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Items: 1 to 20 of 26377

1.

Effect of replacing soybean meal with Hermetia illucens meal on cecal microbiome, liver transcriptome and plasma metabolome of broilers

(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
Series
Accession:
GSE255945
ID:
200255945
2.

The neural-progenitor/stem-cell (NPSC) properties of hindbrain boundary cells

(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
Series
Accession:
GSE230804
ID:
200230804
3.

Single-cell RNA seq mapping of chicken leukocytes

(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
Series
Accession:
GSE224329
ID:
200224329
4.

Aberrant expression of the DCT gene is implicated in the hyperpigmentation of the visceral peritoneum of the chicken

(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
Series
Accession:
GSE246996
ID:
200246996
5.

Replacement of dietary vitamin E by an extract rich in hydrox-ytyrosol, from the olive oil by-product “alperujo”, in broiler chickens: part II - effects on liver traits, oxidation, lipid profile and transcriptome.

(Submitter supplied) The present study aims to evaluate the impact of replacing vitamin E (VE) by a liquid obtained from alpeorujo, an olive oil by-product rich in hydroxytyrosol (HT), on broiler liver traits, oxi-dation, lipid profile and transcriptomic analysis. There were 5 diets that differed only in the substitution of supplemental VE (0 to 40 mg/kg with differences of 10 mg/kg) by HT (30 to 0 mg/kg with differences of 7.5 mg/kg). more...
Organism:
Gallus gallus
Type:
Expression profiling by array
Platform:
GPL19014
30 Samples
Download data: CEL, XLSX
Series
Accession:
GSE240099
ID:
200240099
6.

Newcastle disease virus activates methylation-related enzymes to reprogram m6A Methylation in infected cells

(Submitter supplied) To investigate the role of m6A modification during Newcastle disease virus (NDV) infection We then performed gene expression profiling analysis using data obtained from RNA-seq and MeRIP-seq of NDV infected CEF cells and normal cells.
Organism:
Gallus gallus
Type:
Other
Platform:
GPL26853
12 Samples
Download data: TXT
Series
Accession:
GSE220921
ID:
200220921
7.

Genome-wide association analysis and genome resequencing reveal a genomic duplication possibly concerning a novel chicken comb morphology

(Submitter supplied) Here, we report on a novel chicken comb phenotype, designated Antler-comb. Using a 600K Axiom® Genome-Wide Chicken Genotyping Array, we separately genotyped 12 and 24 female Hetian Wildtype-comb and Antler-comb chickens, respectively. Meanwhile, we sequenced the genomes of 10 Hetian Antler-comb and 10 Wildtype-comb chickens to interrogate the GWAS results and explore the potential genetic variants underlying this phenotype. more...
Organism:
Gallus gallus
Type:
SNP genotyping by SNP array; Genome variation profiling by SNP array
Platform:
GPL23815
36 Samples
Download data: CEL, XLSX
Series
Accession:
GSE145948
ID:
200145948
8.

Differences in the microbiome of the small intestine of Leghorn lines divergently selected for antibody titer to sheep erythrocytes suggest roles for commensals in host humoral response

(Submitter supplied) For forty generations, two lines of White Leghorn chickens have been selected for high (HAS) or low (LAS) antibody response to a low dose injection of sheep red blood cells (SRBCs). Their gut is home to billons of microorganisms and the largest number of immune cells in the body; therefore, the objective of this experiment was to gain understanding of the ways the microbiome may influence the differential antibody response observed in these lines. more...
Organism:
Gallus gallus
Type:
Other
Platform:
GPL33684
36 Samples
Download data: XLSX
Series
Accession:
GSE240908
ID:
200240908
9.

Integrated single-cell multiomics uncovers foundational regulatory mechanisms of lens development and pathology.

(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:
GPL24517 GPL26853
37 Samples
Download data
Series
Accession:
GSE236905
ID:
200236905
10.

Integrated single-cell multiomics uncovers foundational regulatory mechanisms of lens development and pathology [CUT&RUN]

(Submitter supplied) Ocular lens development entails epithelial to fiber cell differentiation, defects in which cause congenital cataract. We report the first single-cell multiomic atlas of lens development, leveraging snRNA-seq, snATAC-seq, and CUT&RUN-seq to discover novel mechanisms of cell fate determination and cataract-linked regulatory networks. A comprehensive profile of cis- and trans-regulatory interactions, including for the cataract-linked transcription factor MAF, is established across a temporal trajectory of fiber cell differentiation. more...
Organism:
Gallus gallus
Type:
Other
Platform:
GPL24517
20 Samples
Download data: NARROWPEAK
Series
Accession:
GSE236904
ID:
200236904
11.

Integrated single-cell multiomics uncovers foundational regulatory mechanisms of lens development and pathology [Multiome snRNA/snATAC]

(Submitter supplied) Ocular lens development entails epithelial to fiber cell differentiation, defects in which cause congenital cataract. We report the first single-cell multiomic atlas of lens development, leveraging snRNA-seq, snATAC-seq, and CUT&RUN-seq to discover novel mechanisms of cell fate determination and cataract-linked regulatory networks. A comprehensive profile of cis- and trans-regulatory interactions, including for the cataract-linked transcription factor MAF, is established across a temporal trajectory of fiber cell differentiation. more...
Organism:
Gallus gallus
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL26853
4 Samples
Download data: H5
Series
Accession:
GSE236903
ID:
200236903
12.

Integrated single-cell multiomics uncovers foundational regulatory mechanisms of lens development and pathology [scRNA-seq]

(Submitter supplied) Ocular lens development entails epithelial to fiber cell differentiation, defects in which cause congenital cataract. We report the first single-cell multiomic atlas of lens development, leveraging snRNA-seq, snATAC-seq, and CUT&RUN-seq to discover novel mechanisms of cell fate determination and cataract-linked regulatory networks. A comprehensive profile of cis- and trans-regulatory interactions, including for the cataract-linked transcription factor MAF, is established across a temporal trajectory of fiber cell differentiation. more...
Organism:
Gallus gallus
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL24517 GPL26853
13 Samples
Download data: CSV, MTX
Series
Accession:
GSE236902
ID:
200236902
13.

Single-cell RNA transcriptome reveals heterogeneity and dynamics of cells during skeletal muscle development in different chicken breeds

(Submitter supplied) Different chicken breeds exhibit distinct muscle phenotypes resulting from selective breeding, but little is known about the molecular mechanisms responsible for this phenotypic difference. Skeletal muscle is composed of a large number of heterogeneous cell populations. Differences in differentiation and interaction of cell populations play a key role in the difference of skeletal muscle phenotype. Here, skeletal muscle single-cell RNA sequencing in three developmental stages was performed on Daheng broiler (cultivated breed) and Tibetan chicken (native breed).
Organism:
Gallus gallus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL26853
6 Samples
Download data: MTX, TSV
Series
Accession:
GSE251682
ID:
200251682
14.

Daily Patterns of Retinal and Choroidal Gene Expression and Circadian Biology in Myopia Pathogenesis

(Submitter supplied) We investigated diurnal changes in gene expression in the retina and choroid at the onset of experimental myopia. We induced visual form deprivation myopia in young chicks, and isolated retinal and choroidal tissues separately in form- deprived and contralateral control eyes every 4 hours over a single 24-hour period.
Organism:
Gallus gallus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL26853
142 Samples
Download data: TXT
Series
Accession:
GSE227724
ID:
200227724
15.

High-resolution genome-wide mapping of MEF2A binding sites by CUT&Tag-seq in chicken primary myoblasts

(Submitter supplied) In this study, CUT&Tag-seq technology was employed to investigate MEF2A binding sites across the entire genome of chicken primary myoblasts. CUT&Tag was performed using CUT&Tag Assay Kit for Illumina Pro (TD904-1) from Vazyme. Antibody targeting MEF2A as well as IgG were used.The final DNA library on a HiSeq PE150 platform was subjected for the analyses. This study provides a wide landscape of MEF2A target genes from chicken primary myoblasts, which supports the active role of MEF2A in avian muscle development.
Organism:
Gallus gallus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL26853
3 Samples
Download data: BED, BEDGRAPH, BW
Series
Accession:
GSE249097
ID:
200249097
16.

Transcriptome profiling of the liver and pectoralis major muscle in slow-growing chickens under an organic raising system

(Submitter supplied) The strategy to improve the competitiveness of smallholder farmers and to serve highly nutritious meat for consumers is the major goal of Korat chicken (KRC) production in Thailand. Organic KRC meat contains high n-3 polyunsaturated fatty acids (PUFA) and docosahexaenoic acid (DHA), which have a wide range of health-related benefits. However, limited scientific investigations have been conducted on the modulations of PUFA and DHA in KRC. more...
Organism:
Gallus gallus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL26853
20 Samples
Download data: XLSX
Series
Accession:
GSE231912
ID:
200231912
17.

Interspecific single-cell transcriptomic analysis reveals differences in signaling pathways governing gonadal primordial germ cells between chicken and zebra finch (Taeniopygia guttata) [chicken scRNA-seq]

(Submitter supplied) Primordial germ cells (PGCs), major cell resource used in the production of germline chimeras in birds, have been used in conservation of avian genetic resources and production of transgenic animals. Numerous bird species have been put on the brink of extinction due to habitat loss and degradation caused by environmental destruction and climate change, but research on PGCs is limited to specific poultry, such as chickens. more...
Organism:
Gallus gallus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL19787
2 Samples
Download data: MTX, TSV
Series
Accession:
GSE208178
ID:
200208178
18.

Histone lactylation couples cellular metabolism with the activation of developmental gene regulatory networks [CUT&RUN control and SOX9/TEA1-VPR over-expressing]

(Submitter supplied) Embryonic cells engage in diverse types of metabolism to execute specialized tasks in the developing embryo. Recent studies have demonstrated that metabolic reprogramming can also drive changes in cell identity and behavior by affecting the expression of developmental genes. However, the connection between cellular metabolism and differential gene expression is still not well understood. Here we report found that histone lactylation, an epigenetic mark derived from glycolysis-derived lactate, couples the metabolic state of embryonic cells with gene expression and the activation of gene regulatory networks. more...
Organism:
Gallus gallus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL19787
4 Samples
Download data: BEDGRAPH, BW
Series
Accession:
GSE241256
ID:
200241256
19.

Histone lactylation couples cellular metabolism with the activation of developmental gene regulatory networks

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Gallus gallus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL19787 GPL26853
25 Samples
Download data: BEDGRAPH, BW, TXT
Series
Accession:
GSE228343
ID:
200228343
20.

Histone lactylation couples cellular metabolism with the activation of developmental gene regulatory networks [R-GNE-140 ATAC-seq]

(Submitter supplied) Embryonic cells engage in diverse types of metabolism to execute specialized tasks in the developing embryo. Recent studies have demonstrated that metabolic reprogramming can also drive changes in cell identity and behavior by affecting the expression of developmental genes. However, the connection between cellular metabolism and differential gene expression is still not well understood. Here we report found that histone lactylation, an epigenetic mark derived from glycolysis-derived lactate, couples the metabolic state of embryonic cells with gene expression and the activation of gene regulatory networks. more...
Organism:
Gallus gallus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL19787
4 Samples
Download data: BW
Series
Accession:
GSE228342
ID:
200228342
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