GEO DataSets

(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:

GPL18413

28 Samples

Download data

(Submitter supplied) Brg1 and Brm function as alternative core enzymatic ATPases of SWI/SNF complex in vertebrates, with clear homologs in zebrafish. Brg1 (but not Brm) is required for early cleavage-stage transcription in mice, but where and how Brg1 or Brm impact chromatin in early embryos remains unexplored. Here, we utilize zebrafish embryos to provide the first simultaneous genome-wide profiling of Brg1 and Brm occupancy in any organism/cell type, alongside our profiling of open chromatin and RNA polymerase II. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18413

5 Samples

Download data: XLSX

(Submitter supplied) Brg1 and Brm function as alternative core enzymatic ATPases of SWI/SNF complex in vertebrates, with clear homologs in zebrafish. Brg1 (but not Brm) is required for early cleavage-stage transcription in mice, but where and how Brg1 or Brm impact chromatin in early embryos remains unexplored. Here, we utilize zebrafish embryos to provide the first simultaneous genome-wide profiling of Brg1 and Brm occupancy in any organism/cell type, alongside our profiling of open chromatin and RNA polymerase II. more...

Organism:

Danio rerio

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18413

23 Samples

Download data: BW

(Submitter supplied) Melanogenesis is the biological process regulating the synthesis of melanin pigments in melanocytes. Defective melanogenesis is associated with numerous human skin diseases, including, but not limited to, albinism, vitiligo, melasma, hypo- and hyperpigmentation disorders. Tyrosinase is the rate-limiting enzyme controlling melanogenesis, and hence tremendous efforts have been made to identify potent and safe inhibitors of tyrosinase function. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20828

24 Samples

Download data: TXT

(Submitter supplied) Li-Fraumeni syndrome (LFS) is a hereditary cancer predisposition syndrome associated with a highly penetrant and diverse tumor spectrum characterized by germline mutations in the TP53 tumor suppressor gene. To better understand how TP53 mutations predispose individuals with LFS to cancer development, we characterized tp53 R217H and R242H zebrafish lines as the first zebrafish p53 hotspot mutants (human R248 and R273H). more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24995

24 Samples

Download data: TXT

(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

(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

(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

(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

(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

(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

(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

(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

(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

(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

(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

(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

(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

(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

(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