GEO DataSets

(Submitter supplied) Primordial germ cells (PGCs) are lineage restricted precursor cells of sperm and eggs. While avian PGCs from chicken can be cultured and modified to produce genome-edited chickens, the long-term culture of PGCs from other bird species has not been achieved. Here, we explored the effects of a cell-matrix interaction on the in vitro propagation of chicken PGCs. Blocking integrin signaling severely reduced the self-renewal of the PGC, indicating that a PGC-matrix interaction is an essential process for self-renewal. more...

Organism:

Gallus gallus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL31227

6 Samples

Download data: TXT

(Submitter supplied) The histone variant H2A.Z is one of the most evolutionally conserved histone variants. Here, we identified a cancer-associated mutation in H2A.Z and evaluate the mutation. Structural and biochemical in vitro analyses showed that the H2A.Z mutation destabilizes nucleosome containing it. Then we applied the genetic complementation analysis to analyze cellular functions of the H2A.Z mutant. Although the H2A.Z mutant is deposited into nucleosome and rescues the lethality of H2A.Z DKO cells, the mutant does not complement mitotic defects of H2A.Z DKO cells, suggesting that stability of H2A.Z nucleosome is required for proper mitotic progression. more...

Organism:

Gallus gallus

Type:

Expression profiling by array

Platform:

GPL13790

2 Samples

Download data: TXT

(Submitter supplied) The aim of this study was to explore whether, and if so, how Bacillus subtilis KC1 can enhance the growth performance of broilers that have been adversely affected by Mycoplasma gallisepticum (MG) infection. A total of 96 1-day-old male broilers were randomly divided into 4 groups: the control group (basal diet), the MG group (basal diet + MG challenge), the Bacillus subtilis KC1 group (basal diet + Bacillus subtilis KC1 supplementation), the Bacillus subtilis KC1 + MG group (basal diet + Bacillus subtilis KC1 supplementation + MG challenge). more...

Organism:

Gallus gallus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30495

36 Samples

Download data: XLS

(Submitter supplied) The histone variant H2A.Z is evolutionarily conserved from yeast to vertebrates. H2A.Z regulates gene expression when localized to promoter region. Recently, we identified two genes encoding H2A.Z, H2A.Z-1 and H2A.Z-2 in vertebrate genome. However, it is not clear that both H2A.Z-1 and H2A.Z-2 were required for the function of H2A.Z in gene regulation. To address this issue, we generated the H2A.Z-1 and H2A.Z-2 single knockout cells in chicken DT40 cells.We used microarrays to analysis the alternation of gene expression profiles in H2A.Z-1 KO and H2A.Z-2 KO cells and identify classes of up or down regulated gene by H2A.Z-1 and H2A.Z-2.

Organism:

Gallus gallus

Type:

Expression profiling by array

Platform:

GPL3213

2 Samples

Download data: CEL, CHP

(Submitter supplied) In mice, genome-wide DNA methylation is actively erased at the onset of fertilisation, followed by remethylation in epiblasts after implantation, leading to inactive chromatin formation as a preliminary step to somatic cell differentiation, and then demethylation again during primitive streak formation and the determination of primordial germ cells (PGCs). This sequence of DNA methylation changes is accompanied by dynamic epigenetic reprogramming, including nuclear structure, histone modification, and intranuclear re-localisation of chromosomes, during totipotency acquisition of the fertilised egg and germline development. more...

Organism:

Gallus gallus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL16133

16 Samples

Download data: BW

(Submitter supplied) In the avian host, comprehensively cataloging immune cell types, their transcriptome profiles, and varying molecular responses to pathogen challenges are necessary steps toward a better understanding of the interplay between genetics and disease resilience. We present a first nuclei atlas of immune cell types derived from the three main immune organs of layer chickens, including spleen, bursa, and thymus. more...

Organism:

Gallus gallus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26853

2 Samples

Download data: H5

(Submitter supplied) Chickens are the most abundant agricultural animals globally, with controlling abdominal fat deposition (AFD) being a key objective in poultry breeding. While GWAS can identify genetic variants associated with AFD traits, the precise roles and mechanisms of these variants remain largely unclear. This study used two distinct chicken lines, selectively bred for differing AFD, as experimental models. Through the integration of genomic, epigenomic, 3D genomic, and transcriptomic data, a comprehensive chromatin 3D regulatory network map was developed to reveal the genetic regulatory mechanisms that influence AFD traits. more...

Organism:

Gallus

Type:

Other

Platform:

GPL34258

6 Samples

Download data: HIC

(Submitter supplied) Chickens are the most abundant agricultural animals globally, with controlling abdominal fat deposition (AFD) being a key objective in poultry breeding. While GWAS can identify genetic variants associated with AFD traits, the precise roles and mechanisms of these variants remain largely unclear. This study used two distinct chicken lines, selectively bred for differing AFD, as experimental models. Through the integration of genomic, epigenomic, 3D genomic, and transcriptomic data, a comprehensive chromatin 3D regulatory network map was developed to reveal the genetic regulatory mechanisms that influence AFD traits. more...

Organism:

Gallus gallus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL26853

6 Samples

Download data: NARROWPEAK

(Submitter supplied) Paddy rice with husk can be availbale for chicken dietary resource instead of yellow corn. Ingestion of paddy rice potentially affects on gastrointestinal physiology and function including digestion/absorption of nutrients and gut barrier function such as mucosal immunity, but the details of changes is unknown. To obtain insight into the physiological modifications in the small intestine of chickens fed paddy rice, we conducted a comprehensive analysis of gene expression in small intestine by DNA microarray. more...

Organism:

Gallus gallus

Type:

Expression profiling by array

Platform:

GPL3213

2 Samples

Download data: CEL, CHP

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

Organism:

Gallus gallus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32831

1 Sample

Download data: MTX, TSV

(Submitter supplied) Combinations of transcription factors govern the identity of cell types, which is reflected by genomic enhancer codes. We utilized deep learning to characterize these enhancer codes and devised three novel metrics to compare cell types in the telencephalon between mammals and birds. To this end, we generated single-cell multiome and spatially-resolved transcriptomics data of the chicken telencephalon. more...

Organism:

Gallus gallus

Type:

Other

Platform:

GPL30495

1 Sample

Download data: H5, TAR, TXT

(Submitter supplied) Combinations of transcription factors govern the identity of cell types, which is reflected by genomic enhancer codes. We utilized deep learning to characterize these enhancer codes and devised three novel metrics to compare cell types in the telencephalon between mammals and birds. To this end, we generated single-cell multiome and spatially-resolved transcriptomics data of the chicken telencephalon. more...

Organism:

Gallus gallus

Type:

Other

Platform:

GPL34823

2 Samples

Download data: PICKLE, TIFF, TXT

(Submitter supplied) The laying hen is the only spontaneous model of ovarian tumor. But no studies have systematically compared the molecular mechanisms of ovarian cancer in hens and women. We performed RNA sequencing of nine chicken ovarian tumor samples and four normal ovarian samples.

Organism:

Gallus gallus

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platform:

GPL24996

26 Samples

Download data: CSV

(Submitter supplied) The beneficial effects of feeding probiotic Bacillus subtilis DSM 32315 (BS) and Bacillus velezensis CECT 5940 (BV) to chickens in vivo are well-documented, with potential immune modulation as a key mechanism. In this study, we investigated the direct interactions of chicken peripheral blood mononuclear cells (PBMCs) with BS or BV in vitro through whole transcriptome profiling and cytokine array analysis. more...

Organism:

Gallus gallus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26853

24 Samples

Download data: TSV

(Submitter supplied) To investigate transcriptomic changes that facilitate the reprogramming of retinal pigment epithelium (RPE) cells to neural retina, chicken RPE explants were cultured for 24 or 48 hours in the presence or absence of the reprogramming factor FGF2. To further interrogate the metabolic requirements of reprogramming, RPE explants were additionally cultured in the presence of the pyruvate dehydrogenase kinase inhibitor dichloroacetate in the presence or absence of FGF2.

Organism:

Gallus gallus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24517

24 Samples

Download data: TSV

(Submitter supplied) Although connective tissues play critical roles in development, our understanding of connective tissue fibroblast developmental programs lag behind that of other components of the musculoskeletal system mainly because fibroblasts are highly heterogeneous and poorly characterized. Combining single-cell RNA-sequencing-based strategies, including trajectory inference, and in situ hybridization analyses, we address the diversity of connective tissue fibroblasts and their developmental trajectories during chicken limb foetal development. more...

Organism:

Gallus gallus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19787

2 Samples

Download data: MTX, TSV

(Submitter supplied) Hox genes are highly conserved, master regulators of spatial patterning in the embryo, but how these factors trigger regional morphogenesis has largely remained a mystery. In the developing gut, Hox genes help demarcate identities of the small and large intestines early in embryogenesis, which ultimately leads to their specialization in both form and function. While the midgut forms villi, the hindgut develops flat, brain-like sulci that resolve into heterogeneous outgrowths. more...

Organism:

Gallus gallus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19787

12 Samples

Download data: CSV

(Submitter supplied) Hox genes are highly conserved, master regulators of spatial patterning in the embryo, but how these factors trigger regional morphogenesis has largely remained a mystery. In the developing gut, Hox genes help demarcate identities of the small and large intestines early in embryogenesis, which ultimately leads to their specialization in both form and function. While the midgut forms villi, the hindgut develops flat, brain-like sulci that resolve into heterogeneous outgrowths. more...

Organism:

Gallus gallus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26853

5 Samples

Download data: FA, GTF, RDS

(Submitter supplied) Chicken infectious anaemia (CIA) is an immunosuppressive disease caused by chicken infectious anaemia virus (CIAV). Due to immunosuppression, the disease is often leads to mixed infections and secondary infections, exacerbating viral, bacterial, and fungal infections, which can be highly detrimental. Therefore, it is imperative to identify the immune genes involved in regulating CIAV infection. In this study, comprehensive transcriptome sequencing was employed to determine the expression levels of regulated immune genes including mRNAs, microRNAs, lncRNAs, and circRNAs in CIAV-infected MDCC-MSB1 cells. more...

Organism:

Gallus gallus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL16133

6 Samples

Download data: XLSX

(Submitter supplied) Chicken infectious anaemia (CIA) is an immunosuppressive disease caused by chicken infectious anaemia virus (CIAV). Due to immunosuppression, the disease is often leads to mixed infections and secondary infections, exacerbating viral, bacterial, and fungal infections, which can be highly detrimental. Therefore, it is imperative to identify the immune genes involved in regulating CIAV infection. In this study, comprehensive transcriptome sequencing was employed to determine the expression levels of regulated immune genes including mRNAs, microRNAs, lncRNAs, and circRNAs in CIAV-infected MDCC-MSB1 cells. more...

Organism:

Gallus gallus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26853

6 Samples

Download data: XLSX