mechanisms that control ear specification from these progenitors. Using a multi-omics approach combined with loss-of-function experiments we identify a core transcriptional circuit that imparts ear identity, along with non-coding elements that integrate this information. more...

Organism:

Gallus gallus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23499

8 Samples

Download data: TSV

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Gallus gallus; Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing; Other

6 related Platforms

46 Samples

Download data: BED, BEDGRAPH, BIGWIG, BW, COOL, NARROWPEAK, TXT

(Submitter supplied) Modifications in gene regulation during development are considered to be a driving force in the evolution of organisms. Part of these changes involve rapidly evolving cis-regulatory elements (CREs), which interact with their target genes through higher-order 3D chromatin structures. How such 3D architectures and variations in CREs contribute to transcriptional evolvability nevertheless remains elusive. more...

Organism:

Mus musculus; Gallus gallus

Type:

Other

Platforms:

GPL21103 GPL23499

2 Samples

Download data: BED, COOL, TXT

(Submitter supplied) Modifications in gene regulation during development are considered to be a driving force in the evolution of organisms. Part of these changes involve rapidly evolving cis-regulatory elements (CREs), which interact with their target genes through higher-order 3D chromatin structures. How such 3D architectures and variations in CREs contribute to transcriptional evolvability nevertheless remains elusive. more...

Organism:

Gallus gallus; Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL17021 GPL23499 GPL19005

15 Samples

Download data: BED, BIGWIG, NARROWPEAK

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Gallus gallus

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL23499 GPL24517 GPL26853

26 Samples

Download data

(Submitter supplied) The retinal pigment epithelium (RPE) exhibits a diverse range of plasticity across vertebrates and is a potential source of cells for the regeneration of retinal neurons. Embryonic amniotes possess a transitory ability to regenerate neural retina through the reprogramming of RPE cells in an FGF-dependent manner. Chicken RPE can regenerate neural retina at embryonic day 4 (E4) of development, but RPE neural competence is lost by embryonic day 5 (E5). more...

Organism:

Gallus gallus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL24517 GPL23499

8 Samples

Download data: CSV

(Submitter supplied) Cytosine DNA methylation is a heritable epigenetic mark present in most eukaryotic groups. While the patterns and functions of DNA methylation have been extensively studied in mouse and human, their conservation in other vertebrates remain poorly explored. In this study, we interrogated the distribution and function of DNA methylation in primary cells of seven vertebrate species including bio-medical models and key livestock species.

Organism:

Homo sapiens; Bos taurus; Sus scrofa; Oryctolagus cuniculus; Canis lupus familiaris; Gallus gallus; Mus musculus

Type:

Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing

9 related Platforms

62 Samples

Download data: BW, IGV

(Submitter supplied) The lean and fat broilers were derived from the 21st generation of the Northeast Agricultural University broiler lines divergently selected for abdominal fat content (NEAUHLF). In brief, broilers in the two lines (lean line and fat line) of the NEAUHLF have the same Arbor Acres ancestry, but were divergently selected by the concentration of very low-density lipoprotein and abdominal fat percentage (AFP) at 7 weeks old. more...

Organism:

Gallus gallus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23499

80 Samples

Download data: TXT