GEO DataSets

(Submitter supplied) Orofacial clefts are the most common form of congenital craniofacial malformations worldwide. The etiology of these birth defects is multifactorial, involving genetic and environmental factors. In most cases, however, the underlying causes remain unexplained, precluding molecular understanding of disease mechanisms. Here, we integrated genome-wide association data, targeted re-sequencing of case and control cohorts, cell type-specific epigenomic profiling, and genome architecture analyses, to functionally and molecularly dissect a genomic locus associated with an increased risk of non-syndromic orofacial cleft. more...

Organism:

Gallus gallus; Homo sapiens

Type:

Other

Platforms:

GPL19005 GPL16791

5 Samples

Download data: BEDGRAPH

(Submitter supplied) Unidirectional airflow in the avian lung enables gas exchange during both inhalation and exhalation. Stereo-seq spatial transcriptomics reveal a third, chicken-specific alveolar cell type expressing KRT14, hereby named luminal cells. Luminal, alveolar type 2, and alveolar type 1 cells sequentially occupy concentric zones radiating from the parabronchial lumen. Our study explores the evolutionary space of lung diversification and lays the foundation for functional analysis of species-specific genetic determinants.

Organism:

Gallus gallus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30495

1 Sample

Download data: H5, H5AD, TAR

(Submitter supplied) Alveolar development of the chicken lung has largely been studied by histology only. We conducted a study to uncover the transcriptomic profile of the lung alveolar cell types in the chicken by single-cell RNA-seq (scRNA-seq) and multiome.

Organism:

Gallus gallus

Type:

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

Platform:

GPL26853

4 Samples

Download data: CLOUPE, H5, MTX, TBI, TSV

(Submitter supplied) Understanding and manipulating the avian gastrointestinal tract, where nutrient absorption and vital host-pathogen interactions occur, is critical for improving poultry health and productivity. To advance research in this area, chicken three-dimensional intestinal enteroid models have been developed and characterised. In this study, we report a comprehensive transcriptome atlas for 43,587 intestinal enteroid cells derived from broiler and layer chickens. more...

Organism:

Gallus gallus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32831

8 Samples

Download data: MTX, TSV

(Submitter supplied) Despite the incredible morphological diversity found within vertebrates, embryonic development is often regulated by shared foundational mechanism maintained from a common ancestor. For instance, the tetrapod limb displays tremendous variation in size and shape but largely develops according to conserved gene regulatory networks, including signaling pathways, transcription factors, and enhancers. more...

Organism:

Alligator mississippiensis; Mus musculus; Anolis sagrei; Gallus gallus; Trachemys scripta

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Third-party reanalysis

7 related Platforms

76 Samples

Download data: BED, BW, NARROWPEAK, TXT

(Submitter supplied) Coloboma is a developmental eye disorder characterised by failure of epithelial fusion during optic fissure closure (OFC). The incomplete identification of genes and molecular pathways that directly regulate fusion restricts current understanding of OFC mechanisms and coloboma causation. The recent identification of pioneer cells at the edges of the fissure margins provides an opportunity to molecularly characterise OFC. more...

Organism:

Gallus gallus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32831

10 Samples

Download data: TXT

(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; Other

Platforms:

GPL19787 GPL26853

42 Samples

Download data: BED, BIGWIG, COOL, NARROWPEAK

(Submitter supplied) The integument plays a critical role in functional adaptation, with macro-regional specification forming structures like beaks, combs, feathers, and scales, while micro-regional specification modifies skin appendage shapes. However, the molecular mechanisms remain largely unknown. Craniofacial integument displays dramatic diversity, exemplified by the Polish chicken (PC) with a homeotic transformation of comb-to-crest feathers, caused by a 195–base pair (bp) duplication in HoxC10 intron. more...

Organism:

Gallus gallus

Type:

Other

Platform:

GPL26853

4 Samples

Download data: BED, COOL, FA, GTF

(Submitter supplied) The integument plays a critical role in functional adaptation, with macro-regional specification forming structures like beaks, combs, feathers, and scales, while micro-regional specification modifies skin appendage shapes. However, the molecular mechanisms remain largely unknown. Craniofacial integument displays dramatic diversity, exemplified by the Polish chicken (PC) with a homeotic transformation of comb-to-crest feathers, caused by a 195–base pair (bp) duplication in HoxC10 intron. more...

Organism:

Gallus gallus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL26853

10 Samples

Download data: BED, BIGWIG, FA, GTF, NARROWPEAK

(Submitter supplied) The integument plays a critical role in functional adaptation, with macro-regional specification forming structures like beaks, combs, feathers, and scales, while micro-regional specification modifies skin appendage shapes. However, the molecular mechanisms remain largely unknown. Craniofacial integument displays dramatic diversity, exemplified by the Polish chicken (PC) with a homeotic transformation of comb-to-crest feathers, caused by a 195–base pair (bp) duplication in HoxC10 intron. more...

Organism:

Gallus gallus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL26853 GPL19787

28 Samples

Download data: FA, GTF, TXT

(Submitter supplied) Birds exhibit a remarkable diversity in limb morphology. Zic3, a transcription factor highly expressed in the anterior of the limb, has differential expression among bird species. To study how it regulates digit morphogenesis in birds, we overexpressed the chicken-Zic3 gene in the lateral plate mesoderm (LPM) of developing chicken hindlimbs at Hamburger Hamilton (HH) stage 10 using the RCAS avian retrovirus. more...

Organism:

Gallus gallus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26853

6 Samples

Download data: TXT

(Submitter supplied) Exposure to chronic heat stress not only reduces body weight gain in growing broilers, but also enhances fat deposition in the abdomen, subcutaneous, and intramuscular. To elucidate this phenomenon, numerous studies have examined changes in the transcripts, protein, and metabolic levels in the liver, the primary site of de novo fat synthesis in birds. On the other hand, changes in adipose tissue, the direct site of fat deposition, have not been unclear. more...

Organism:

Gallus gallus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26853

6 Samples

Download data: XLSX

(Submitter supplied) High pathogenicity avian influenza viruses pose a growing threat to poultry, livestock, wildlife, and humans as they undergo accelerated expansion of host and geographical ranges. Since 2020, these viruses have driven a panzootic characterized by extensive viral diversification and spillover into species previously considered to be resistant. There is currently a lack of physiologically relevant in vitro models that can be used to screen the rapidly changing viral landscape. more...

Organism:

Gallus gallus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34854

2 Samples

Download data: RDATA

(Submitter supplied) High pathogenicity avian influenza viruses pose a growing threat to poultry, livestock, wildlife, and humans as they undergo accelerated expansion of host and geographical ranges. Since 2020, these viruses have driven a panzootic characterized by extensive viral diversification and spillover into species previously considered to be resistant. There is currently a lack of physiologically relevant in vitro models that can be used to screen the rapidly changing viral landscape. more...

Organism:

Gallus gallus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34854

18 Samples

Download data: XLSX

(Submitter supplied) The amniote pallium contains sensory circuits structurally and functionally equivalent, yet their evolutionary relationshipremains unresolved. Our study employs birthdating analysis, single-cell RNA and spatial transcriptomics, and mathematical modeling to compare the development and evolution of known pallial circuits across birds (chick), lizards (gecko)and mammals (mouse). Wereveal that neurons within these circuits' stations are generated at varying developmental times and brain regions across species, and foundan early developmental divergence in the transcriptomic progression of glutamatergic neurons. more...

Organism:

Gallus gallus; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL26853 GPL24247

6 Samples

Download data: RDS, TAR, TXT

(Submitter supplied) Embryonic gene expression is remarkably conserved across vertebrates as observed, for instance, in the developing hearts of chicken and mouse which diverged >300 million years ago. However, most cis regulatory elements (CREs) are highly divergent, which makes orthology tracing based on sequence similarity difficult, especially at larger evolutionary distances. Some evidence suggests functional conservation of CREs despite sequence divergence. more...

Organism:

Gallus gallus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL26853

21 Samples

Download data: BW

(Submitter supplied) Embryonic gene expression is remarkably conserved across vertebrates as observed, for instance, in the developing hearts of chicken and mouse which diverged >300 million years ago. However, most cis regulatory elements (CREs) are highly divergent, which makes orthology tracing based on sequence similarity difficult, especially at larger evolutionary distances. Some evidence suggests functional conservation of CREs despite sequence divergence. more...

Organism:

Gallus gallus

Type:

Other

Platform:

GPL26853

2 Samples

Download data: HIC

(Submitter supplied) Embryonic gene expression is remarkably conserved across vertebrates as observed, for instance, in the developing hearts of chicken and mouse which diverged >300 million years ago. However, most cis regulatory elements (CREs) are highly divergent, which makes orthology tracing based on sequence similarity difficult, especially at larger evolutionary distances. Some evidence suggests functional conservation of CREs despite sequence divergence. more...

Organism:

Mus musculus; Gallus gallus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL26853 GPL24247

12 Samples

Download data: BW

(Submitter supplied) Embryonic gene expression is remarkably conserved across vertebrates as observed, for instance, in the developing hearts of chicken and mouse which diverged >300 million years ago. However, most cis regulatory elements (CREs) are highly divergent, which makes orthology tracing based on sequence similarity difficult, especially at larger evolutionary distances. Some evidence suggests functional conservation of CREs despite sequence divergence. more...

Organism:

Gallus gallus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26853

4 Samples

Download data: BW

(Submitter supplied) We performed scRNA-seq for PBMCs isolated from 35-day-old healthy male SPF chicken at the onset or upon vaccination with live-attenuated or inactivated IBV vaccines.

Organism:

Gallus gallus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24517

8 Samples

Download data: MTX, TSV