GEO DataSets

(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) Limb development is a well-established model for understanding cell fate decisions, and the formation of skeletal elements is coordinated through a sequence of events that control chondrogenesis spatiotemporally. It has been established that epigenetic control participates in cartilage maturation. Our research has shown for the first time that the inhibition of DNA methylation in interdigital tissue with 5-azacytidine results in the formation of an ectopic digit. more...

Organism:

Gallus gallus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL26853

4 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:

GPL19005 GPL19787

7 Samples

Download data

(Submitter supplied) Chicken primordial germ cells (PGCs) have an epigenetic signature which differs from the one that mammalian PGCs acquire with their epigenome reprogramming during early embryonic development. In particular, chicken PGCs display a high global amount of histone H3 lysine 9 trimethylation (H3K9me3) compared to somatic cell types. We performed the genome-wide profiling of H3K9me3 and the transcriptome analysis on chicken PGCs compared to embryonic stem cells (ESCs) as a closely related, non germinal cell type.

Organism:

Gallus gallus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19005

3 Samples

Download data: CSV

(Submitter supplied) Chicken primordial germ cells (PGCs) have an epigenetic signature which differs from the one that mammalian PGCs acquire with their epigenome reprogramming during early embryonic development. In particular, chicken PGCs display a high global amount of histone H3 lysine 9 trimethylation (H3K9me3) compared to somatic cell types. We performed the genome-wide profiling of H3K9me3 and the transcriptome analysis on chicken PGCs compared to embryonic stem cells (ESCs) as a closely related, non germinal cell type.

Organism:

Gallus gallus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19787

4 Samples

Download data: CSV

(Submitter supplied) Birds have a sex chromosome system in which females are heterogametic (ZW) and males are homogametic (ZZ). The differentiation of avian sex chromosomes from ancestral autosomes entailed the loss of most genes from the W chromosome during evolution. However, to what extent mechanisms evolved that counterbalance the consequences of this extensive gene dosage reduction in female birds has remained unclear. more...

Organism:

Gallus gallus

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL27748 GPL32831

96 Samples

Download data: RDS

(Submitter supplied) We used the RCAS avian retrovirus to overexpress SOCS2 in the developing chicken limb buds and transcriptome sequencing (mRNA-Seq) revealed changes in expression of genes known to be associated with growth and development in forelimbs with overexpressed SOCS2.

Organism:

Gallus gallus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26853

2 Samples

Download data: TXT

(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) To investigate the transcriptional regulation network of thesuppression of ILTV infection by PP1 and PP2 in chickenLMH cells, we treated LMH cells with PP1 or PP2 upon ILTV infection. We then performed gene expression profiling analysis using data obtained from RNA-seq of LMH cells.

Organism:

Gallus gallus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19005

16 Samples

Download data: TXT

(Submitter supplied) Three-dimensional organization of mitotic chromosomes is established by cohesin and condensin complexes. In the centromere, cohesin maintains sister chromatid pairing until anaphase onset, while condensin provides elastic resistance to spindle forces. However, how condensin and cohesin structure vertebrate centromeres remains unclear. By super-resolution imaging, Capture-C analysis and polymer modeling we show that vertebrate centromeres are partitioned into two condensin-dependent subdomains during mitosis. more...

Organism:

Gallus gallus

Type:

Other

Platforms:

GPL26853 GPL19005

60 Samples

Download data: BEDGRAPH

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

Organism:

Gallus gallus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL32831 GPL19005 GPL26853

100 Samples

Download data: BEDGRAPH, BW

(Submitter supplied) Three-dimensional organization of mitotic chromosomes is established by cohesin and condensin complexes. In the centromere, cohesin maintains sister chromatid pairing until anaphase onset, while condensin provides elastic resistance to spindle forces. However, how condensin and cohesin structure vertebrate centromeres remains unclear. By super-resolution imaging, Capture-C analysis and polymer modeling we show that vertebrate centromeres are partitioned into two condensin-dependent subdomains during mitosis. more...

Organism:

Gallus gallus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL26853 GPL19005

8 Samples

Download data: BW

(Submitter supplied) Three-dimensional organization of mitotic chromosomes is established by cohesin and condensin complexes. In the centromere, cohesin maintains sister chromatid pairing until anaphase onset, while condensin provides elastic resistance to spindle forces. However, how condensin and cohesin structure vertebrate centromeres remains unclear. By super-resolution imaging, Capture-C analysis and polymer modeling we show that vertebrate centromeres are partitioned into two condensin-dependent subdomains during mitosis. more...

Organism:

Gallus gallus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL32831

32 Samples

Download data: BW

(Submitter supplied) Neurocristopathies such as CHARGE syndrome result from aberrant neural crest development. A large proportion of CHARGE cases are attributed topathogenic variantsin the gene encoding CHD7, chromodomain helicase DNA binding protein 7, which remodels chromatin. While the role for CHD743in neural crest development is well documented,how this factor is specifically upregulated in neural crest cells is not understood. more...

Organism:

Gallus gallus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19005

6 Samples

Download data: BED, BW

(Submitter supplied) Background: MYCN gene is a transcription factor whose amplification and overexpression can lead to tumorigenesis. In retina, MYCN overexpression is related to tumorigenesis of retinoblastoma, a childhood cancer. Purpose: To find out differentially expressed genes in MYCN-overexpressing cells, which will give information of MYCN-related gene expression and possibly find out new pathways in mechanism of retinoblastoma tumorigenesis with MYCN overexpression. more...

Organism:

Gallus gallus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26853

12 Samples

Download data: TXT

(Submitter supplied) Eimeria (E.) maxima parasite infects the midgut disrupting the jejunal and ileal mucosal lining causing high morbidity and mortality in chickens. Heat stress (HS) is a seasonal stressor that affects biological functions leading to poor performance. Our objective was to elucidate how HS, E. maxima infection, and their combination affect the ileum transcriptome. Two-hundred and forty 2-week-old males Ross708 chickens were randomly allocated into four treatment groups: thermoneutral control (TNc), thermoneutral infected (TNi), heat stress control (HSc), and heat stress infected (HSi), with 6 replicates each of 10 birds. more...

Organism:

Gallus gallus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16133

20 Samples

Download data: TXT

(Submitter supplied) Despite the existence of a number of studies investigating the effect of insect meal on the growth performance of broilers, knowledge about the metabolic effects of insect meal in broilers is still scarce. Thus, the present study investigated the effect of partial replacement of soybean meal with Hermetia illucens (HI) larvae meal on the liver transcriptome, the plasma metabolome and the cecal microbiome in broilers. more...

Organism:

Gallus gallus

Type:

Expression profiling by array

Platform:

GPL19014

18 Samples

Download data: CEL

(Submitter supplied) Hindbrain boundary cells of st. 18 HH chick embryo express the ECM molecule Chondrotin sulphate proteoglycan (CSPG). To determine whether the ventricular zone of hindbrain boundaries act as reservoirs of NPSCs, we separated between hindbrain boundary cells and the rest of hindbrain cells based on the expression pattern of CSPG which seemed membrane-bound. FACS approach was used to isolate CSPG-positive cells and CSPG-negative cells. more...

Organism:

Gallus gallus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32831

10 Samples

Download data: XLSX

(Submitter supplied) The immune system is a complex infrastructure where many cells interact with each other and perform duties depending on their type and function. When using traditional immunological methods in studying non-traditional model organisms, such as birds, challenges arise. These are often associated with a lack of knowledge surrounding the organism in question—particularly, the expected leukocytes, their cell-specific marker genes, and associated reagents. more...

Organism:

Gallus gallus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26853

4 Samples

Download data: MTX, TSV, XLSX

(Submitter supplied) Hyperpigmentation of the visceral peritoneum (HVP) has recently garnered significant attention within the poultry industry due to its potential implications for the health of afflicted animals and its adverse effects on the appearance of commercial chicken carcasses. Unfortunately, the heritable characteristics of HVP are not yet fully understood. Motivated by poultry industry demand, we deployed multi-omics comparing the clinical HVP and normal samples profiling the potential regulating molecular landscape in cell and genome resolution, specifically, aiming to decipher the precise molecular genomic marker. more...

Organism:

Gallus gallus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26853

2 Samples

Download data: MTX, TSV