GEO DataSets

(Submitter supplied) The splicing factor Bcas2 is involved in several biological processes including tumorigenesis, gametogenesis, and hematopoiesis. The alternative splicing events and downstream genes regulated by Bcas2 have not yet been investigated at the transcriptome level in zebrafish. In this study, we conducted RNA-sequencing analysis on the WT and bcas2 knockout zebrafish embryos (3 dpf) to identify the global differentially expressed genes (DEGs) and differential splicing events (DSEs). more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL14875

6 Samples

Download data: TXT

(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

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

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL14875

24 Samples

Download data

(Submitter supplied) Gene functional study and the emerging mRNA therapy technology heavily rely on in vitro transcribed (IVT) mRNA, but the double-stranded RNA (dsRNA) by-product generated during IVT is often recognized by cells as a marker of virus replication, leading to the integrated stress response (ISR).The biological effects of dsRNA in undifferentiated cells differ significantly from those of differentiated counterparts.Here, we found that dsRNA triggered an unprecedented ISR in zebrafish early embryos, leading to developmental delay, severe cell necrosis, and lethal malformations.Mechanistically, dsRNA stimulation caused a PKR-eIF2α independent global translation inhibition and a burst of p53 signaling. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL14875

12 Samples

Download data: TXT

(Submitter supplied) Gene functional study and the emerging mRNA therapy technology heavily rely on in vitro transcribed (IVT) mRNA, but the double-stranded RNA (dsRNA) by-product generated during IVT is often recognized by cells as a marker of virus replication, leading to the integrated stress response (ISR).The biological effects of dsRNA in undifferentiated cells differ significantly from those of differentiated counterparts.Here, we found that dsRNA triggered an unprecedented ISR in zebrafish early embryos, leading to developmental delay, severe cell necrosis, and lethal malformations.Mechanistically, dsRNA stimulation caused a PKR-eIF2α independent global translation inhibition and a burst of p53 signaling. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL14875

12 Samples

Download data: XLS, XLSX

(Submitter supplied) We have evaluated the possible use of zebrafish to study antiviral RNAi with sindbis virus (SINV), vesicular stomatitis virus (VSV), and nodamura virus (NoV). We find that SINV and NoV viruses induce the production of virus-derived small interfering RNAs (vsiRNAs), the hallmark of antiviral RNAi, with a preference of 22 nucleotides in length after infection of larval zebrafish. Meanwhile, the suppressor of RNAi (VSR) protein, NoV B2, may affect the accumulation of the NoV virus in zebrafish.

Organism:

Danio rerio

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL14875 GPL18413

5 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; Methylation profiling by high throughput sequencing

Platforms:

GPL14875 GPL18413

12 Samples

Download data: TXT

(Submitter supplied) Myelodysplastic Syndrome (MDS) is a heterogenous group of clonal hematopoietic disorders characterized by ineffective hematopoiesis, cytopenias and dysplasia. The gene encoding Ten-ele¬ven translocation 2 (TET2), a dioxygenase enzyme that catalyzes the conversion of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine, is a recurrently mutated tumor suppressor gene in MDS and other myeloid malignancies. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL14875

4 Samples

Download data: TXT

(Submitter supplied) The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules, yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm-generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL14875

1536 Samples

Download data: CSV, RDS, TXT

(Submitter supplied) Wastewater treatment plant (WWTP) effluent-dominated streams provide critical habitat for aquatic and terrestrial organisms but also continually expose them to complex mixtures of pharmaceuticals that can potentially impair growth, behavior, and reproduction. Currently, few biomarkers are available that relate to pharmaceutical-specific mechanisms of action. In the experiment reported in this paper, zebrafish (Danio rerio) embryos at two developmental stages were exposed to water samples from three sampling sites (0.1 km upstream of the outfall, at the effluent outfall, and 0.1 km below the outfall) during base-flow conditions from two months (January and May) of a temperate-region effluent-dominated stream containing a complex mixture of pharmaceuticals and other contaminants of emerging concern. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL14875

58 Samples

Download data: TSV

(Submitter supplied) We used single cell RNA sequencing to analyze the diversity of intestinal cells under conventional conditions and the effect of an acute, natural Vibrio cholerae infection on the intestinal transcriptome.

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL14875

2 Samples

Download data: MTX, TSV

(Submitter supplied) we profiled chromatin accessibility of zebrafish endothelial cells after amputation injury and identify an mmp14b endothelial enhancer induced by heart injury in zebrafish. We show that the enhancer is required for mmp14b expression and regeneration in response to heart injury. Moreover, the enhancer depends on a consensus TEAD-binding motif, suggesting a role for Hippo signaling upstream of mmp14b.

Organism:

Danio rerio

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL14875

9 Samples

Download data: BIGWIG

(Submitter supplied) We compare mettl4 KO and WT samples from different species to understand how mettl4 affects the alterative splicing

Organism:

Homo sapiens; Schizosaccharomyces pombe; Danio rerio; Drosophila melanogaster; Mus musculus

Type:

Expression profiling by high throughput sequencing

5 related Platforms

23 Samples

Download data: MATRIX

(Submitter supplied) RNA surveillance pathways detect and degrade defective transcripts to ensure RNA fidelity. We find disrupted nuclear RNA surveillance is oncogenic. Cyclin Dependent Kinase 13 (CDK13) is mutated in melanoma and patient-mutated CDK13 accelerates zebrafish melanoma. CDK13 mutation causes aberrant RNA stabilization. CDK13 is required for ZC3H14 phosphorylation, which is necessary and sufficient to promote nuclear RNA degradation. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL14875

6 Samples

Download data: TXT

(Submitter supplied) RNA surveillance pathways detect and degrade defective transcripts to ensure RNA fidelity. We find disrupted nuclear RNA surveillance is oncogenic. Cyclin Dependent Kinase 13 (CDK13) is mutated in melanoma and patient-mutated CDK13 accelerates zebrafish melanoma. CDK13 mutation causes aberrant RNA stabilization. CDK13 is required for ZC3H14 phosphorylation, which is necessary and sufficient to promote nuclear RNA degradation. more...

Organism:

Mus musculus; Danio rerio; Homo sapiens

Type:

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

4 related Platforms

87 Samples

Download data: BW, TXT

(Submitter supplied) RNA surveillance pathways detect and degrade defective transcripts to ensure RNA fidelity. We find disrupted nuclear RNA surveillance is oncogenic. Cyclin Dependent Kinase 13 (CDK13) is mutated in melanoma and patient-mutated CDK13 accelerates zebrafish melanoma. CDK13 mutation causes aberrant RNA stabilization. CDK13 is required for ZC3H14 phosphorylation, which is necessary and sufficient to promote nuclear RNA degradation. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL14875

9 Samples

Download data: TXT

(Submitter supplied) RNA surveillance pathways detect and degrade defective transcripts to ensure RNA fidelity. We find disrupted nuclear RNA surveillance is oncogenic. Cyclin Dependent Kinase 13 (CDK13) is mutated in melanoma and patient-mutated CDK13 accelerates zebrafish melanoma. CDK13 mutation causes aberrant RNA stabilization. CDK13 is required for ZC3H14 phosphorylation, which is necessary and sufficient to promote nuclear RNA degradation. more...

Organism:

Danio rerio

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL14875

6 Samples

Download data: BW

(Submitter supplied) RNA-seq of 6 samples, 3 of them are Ttdmt1 knockout in zebrafish named ZF-TKO and 3 of them are control group named ZF-Control.

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL14875

6 Samples

Download data: TXT

(Submitter supplied) Meckel Syndrome, Nephronophthisis, Joubert Syndrome, and Bardet-Biedl Syndrome have mutations in proteins that localize to the ciliary transition zone (TZ). The phenotypically distinct syndromes suggest these TZ proteins have differing functions. However, mutations in a single TZ gene can result in multiple syndromes suggesting the phenotype is influenced by modifier genes. We performed a comprehensive analysis of ten zebrafish TZ mutants including mks1, tmem216, tmem67, rpgrip1l, cc2d2a, b9d2, cep290, tctn1, nphp1, and nphp4, as well as mutants in ift88 and ift172. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL14875

26 Samples

Download data: TXT

(Submitter supplied) Certain cranial neural crest cells are uniquely endowed with the ability to make skeletal cell types otherwise only derived from mesoderm. As these cells migrate into the pharyngeal arches, they downregulate neural crest specifier genes and upregulate so-called ectomesenchyme genes characteristic of skeletal progenitors. While both external and cell-autonomous factors have been proposed as triggers of this transition, the details remain obscure. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL14875

4 Samples

Download data: TXT