GEO DataSets

(Submitter supplied) Mycobacterial granulomas lie at the center of tuberculosis (TB) pathogenesis and represent a unique niche where infecting bacteria survive in nutrient-restricted conditions and in the face of a host immune response. The granuloma’s necrotic core, where bacteria reside extracellularly in humans, is difficult to assess in many experimentally tractable models. Here, using necrotic mycobacterial granulomas in adult zebrafish, we develop dual RNA-seq across different host genotypes to profile transcriptional alterations that enable bacteria to survive and take advantage of host immune responses. more...

Organism:

Mycobacterium marinum; Danio rerio

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL35418 GPL29034

17 Samples

Download data: TSV

(Submitter supplied) Climate change increases both the frequency and duration of heat events. Direct negative effects of such heat stress may be exacerbated through heat-induced stress propagation (via stress metabolites) between aquatic animals. Whilst early life stages are vulnerable to stress-induced damage, they also deploy cellular mechanisms to protect cells against their naturally mutagenic environment. Little is known about the fate and performance of fish embryos which have experienced direct or indirect heat stress in a mutagenic environment. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24995

12 Samples

Download data: TAB

(Submitter supplied) Zebrafish heart regeneration is a complex process consisting of tempo-spatial coordination of cardiomyocyte (CM) and endothelial cell (EC) regeneration, fibrosis and inflammation. While myocardial, endocardial, and epicardial signaling have been reported to modulate this process, little is known about how leukocyte especially platelet signaling is involved in this regenerative process. Here we report that cloche/npas4l (neuronal PAS domain protein 4 like) is a pro-regenerative platelet factor for adult zebrafish heart regeneration. more...

Organism:

Danio rerio

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24995

2 Samples

Download data: NARROWPEAK

(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

18 Samples

Download data: MTX, TSV, TXT

(Submitter supplied) Zebrafish heart regeneration is a complex process consisting of tempo-spatial coordination of cardiomyocyte (CM) and endothelial cell (EC) regeneration, fibrosis and inflammation. While myocardial, endocardial, and epicardial signaling have been reported to modulate this process, little is known about how leukocyte especially platelet signaling is involved in this regenerative process. Here we report that cloche/npas4l (neuronal PAS domain protein 4 like) is a pro-regenerative platelet factor for adult zebrafish heart regeneration. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24995

6 Samples

Download data: MTX, TSV

(Submitter supplied) Zebrafish heart regeneration is a complex process consisting of tempo-spatial coordination of cardiomyocyte (CM) and endothelial cell (EC) regeneration, fibrosis and inflammation. While myocardial, endocardial, and epicardial signaling have been reported to modulate this process, little is known about how leukocyte especially platelet signaling is involved in this regenerative process. Here we report that cloche/npas4l (neuronal PAS domain protein 4 like) is a pro-regenerative platelet factor for adult zebrafish heart regeneration. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24995

10 Samples

Download data: TXT

(Submitter supplied) The objectives of this study were to identify biomarkers for teratogenic response in a dose and time resolved manner and align the findings with morphological alterations found ZET assay. For this purpose triadimefon was selected as a model compound with teratogenic effects and known mode of action.

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24995

57 Samples

Download data: TXT

(Submitter supplied) The meninges are a set of connective tissue layers that surround the central nervous system, protecting the brain from mechanical shock, supporting its buoyancy, guarding it from infection and injury, and maintaining brain homeostasis. Despite their critical role, the molecular identity, developmental origins, and functional properties of the cell types populating the meninges remain poorly characterized. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24995

2 Samples

Download data: H5

(Submitter supplied) Splicing is a complex process, required to create the transcriptomic diversity needed for specialised functions in higher eukaryotes. The spliceosome contains more than 100 proteins and RNA molecules which coordinate this dynamic process, and interestingly, despite the ubiquity of splicing, pathogenic variants in spliceosomal components often cause a tissue-specific phenotype, hinting at further complexities which are not yet fully understood. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24995

6 Samples

Download data: TXT

(Submitter supplied) The generation of self-tolerant repertoires of T cells depends on the expression of peripheral self antigens in the thymic epithelium, and the presence of small populations of cells mimicking the diverse phenotypes of peripheral tissues. Whereas the molecular underpinnings of self-antigen expression have been extensively studied, the developmental origins and differentiation pathways of thymic mimetic cells remain to be identified. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24995

6 Samples

Download data: TSV

(Submitter supplied) Spatial transcriptome sequencing technology has provided high-resolution transcriptome data for studying the molecular mechanism of Tau P301S mediating Alzheimer's disease-like pathological changes in zebrafish, providing a unique insight into the pathogenesis of tau pathology-mediated cell-cell interactions in AD.

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30277

4 Samples

Download data: GEF, H5, JPG, TAR

(Submitter supplied) Cytochrome P450 1B1 (CYP1B1) is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma (PCG), however CYP1B1’s role in PCG development and related eye disorders is poorly understood. To explore CYP1B1’s role an in vivo zebrafish (Danio rerio) model was used. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30614

40 Samples

Download data: CSV

(Submitter supplied) Circadian clocks temporally orchestrate the behavioural and physiological rhythms. The core molecules establishing the circadian clock are clear; however, the critical signalling pathways that cause or favour the homeostasis are poorly understood. Here, we report that anti-Müllerian hormone (Amh)-mediated signalling plays an important role in sustaining circadian homeostasis in zebrafish. Remarkably, amh knockout dampens molecular clock oscillations and disrupts both behavioural and hormonal circadian rhythms, which were recapitulated in bmpr2a null mutants. more...

Organism:

Danio rerio

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24995

12 Samples

Download data: BW

(Submitter supplied) Circadian clocks temporally orchestrate the behavioural and physiological rhythms. The core molecules establishing the circadian clock are clear; however, the critical signalling pathways that cause or favour the homeostasis are poorly understood. Here, we report that anti-Müllerian hormone (Amh)-mediated signalling plays an important role in sustaining circadian homeostasis in zebrafish. Remarkably, amh knockout dampens molecular clock oscillations and disrupts both behavioural and hormonal circadian rhythms, which were recapitulated in bmpr2a null mutants. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20828

2 Samples

Download data: MTX, TSV

(Submitter supplied) Understanding how mechanical stimulation affects cellular behaviors during tissue regeneration offers valuable insight into the mechanisms that regulate injury repair. We incorporated a swim tunnel exercise regimen during zebrafish caudal fin regeneration to explore exercise loading impacts on a robust model of tissue regeneration. Early exercise loading, initiated before or during blastema formation, resulted in reduced regenerative outcomes. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24995

10 Samples

Download data: H5

(Submitter supplied) Shwachman-Diamond syndrome (SDS) is characterized by neutropenia, exocrine pancreatic insufficiency, and bony abnormalities with an increased risk of myeloid neoplasia. Almost all cases of SDS result from biallelic mutations in SBDS. SBDS interacts with EFL1 to displace EIF6 from the 60S ribosomal subunit. Released EIF6 permits the assembly of ribosomal large and small subunits in the cytoplasm. Decreased EIF6 levels due to haploinsufficiency or missense mutations which lead to decreased protein expression may provide a somatic genetic rescue and anti-leukemic effects. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24776

6 Samples

Download data: XLSX

(Submitter supplied) CCSER1, a gene with limited prior knowledge in neurological conditions has emerged as a potential tumor suppressor and regulator of neurodevelopment. Our analysis reveals that CCSER1 downregulation correlates with down regulation of DNA repair and DNA replication pathways and up regulation of neurodevelopmental pathways, including calcium signaling and neuroactive ligand-receptor interaction, in CCSER1-deficient zebrafish. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16509

29 Samples

Download data: TXT

(Submitter supplied) Regeneration and homeostatic turnover of solid tissues depend on the proliferation of symmetrically dividing adult stem cells, which either remain stem cells or differentiate based on their niche position. Here we demonstrate that in zebrafish lateral line sensory organs, stem and progenitor cell proliferation are independently regulated by two cyclinD genes. Loss of ccnd2a impairs stem cell proliferation during development, while loss of ccndx disrupts hair cell progenitor proliferation but allows normal differentiation. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30614

4 Samples

Download data: H5

(Submitter supplied) Successful initiation of animal development requires activation of the egg immediately prior to fusion of gamete pronucleii. In all taxa, this is initiated by waves of calcium transients which transverse across the egg. Calcium waves also occur at cleavage furrows during later blastula cytokinesis. Calcium is released from the endoplasmic reticulum through activation of 1,4,5-trisphosphate (IP3) receptors. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24995

9 Samples

Download data: XLS

(Submitter supplied) Proteins without transmembrane domains could be anchored to the cell surface for regulating various biological processes when covalently linked to glycosylphosphatidylinositol (GPI) molecules by the GPI transamidase (GPIT) complex. However, it remains poorly understood whether and how the GPIT complex affects primordial germ cell (PGC) development. In this study, we report the important roles of GPI transamidase in PGC migration and development in zebrafish embryos. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20828

8 Samples

Download data: TXT