GEO DataSets

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL21741 GPL20828

16 Samples

Download data: TSV, TXT

(Submitter supplied) Quality control of translation is crucial for maintaining cellular and organismal homeostasis. Obstacles in translation elongation induce ribosome collision, which is monitored by multiple sensor mechanisms in eukaryotes. The E3 ubiquitin ligase Znf598 recognizes collided ribosomes, triggering ribosome-associated quality control (RQC) to rescue stalled ribosomes and no-go decay (NGD) to degrade stall-prone mRNAs. more...

Organism:

Danio rerio

Type:

Other; Expression profiling by high throughput sequencing

Platform:

GPL21741

4 Samples

Download data: TXT

(Submitter supplied) The FAM83 (Family with sequence similarity 83) family is highly conserved in vertebrates, yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family, FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed, two pathways often dysregulated in disease. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21741

54 Samples

Download data: RESULTS

(Submitter supplied) Artificially sweetened beverages containing noncaloric monosaccharides were suggested as healthier alternatives to sugar-sweetened beverages. Nevertheless, the potential detrimental effects of these noncaloric monosaccharides on blood vessel function remain inadequately understood. Presently, we have established a zebrafish model that exhibits significant excessive angiogenesis induced by high glucose. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21741

2 Samples

Download data: MTX, TSV

(Submitter supplied) Mutations in the transcription factor EBF3 results in a neurodevelopmental disorder, and studies in animal models indicate that it has a critical role in neuronal differentiation. The molecular pathways and neuron types disrupted by its loss, however, have not been thoroughly investigated. Nor have the outcomes of these changes on behavior and brain activity. Here, we generated and characterized a zebrafish ebf3a loss-of-function mutant. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21741

10 Samples

Download data: TXT

(Submitter supplied) Neural crest cells give rise to the neurons of the enteric nervous system (ENS) that innervate the gastrointestinal tract to regulate gut motility. The immense size and distinct subregions of the gut present a challenge to understanding the spatial organization and sequential differentiation of different neuronal subtypes. Here, we profile enteric neurons and progenitors at single cell resolution during zebrafish embryonic and larval development to provide a near complete picture of transcriptional changes that accompany emergence of ENS neurons throughout the gastrointestinal tract. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21741

5 Samples

Download data: H5AD

(Submitter supplied) The innate immune response is triggered rapidly after injury and its spatiotemporal dynamics are critical for regeneration, but many questions remain about its exact role. Here we show that MyD88, a key component of the innate immune response, controls not only the inflammatory but also the fibrotic response during zebrafish cardiac regeneration. We find in cryoinjured myd88-/- ventricles a significant reduction in neutrophil and macrophage numbers as well as the expansion of a collagen-rich endocardial population. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21741

6 Samples

Download data: TXT

(Submitter supplied) Craniofacial dysmorphisms are among the most common birth defects. Proteasome mutations frequently result in craniofacial dysmorphisms including lower jaw malformations; however, the underlying mechanisms are unknown. Here we use a zebrafish proteasome subunit beta 1 (psmb1) mutant to define the cellular mechanisms underlying proteasome mutation-induced craniofacial dysmorphisms. psmb1 mutants exhibit a flattened ceratohyal and smaller Meckel’s and palatoquadrate cartilages. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL21741 GPL24995

14 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Danio rerio; Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platforms:

GPL21741 GPL20301 GPL20828

40 Samples

Download data: NARROWPEAK, TSV

(Submitter supplied) Developmental signaling pathways associated with growth factors such as TGFb are commonly dysregulated in melanoma. Here we identified a human TGFb enhancer that was specifically activated in melanoma cells treated with TGFB1 ligand. We generated stable transgenic zebrafish with this enhancer driving green fluorescent protein (TIE:EGFP). EGFP was not expressed in normal melanocytes or early melanomas but was expressed in spatially distinct regions of mature melanomas. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21741

6 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Danio rerio; Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing; Other; Expression profiling by high throughput sequencing

5 related Platforms

34 Samples

Download data: BED, BW, COOL, NARROWPEAK, TXT

(Submitter supplied) The existence of homologies between fins and tetrapod limb skeletal parts as well as of the nature of those mechanisms underlying the transition of the former towards the latter, have been a rich source of discussion for more than a century. While the recent use of gene expression patterns to try and infer evolutionary scenarios has been a popular and successful approach, in particular the distribution of Hox transcript domains, it has failed to provide clearcut evidence as to whether fishes do have bony elements related by ancestry to tetrapod hands and feet. more...

Organism:

Danio rerio

Type:

Other

Platform:

GPL21741

3 Samples

Download data: BW, NARROWPEAK

(Submitter supplied) The existence of homologies between fins and tetrapod limb skeletal parts as well as of the nature of those mechanisms underlying the transition of the former towards the latter, have been a rich source of discussion for more than a century. While the recent use of gene expression patterns to try and infer evolutionary scenarios has been a popular and successful approach, in particular the distribution of Hox transcript domains, it has failed to provide clearcut evidence as to whether fishes do have bony elements related by ancestry to tetrapod hands and feet. more...

Organism:

Danio rerio; Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL19057 GPL20828 GPL21741

14 Samples

Download data: BW, NARROWPEAK

(Submitter supplied) Wound healing is impaired by infection; however, how microbe-induced inflammation modulates tissue repair remains unclear. We took advantage of the optical transparency of zebrafish and a genetically tractable microbe, Listeria monocytogenes, to probe the role of infection and inflammation in wound healing. We found a critical window of microbial clearance necessary to limit persistent inflammation and enable efficient wound repair. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21741

9 Samples

Download data: RESULTS

(Submitter supplied) Adult stem cells are important for tissue turnover and regeneration. However, in most adult systems it remains elusive how stem cells assume different functional states and support spatially patterned tissue architecture. Here, we dissected the diversity of neural stem cells in the adult zebrafish brain, an organ that is characterized by pronounced zonation and high regenerative capacity. We combined single-cell transcriptomics of dissected brain regions with massively parallel lineage tracing and in vivo RNA metabolic labeling to analyze regulation of neural stem cells in space and time. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing; Other

4 related Platforms

39 Samples

Download data: CSV, LOOM, MTX, TSV

(Submitter supplied) Each organ of the human body requires locally-adapted blood vessels. The gain of such organotypic vessel specializations is often deemed molecularly unrelated to the process of organ vascularization. Opposing this model, we reveal a molecular mechanism for brain-specific angiogenesis, that operates under the control of Wnt7a/b ligands, well-known blood-brain barrier maturation signals. The control mechanism relies on Wnt7a/b-dependent expression of Mmp25 in brain endothelial cells. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL23274 GPL21741

3 Samples

Download data: TXT, XLSX

(Submitter supplied) This study aimed at understanding the function of Akt signaling in vascular development in Zebrafish.

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21741

2 Samples

Download data: MTX, TSV

(Submitter supplied) Cypermethrin (CYP) and chlorpyrifos (CPF) are pesticides which are frequently used in agricultural areas around the world. These chemicals have been shown to cause serious toxicological damage in the brain of fish, which is non-target organisms. However, circRNAs associated with acute brain toxicity caused by cypermethrin and chlorpyrifos have not been studied yet. In this study, circRNAs were identified and characterized using RNA-seq in Zebrafish brains exposed to acute cypermethrin and chlorpyrifos toxicity. more...

Organism:

Danio rerio

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL21741

9 Samples

Download data: XLSX

(Submitter supplied) The histone variant H2A.Z is central to early embryonic development, determining transcriptional competency through chromatin regulation of gene promoters and enhancers. In addition to genic loci, we find that H2A.Z resides at a subset of evolutionarily young repetitive elements, including DNA transposons, LINEs, and LTRs, during early zebrafish development. Moreover, increases in H2A.Z occur when repetitive elements become transcriptionally active. more...

Organism:

Danio rerio

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21741

6 Samples

Download data: BW

(Submitter supplied) The histone variant H2A.Z is central to early embryonic development, determining transcriptional competency through chromatin regulation of gene promoters and enhancers. In addition to genic loci, we find that H2A.Z resides at a subset of evolutionarily young repetitive elements, including DNA transposons, LINEs, and LTRs, during early zebrafish development. Moreover, increases in H2A.Z occur when repetitive elements become transcriptionally active. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21741

12 Samples

Download data: BW, TXT