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Items: 1 to 20 of 10846

1.

Transcriptome changes with GSK-J4 treatment in an ex vivo post-cataract surgery model

(Submitter supplied) Cell reprogramming to a myofibroblast responsible for the pathological accumulation of extracellular matrix is fundamental to the onset of fibrosis. Here, we explored how condensed chromatin structure marked by H3K72me3 becomes modified to allow for activation of repressed genes to drive emergence of myofibroblasts. In the early stages of myofibroblast precursor cell differentiation, we discovered that H3K27me3 demethylase enzyme UTX creates a delay in the accumulation of H3K27me3 on nascent DNA revealing a period of decondensed chromatin structure. more...
Organism:
Gallus gallus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL26853
6 Samples
Download data: TXT
Series
Accession:
GSE213480
ID:
200213480
2.

Transcriptome Sequencing Reveals Pathways Related to Proliferation and Differentiation of Shitou Goose Myoblasts

(Submitter supplied) In this study, we cultured lion-headed goose myoblasts and induced their differentiation, followed by RNA-seq extraction of total RNA from proliferative and differentiated cells, respectively. The identified lncRNAs and mRNAs were analyzed, including enrichment analysis, alternative splicing, and construction of interaction networks.
Organism:
Gallus gallus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL26853
6 Samples
Download data: TXT
Series
Accession:
GSE213147
ID:
200213147
3.

Development of the chicken lateral plate mesoderm and forelimb mesenchyme

(Submitter supplied) The lateral plate mesoderm (LPM) is a transient tissue that produces a diverse range of differentiated structures, including the limbs. However, the molecular mechanisms that drive early LPM specification and development are poorly understood. In this study, we utilize single-cell transcriptomics to define the cell-fate decisions directing LPM specification, subdivision, and early initiation of the forelimb mesenchyme in chicken embryos. more...
Organism:
Gallus gallus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL32647
3 Samples
Download data: MTX, TSV
Series
Accession:
GSE212985
ID:
200212985
4.

Cell-type identity of the avian utricle

(Submitter supplied) The avian utricle, a vestibular organ of the inner ear, displays turnover of sensory hair cells throughout life. This is in sharp contrast to the mammalian utricle, which shows limited regenerative capacity. Here, we use single-cell RNA-sequencing to identify distinct marker genes for the different sensory hair cell subtypes of the chicken utricle, which we validated in situ . We provide markers for spatially distinct supporting cell populations, and identified two transitional cell populations of dedifferentiating supporting cells and developing hair cells. more...
Organism:
Gallus gallus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL19787
300 Samples
Download data: CSV
Series
Accession:
GSE212831
ID:
200212831
5.

OCT4-SOX2 dimers reshape the epigenome to promote neural crest multipotency [Group1-4]

(Submitter supplied) The transcription factors OCT4 and SOX2 play an essential role in the establishment and maintenance of pluripotent embryonic stem cells (ESCs). Yet, their function in specialized stem cell populations is still poorly understood. Here, we show that the OCT4 and SOX2 work as dimers to regulate the epigenomic landscape of neural crest cells. By isolating primary neural crest cells at a range of developmental stages, we characterized the transcriptomic and epigenomic changes that take place during specification, migration, and early differentiation. more...
Organism:
Gallus gallus; Homo sapiens
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other
Platforms:
GPL27748 GPL21697
14 Samples
Download data: NARROWPEAK, TXT
Series
Accession:
GSE200196
ID:
200200196
6.

Chick Cranial Small RNA-seq

(Submitter supplied) Small RNA-seq of HH9- chick embryo cranial midbrain region
Organism:
Gallus gallus
Type:
Non-coding RNA profiling by high throughput sequencing
Platform:
GPL24517
4 Samples
Download data: TXT
Series
Accession:
GSE171616
ID:
200171616
7.

Chiwi KO Neural Folds

(Submitter supplied) RNA-seq of HH9- chick embryo cranial neural folds comparing Chiwi CRISPR KO to control
Organism:
Gallus gallus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL19005
4 Samples
Download data: TXT
Series
Accession:
GSE171615
ID:
200171615
8.

Mitotic H3K9 acetylation patterns are controlled by phase-specific activity of the histone deacetylases HDAC2, 3 and SIRT1

(Submitter supplied) Histone acetylation play a fundamental role in many biological processes. H3K9ac is tightly linked to active transcription, and enriched in promoters, enhancers and insulators. During mitosis H3k9ac levels are reduced, and the mechanism of this reduction is not clear. Here, we used small molecules inhibitors of histone deacetylases and evaluated by immunofluorescence and western blots the involvement of each of the targeted enzymes in regulating H3K9ac during prophase, metaphase, anaphase, telophase and cytokinesis. more...
Organism:
Gallus gallus; Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL29808
14 Samples
Download data: BED
Series
Accession:
GSE168180
ID:
200168180
9.

Identification of candidate regulatory elements controlling transcriptome during the formation of interphalangeal joints

(Submitter supplied) We report the ChIPseq derived Candidate Enhancer (CE) atlas generated for interphalangeal interzone and phalange, tissues collected during synovial joint formation. Three replicates for interzone and three replicated for phalange were immunoprecipitated (IP) with the H3K27ac antibodies. Also, two replicates for interzone and two replicates for phalange were immunoprecipitated with H3K4me1 antibodies. more...
Organism:
Gallus gallus
Type:
Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platforms:
GPL19005 GPL21476
26 Samples
Download data: BROADPEAK, TXT
Series
Accession:
GSE198819
ID:
200198819
10.

Epigenetic and transcriptomic signature reveals Sox8 as an otic master regulator

(Submitter supplied) Previously FGF signalling has been shown to specify otic fate from multipotent pre-placodal ectoderm. Though many FGF target genes have been identified in subsequent studies, none of them is sufficient to induce otic lineage. Profiling and analysing the transcriptome and epigenomical signature during otic specification, we predicted and confirmed Sox8 as an otic master regulator, able to specify otic fate in the pre-placodal ectoderm. more...
Organism:
Gallus gallus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL16133
5 Samples
Download data: BW
Series
Accession:
GSE102825
ID:
200102825
11.

Transcriptome of eight rooster (Leghorn) tissues for identification of differentially expressed genes

(Submitter supplied) The aim of this study is to obtain mRNA profiles of chicken tissues to perform differential transcriptome analysis
Organism:
Gallus gallus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL26853
40 Samples
Download data: TXT
Series
Accession:
GSE133401
ID:
200133401
12.

A method to investigate muscle target-specific transcriptional signatures of single motor neurons

(Submitter supplied) To investigate target-specific transcriptional signatures of single motor neurons, here we combine ex-ovo retrograde axonal labelling in mid-gestation chicken embryos with manual isolation of individual fluorescent cells and Smart-seq2 single-cell RNA-sequencing. We validate our method by injecting the EMR and FDQ wing muscles and harvest a total of 50 fluorescently labeled cells, in which we detect upto 10000 transcribed genes. more...
Organism:
Gallus gallus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL26853
50 Samples
Download data: CSV
Series
Accession:
GSE203595
ID:
200203595
13.

Emergence of sex-specific transcriptomes in a sexually-dimorphic brain nucleus

(Submitter supplied) Sexual dimorphisms in the brain give rise to sex differences in physiology and behavior, yet we have limited understanding of the transcriptomic changes underlying their development. We evaluated developmental transcriptome dynamics for one of the most extreme neuroanatomical sexual dimorphisms in vertebrates - the songbird robust nucleus of the arcopallium (RA). RA is the telencephalic motor output nucleus of the song system. more...
Organism:
Taeniopygia guttata
Type:
Expression profiling by high throughput sequencing
Platform:
GPL27119
22 Samples
Download data: TSV
Series
Accession:
GSE191296
ID:
200191296
14.

Sox8 reprogram ectoderm into ear vesicles and auditory neurons [smartseq2]

(Submitter supplied) The vertebrate inner ear arises from a pool of progenitors with the potential to give rise to all the sense organs and cranial ganglia of the head1-6. Here we explore the molecular mechanisms that control ear specification from these progenitors. Using a multi-omics approach combined with loss-of-function experiments we identify a core transcriptional circuit that imparts ear identity, along with non-coding elements that integrate this information. more...
Organism:
Gallus gallus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL23499
858 Samples
Download data: CSV, LOOM
Series
Accession:
GSE168088
ID:
200168088
15.

Sox8 reprograms ectoderm into ear vesicles and associated neurons [Sox8OE_rnaseq]

(Submitter supplied) The vertebrate inner ear arises from a pool of progenitors with the potential to give rise to all the sense organs and cranial ganglia of the head1-6. Here we explore the molecular mechanisms that control ear specification from these progenitors. Using a multi-omics approach combined with loss-of-function experiments we identify a core transcriptional circuit that imparts ear identity, along with non-coding elements that integrate this information. more...
Organism:
Gallus gallus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL23499
6 Samples
Download data: TSV
Series
Accession:
GSE168087
ID:
200168087
16.

Sox8 reprograms ectoderm into ear vesicles and associated neurons [Lmx1aE1_rnaseq]

(Submitter supplied) The vertebrate inner ear arises from a pool of progenitors with the potential to give rise to all the sense organs and cranial ganglia of the head1-6. Here we explore the molecular mechanisms that control ear specification from these progenitors. Using a multi-omics approach combined with loss-of-function experiments we identify a core transcriptional circuit that imparts ear identity, along with non-coding elements that integrate this information. more...
Organism:
Gallus gallus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL23499
8 Samples
Download data: TSV
Series
Accession:
GSE168084
ID:
200168084
17.

Sox8 reprograms ectoderm into ear vesicles and associated neurons [ChIP-seq]

(Submitter supplied) The vertebrate inner ear arises from a pool of progenitors with the potential to give rise to all the sense organs and cranial ganglia of the head1-6. Here we explore the molecular mechanisms that control ear specification from these progenitors. Using a multi-omics approach combined with loss-of-function experiments we identify a core transcriptional circuit that imparts ear identity, along with non-coding elements that integrate this information. more...
Organism:
Gallus gallus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL22626
4 Samples
Download data: BROADPEAK
Series
Accession:
GSE168083
ID:
200168083
18.

Sox8 reprograms ectoderm into ear vesicles and associated neurons [ATAC-seq]

(Submitter supplied) The vertebrate inner ear arises from a pool of progenitors with the potential to give rise to all the sense organs and cranial ganglia of the head1-6. Here we explore the molecular mechanisms that control ear specification from these progenitors. Using a multi-omics approach combined with loss-of-function experiments we identify a core transcriptional circuit that imparts ear identity, along with non-coding elements that integrate this information. more...
Organism:
Gallus gallus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL19005
1 Sample
Download data: NARROWPEAK
Series
Accession:
GSE168082
ID:
200168082
19.

Bulk 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
6 Samples
Download data: TXT
Series
Accession:
GSE199162
ID:
200199162
20.

Changes of miRNA expression profile after avian reovirus infection

(Submitter supplied) We infected DF-1 cells with avian reovirus, and then used high-throughput sequencing to detect changes in miRNA expression profiles. This research provides a more comprehensive understanding of the interaction between viruses and host cells
Organism:
Gallus gallus
Type:
Non-coding RNA profiling by high throughput sequencing
Platform:
GPL24517
2 Samples
Download data: TXT, XLSX
Series
Accession:
GSE181193
ID:
200181193
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