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Items: 1 to 20 of 45554

1.

Increase in ER-mitochondria contacts and mitochondrial fusion are hallmarks of mitochondrial activation during embryogenesis

(Submitter supplied) Mitochondrial energy production is essential for development, yet the mechanisms underlying the continuous increase in mitochondrial activity during embryogenesis remain elusive. Using zebrafish as a model system for vertebrate development, we identify two sequentially acting mechanisms that could contribute to the rise in mitochondrial activity: an increased association between mitochondria and the endoplasmic reticulum (ER) at early stages, followed by the fusion of mitochondria leading to their elongated morphology at later embryonic stages. more...
Organism:
Danio rerio
Type:
Expression profiling by high throughput sequencing
Platform:
GPL30614
24 Samples
Download data: TSV
Series
Accession:
GSE267318
ID:
200267318
2.

Transcriptional profiles of venous and lymphatic endothelial cells from tie1 mutant zebrafish

(Submitter supplied) To investigate what kind of gene expression is regulated downstream of Tie1 signaling, we performed RNA-seq analyses on venous and lymphatic endothelial cells (ECs) between homozygous tie1 mutant embryos and their wild-type and heterozygous siblings during secondary sprouting, respectively. Our analyses indicate that Tie1 signaling controls a series of gene expression involved in lymphatic development including EC migration, proliferation, and differentiation.
Organism:
Danio rerio
Type:
Expression profiling by high throughput sequencing
Platform:
GPL20828
4 Samples
Download data: CSV
Series
Accession:
GSE240329
ID:
200240329
3.

Transcriptomic analysis of 52 hpf mbd5 KO & KD embryos and 7 dpf mb5 KO & OE larves

(Submitter supplied) To dissect the molecular function of mbd5 in zebrafish embryonic development, we carried out transcriptomic analyses at those two developmental stages.
Organism:
Danio rerio
Type:
Expression profiling by high throughput sequencing
Platform:
GPL23085
14 Samples
Download data: TXT
Series
Accession:
GSE225204
ID:
200225204
4.

MBD5, a m5C RNA reader, regulates histone ubiquitylation in development and function

(Submitter supplied) Methyl-CpG-binding domain (MBD)-containing proteins are readers of epigenetic information. The founding member, MeCP2, mutated in the Rett Syndrome, binds to methylated CpG DNAs. MBD5 is an evolutionarily conserved MBD family member associated with epilepsy, autism spectrum disorders (ASD), and early onset dementia. The mechanism of action of MBD5 remains unclear. Here we report that mbd5 regulates embryonic development, erythrocyte differentiation, iron metabolism, and behavior in zebrafish. more...
Organism:
Danio rerio
Type:
Expression profiling by high throughput sequencing; Other
Platform:
GPL24995
18 Samples
Download data: XLSX
Series
Accession:
GSE222803
ID:
200222803
5.

Integration of ATAC and RNA-Sequencing identifies chromatin and transcriptomic signatures in classical and non-classical zebrafish osteoblasts and indicates mechanisms of entpd5a regulation [RNA]

(Submitter supplied) Two types of osteoblasts are required to assemble the zebrafish embryonic skeleton: classical osteoblasts homologous to the mammalian situation, and notochord sheath cells, which serve as non-classical osteoblasts. The gene entpd5a is critically required for ossification via both types of osteoblasts. Despite the usefulness of zebrafish models in vertebrate research, the genetic regulation of bone formation, as well as mechanisms of transcriptional control of entpd5a, remain largely unknown. more...
Organism:
Danio rerio
Type:
Expression profiling by high throughput sequencing
Platform:
GPL24995
12 Samples
Download data: TXT
Series
Accession:
GSE267333
ID:
200267333
6.

Integration of ATAC and RNA-Sequencing identifies chromatin and transcriptomic signatures in classical and non-classical zebrafish osteoblasts and indicates mechanisms of entpd5a regulation [ATAC]

(Submitter supplied) Two types of osteoblasts are required to assemble the zebrafish embryonic skeleton: classical osteoblasts homologous to the mammalian situation, and notochord sheath cells, which serve as non-classical osteoblasts. The gene entpd5a is critically required for ossification via both types of osteoblasts. Despite the usefulness of zebrafish models in vertebrate research, the genetic regulation of bone formation, as well as mechanisms of transcriptional control of entpd5a, remain largely unknown. more...
Organism:
Danio rerio
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL20828
12 Samples
Download data: BED
Series
Accession:
GSE267332
ID:
200267332
7.

Valbenazine promotes body growth via growth hormone signaling during zebrafish embryonic development

(Submitter supplied) To study the embryonic developmental toxicity of a VMAT-2 inhibitor Valbenazine (VBZ).
Organism:
Danio rerio
Type:
Expression profiling by high throughput sequencing
Platform:
GPL24995
2 Samples
Download data: TXT
Series
Accession:
GSE232468
ID:
200232468
8.

Differential expression in Muller glia of injured zebrafish in a mycb-/- context

(Submitter supplied) This experiment studies retinal regeneration using a zebrafish model with a focus on Muller glia reprogramming.
Organism:
Danio rerio
Type:
Expression profiling by high throughput sequencing
Platform:
GPL24995
6 Samples
Download data: TXT
Series
Accession:
GSE249116
ID:
200249116
9.

Differential expression in Muller glia of injured zebrafish in a mych-/- context

(Submitter supplied) This experiment studies retinal regeneration using a zebrafish model with a focus on Muller glia reprogramming.
Organism:
Danio rerio
Type:
Expression profiling by high throughput sequencing
Platform:
GPL24995
9 Samples
Download data: TXT
Series
Accession:
GSE249115
ID:
200249115
10.

Differential expression in Zebrafish retinal muller glia under injured and knockout

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Danio rerio
Type:
Expression profiling by high throughput sequencing
Platform:
GPL24995
15 Samples
Download data
Series
Accession:
GSE249117
ID:
200249117
11.

Single-cell transcriptome profiling of zebrafish pancreatic beta-cells segregated by CaMPARI-based calcium labeling.

(Submitter supplied) Coordination of cell activity trough Ca2+ waves enables pancreatic β-cells to secrete precise quantities of insulin in response to blood sugar. However, how the coordinating Ca2+ waves are orchestrated in space and time remains unknown. By applying functional Ca2+ imaging using CaMPARI and single-molecule RNA detection, we reveal a gene-signature depicting a molecularly and metabolically distinct state of first responder β-cells. more...
Organism:
Danio rerio
Type:
Expression profiling by high throughput sequencing
Platform:
GPL20828
191 Samples
Download data: CSV
Series
Accession:
GSE237867
ID:
200237867
12.

The evolutionarily conserved zebrafish choroid plexus maintains the size of brain ventricles

(Submitter supplied) The choroid plexus produces cerebrospinal fluid (CSF) by transport of electrolytes and water from the vasculature to the brain ventricles. The choroid plexus plays additional roles in brain development and homeostasis by secreting neurotrophic molecules, and by serving as a CSF-blood barrier and immune interface. Prior studies have identified transporters on the epithelial cells that transport water and ions into the ventricles and tight junctions involved in the CSF-blood barrier. more...
Organism:
Danio rerio
Type:
Expression profiling by high throughput sequencing
Platform:
GPL24995
2 Samples
Download data: CSV, TXT
Series
Accession:
GSE246851
ID:
200246851
13.

Single cell sequencing data of zebrafish spinal cord injury

(Submitter supplied) After spinal cord injury in adult zebrafish, the spinal cord was taken out for single-cell data sequencing
Organism:
Danio rerio
Type:
Expression profiling by high throughput sequencing
Platform:
GPL24995
3 Samples
Download data: MTX, TSV
Series
Accession:
GSE202429
ID:
200202429
14.

CUT&Tag Reveals a Return of Embryonic H3K4me3 Patterns During Zebrafish Tail Fin Regeneration

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Danio rerio
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL24995
20 Samples
Download data: BW
Series
Accession:
GSE261540
ID:
200261540
15.

CUT&Tag Reveals a Return of Embryonic H3K4me3 Patterns During Zebrafish Tail Fin Regeneration (RNA-Seq)

(Submitter supplied) The regenerative potential is governed by a complex process of transcriptional reprogramming, involving nuclear reorganization and dynamics in transcription factor binding patterns throughout the genome. The degree to which chromatin and epigenetic changes influence this process remains only partially understood. Here we provide a modified CUT&Tag protocol suitable for improved characterization and interrogation of epigenetic changes during of zebrafish caudal fin regeneration. more...
Organism:
Danio rerio
Type:
Expression profiling by high throughput sequencing
Platform:
GPL24995
2 Samples
Download data: BW
Series
Accession:
GSE261539
ID:
200261539
16.

CUT&Tag Reveals a Return of Embryonic H3K4me3 Patterns During Zebrafish Adult Tail Fin Regeneration (CUT&Tag)

(Submitter supplied) Regenerative potential is governed by a complex process of transcriptional reprogramming, involving chromatin reorganization and dynamics in transcription factor binding patterns throughout the genome. The degree to which chromatin and epigenetic changes contribute to this process remains partially understood. Here we provide a modified CUT&Tag protocol suitable for improved characterization and interrogation of epigenetic changes during adult fin regeneration in zebrafish. more...
Organism:
Danio rerio
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL24995
18 Samples
Download data: BW
Series
Accession:
GSE261538
ID:
200261538
17.

New insights into benzo[⍺]pyrene osteotoxicity in zebrafish

(Submitter supplied) Persistent and ubiquitous organic pollutants, such as the polycyclic aromatic hydrocarbon benzo[⍺]pyrene (BaP), represent a major threat to aquatic organisms and human health. Beside some well-documented adverse effects on the development and reproduction of aquatic organisms, BaP was recently shown to affect fish bone formation and skeletal development through mechanisms that remain poorly understood. more...
Organism:
Danio rerio
Type:
Expression profiling by high throughput sequencing
Platform:
GPL20828
2 Samples
Download data: TXT
Series
Accession:
GSE174529
ID:
200174529
18.

Double-stranded RNA triggers a distinct integrated stress response in the early embryo [RNA-seq, Ribo-seq]

(Submitter supplied) Double-stranded RNA (dsRNA) is associated with virus infections and is present as by-products during the transcription of synthetic mRNA, which has been widely used in gene gain-of-function studies and serves as a core component in emerging mRNA-based therapies1-4. The presence of dsRNA in host cells induces an integrated stress response that functions to prevent virus replication and infection5,6. Unlike differentiated cells, undifferentiated cells adopt a distinct defense strategy against RNA virus infection7, but the mechanism is unclear. We show a previously unidentified response triggered by dsRNA in the early embryo. Although dsRNA causes a global protein translation inhibition in a PKR-eIF2α independent manner and leads to developmental delay and cell necrosis, it also strongly induces p53 activation, which then upregulates Interferon Stimulated Genes independently of interferon ligands. Importantly, we demonstrate that the burst of p53 signaling dose not result in cell death but functions as a protective mechanism against deleterious translation blockage by slowing down global protein degradation via ISGylation. Our work has identified a distinct dsRNA-induced stress response in the embryo, reflecting an ancient innate immune memory before the establishment of the IFN system. It also raises the provocative question as to the original protective role of p53 during evolution.
Organism:
Danio rerio
Type:
Expression profiling by high throughput sequencing; Other
Platforms:
GPL24995 GPL14875
20 Samples
Download data: TSV, TXT, XLS
Series
Accession:
GSE265771
ID:
200265771
19.

Trim2b mediates protection against SVCV infection by degrading NLRP12-like and viral SVCV-N/SVCV-G proteins

(Submitter supplied) In the present study, we report the functional characterization of zebrafish trim2b. we show that zebrafish trim2b plays a protective role in the host defense against SVCV infection. During SVCV infection, the in vivo studies revealed that trim2b overexpression led to the decreased virus loads and increased survival rate. Zebrafish trim2b deficiency led to the increased virus loads and decreased survival rate. more...
Organism:
Danio rerio
Type:
Expression profiling by high throughput sequencing
Platform:
GPL24995
12 Samples
Download data: FA, TXT
Series
Accession:
GSE232313
ID:
200232313
20.

Tissue-resident trained immunity in hepatocytes protects septic-liver injury in zebrafish

(Submitter supplied) Trained immunity is classically characterized by long-term epigenetic reprogramming of innate immune cells to combat infectious diseases. Infection-induced organ injury is a common clinical severity phenotype of sepsis. However, whether the induction of trained immunity plays a role in protecting septic-organ injury remains largely unknown. Here, through establishing an in vivo β-glucan training and secondary LPS challenge-induced organ injury model in zebrafish larvae, we observe that induction of trained immunity could inhibit the pyroptosis of hepatocytes to alleviate septic-liver injury, with an elevated epigenetic modification of trimethylation at histone 3 lysine 4 (H3K4me3) that targets mitophagy activation. more...
Organism:
Danio rerio
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL24995
4 Samples
Download data: BW, NARROWPEAK
Series
Accession:
GSE245156
ID:
200245156
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