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Items: 1 to 20 of 38083

1.

Effects of a biotechnologically produced Pleurotus sapidus mycelium on gut microbiome, liver transcriptome and plasma metabolome of broilers

(Submitter supplied) Submerged cultivation using low-value agro-industrial side streams allows large-scale and efficient production of fungal mycelia, which has a high nutritional value. As the dietary properties of fungal mycelia in poultry are largely unknown, the present study aimed to investigate the effect of feeding a Pleurotus sapidus (PSA) mycelium as a feed supplement on growth performance, composition of the cecal microbiota and several physiological traits including gut integrity, nutrient digestibility, liver lipids, liver transcriptome and plasma metabolome in broilers. more...
Organism:
Gallus gallus
Type:
Expression profiling by array
Platform:
GPL18368
18 Samples
Download data: CEL, XLSX
Series
Accession:
GSE269154
ID:
200269154
2.

Host transcriptomic response to a bacterial toxin at single-nuclei resolution

(Submitter supplied) We are studying the host immune response to a bacterial toxin in the chicken spleen and bursa. We performed snRNAseq to analyze the various immune cell types that play a role in combating the infection and the cell-type transcriptional response.
Organism:
Gallus gallus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL26853
10 Samples
Download data: MTX, TSV
Series
Accession:
GSE249652
ID:
200249652
3.

An in vivo CRISPR screen in chick embryos reveals a role for MLLT3 in specification of neural cells from the caudal epiblast

(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
Series
Accession:
GSE267653
ID:
200267653
4.

Influence of DNA-methylation at multiple stages of limb chondrogenesis

(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
Series
Accession:
GSE266119
ID:
200266119
5.

Germ cell specific high level of H3K9me3 in chicken PGCs: distribution and role in gene expression control

(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:
GPL19787 GPL19005
7 Samples
Download data
Series
Accession:
GSE248768
ID:
200248768
6.

Germ cell specific high level of H3K9me3 in chicken PGCs: distribution and role in gene expression control [RNA-Seq]

(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
Series
Accession:
GSE248767
ID:
200248767
7.

Germ cell specific high level of H3K9me3 in chicken PGCs: distribution and role in gene expression control [ChIP-Seq]

(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
Series
Accession:
GSE248766
ID:
200248766
8.

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
9.

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
10.

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
11.

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
12.

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
13.

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 GPL26853 GPL19005
100 Samples
Download data: BEDGRAPH, BW
Series
Accession:
GSE254182
ID:
200254182
14.

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

(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
Series
Accession:
GSE254181
ID:
200254181
15.

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

(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
Series
Accession:
GSE254180
ID:
200254180
16.

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
17.

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
18.

Archival chromatin sequencing in eastern water dragon museum specimens

(Submitter supplied) Formalin induces inter- and intra-molecular crosslinks within exposed cells. This cross-linking can be exploited to characterise chromatin state as in the MNase (micrococcal nuclease) assays. Our team aims to optimise these assays for application in museum preserved formalin-exposed specimens. To do so, we applied an optimised MNase assay to fresh-frozen and archival eastern water dragon specimens, as old as 1905. more...
Organism:
Intellagama lesueurii lesueurii
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL34214
8 Samples
Download data: WIG
Series
Accession:
GSE256157
ID:
200256157
19.

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
20.

Hepatic Transcriptomic Responses to Ethinylestradiol in Embryonic Japanese Quail and Double-crested Cormorant

(Submitter supplied) Species difference in susceptibility to toxicants is a critical issue in ecotoxicology. Transcriptomics is being proposed as a strategy to improve toxicity testing for regulatory risk assessment; however, different responses among species have not been extensively explored using this approach. In the present study, we identified dysregulated genes and pathways in Japanese quail (JQ) and double-crested cormorant (DCCO) embryos following exposure to ethinylestradiol (EE2). more...
Organism:
Phalacrocorax auritus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL32719
15 Samples
Download data: TXT
Series
Accession:
GSE214620
ID:
200214620
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