txid9031[Organism:noexp] - GEO DataSets

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Select item 2002575491.

A male-essential microRNA is key for avian sex chromosome dosage compensation

(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

Series

Accession:: GSE257549

ID:: 200257549

Select item 2002526162.

SOCS2 contributes to reduction of the third digit during development of the chicken forelimb

(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

Series

Accession:: GSE252616

ID:: 200252616

Select item 2002640423.

Pronounced early differentiation underlies zebra finch gonadal germ cell development.

(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

Series

Accession:: GSE264042

ID:: 200264042

Select item 2002004584.

Exploration of the transcriptional regulation network of the suppression of ILTV infection by PP1 and PP2 in chickenLMH cells

(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

Series

Accession:: GSE200458

ID:: 200200458

Select item 2002546595.

Centromeric chromatin in mitosis reorganizes into a functional structure stabilized by cohesin [NG-Capture-C]

(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:: GPL19005 GPL26853
60 Samples

Download data: BEDGRAPH

Series

Accession:: GSE254659

ID:: 200254659

Select item 2002541826.

Centromeric chromatin in mitosis reorganizes into a functional structure stabilized by cohesin

(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

Series

Accession:: GSE254182

ID:: 200254182

Select item 2002541817.

Centromeric chromatin in mitosis reorganizes into a functional structure stabilized by cohesin [CENPA-ChIP-seq]

Organism:: Gallus gallus

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platforms:: GPL26853 GPL19005
8 Samples

Download data: BW

Series

Accession:: GSE254181

ID:: 200254181

Select item 2002541808.

Centromeric chromatin in mitosis reorganizes into a functional structure stabilized by cohesin [Halo-ChIP-seq]

Organism:: Gallus gallus

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platform:: GPL32831
32 Samples

Download data: BW

Series

Accession:: GSE254180

ID:: 200254180

Select item 2002614869.

Chromatin remodeller Chd7 is developmentally regulated in the neural crest by tissue - specific transcription factors

(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

Series

Accession:: GSE261486

ID:: 200261486

Select item 20022645810.

Bulk RNA-sequencing of MYCN-overexpressing chicken retinal cell lines

(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

Series

Accession:: GSE226458

ID:: 200226458

PubMed Full text in PMC Similar studies

Select item 20024177711.

Host transcriptome response to heat stress and Eimeria maxima infection in meat-type chickens

(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

Series

Accession:: GSE241777

ID:: 200241777

PubMed Full text in PMC Similar studies

Select item 20025594512.

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

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 20023080413.

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

PubMed Full text in PMC Similar studies

Select item 20022432914.

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

PubMed Full text in PMC Similar studies

Select item 20024699615.

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

Select item 20024009916.

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

Analyze with GEO2R

Select item 20022092117.

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

Select item 20014594818.

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

Select item 20024090819.

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...