GEO DataSets

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

Organism:

Mus musculus; Danio rerio

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24995 GPL24247

52 Samples

Download data: H5

(Submitter supplied) Mice respond to myocardial infarction (MI) by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation after the MI resolves. In contrast, zebrafish can fully regenerate their heart after heart injury. To further investigate the divergent species’ responses to cardiac injury, single cell transcriptomic analyses were performed on the heart, blood, liver, kidney, and pancreatic islets.

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24995

24 Samples

Download data: H5

(Submitter supplied) Single cell transcriptome analyses of whole kidney marrow cells isolated from wild type and rad21 heterozygous mutant adult zebrafish.

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24995

4 Samples

Download data: MTX, TSV

(Submitter supplied) Following amputation, zebrafish regenerate their injured caudal fin through lineage-restricted reprogramming. Although previous studies have charted various genetic and epigenetic dimensions of this process, the intricate gene regulatory programs shared by or unique to different regenerating cell types remain under-investigated. Here, we mapped the regulatory landscape of fin regeneration by applying paired snRNA-seq and snATAC-seq on uninjured and regenerating fin. more...

Organism:

Danio rerio

Type:

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

Platform:

GPL24995

20 Samples

Download data: MTX, TBI, TSV

(Submitter supplied) Soil Aquifer Treatment (SAT) is recognized as a cost-effective approach to reduce contaminants of emerging concern (CECs) from Wastewater Treatment Plant (WWTP) effluents. However, its efficiency in removing the associated biological effects is still poorly understood. Here, we evaluated the efficiency of three pilot SAT systems, two of them enhanced with reactive barriers containing different proportions of sand and organic materials, in removing toxicity associated to CECs. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24995

20 Samples

Download data: TXT, XLSX

(Submitter supplied) Autophagy-lysosomal degradation is an evolutionarily conserved process key to cellular homeostasis, differentiation, and stress survival, which is particularly important to the pathophysiology of the cardiovascular system. What is more, both experimental and clinical observations indicate that autophagy-lysosomal degradation affects correct cardiac morphogenesis, and in particular valve development. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24995

4 Samples

Download data: MTX, TSV

(Submitter supplied) Beta cells are remarkably heterogeneous. However, beta cells response to chronic stress at a single cell level remains largely unknown. Here, we used a chemo-genetic model of beta cell excitotoxcity coupled with single cell RNA sequencing to understand beta cells response to chronic stress. Remarkably, we found that a subset of stressed beta cells progressed towards death while the other group evaded the destruction by dedifferentiation. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24995

697 Samples

Download data: TSV

(Submitter supplied) Molecular underpinnings of vertebrate retinal differentiation and maturation are poorly understood, particularly for non-mammalian species. We generated single-cell transcriptome data from the larval zebrafish retina and characterized gene expression diversity among photoreceptor subtypes and their progenitors.

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24995

1 Sample

Download data: MTX, TSV

(Submitter supplied) Time course analysis of tRNA abundance during zebrafish early embryonic development.

Organism:

Danio rerio

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL24995 GPL20828

18 Samples

Download data: CSV

(Submitter supplied) Traumatic brain injuries (TBIs) represent a large global disease burden and can result in several short- and long-term deficits. Treatment for TBIs are limited, however stem cell therapies involving either transplantation of exogenous stem cells or stimulation of endogenous stem cells have been proposed. These approaches possess issues with survival and differentiation of stem/progenitor cells, which highlights the need to elucidate mechanisms necessary for complete regeneration. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24995

28 Samples

Download data: MTX, TSV

(Submitter supplied) Vertebrate spermatogonial stem cells maintain sperm production over the lifetime of an animal but fertility declines with age. While morphological studies have informed our understanding of typical spermatogenesis, the molecular and cellular mechanisms underlying the maintenance and decline of spermatogenesis are not yet understood. We used single-cell RNA sequencing to generate a developmental atlas of the aging zebrafish testis. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24995

18 Samples

Download data: MTX, TSV

(Submitter supplied) The hypoxia signaling pathway controls hypoxia adaptation and tolerance of organisms, which is regulated by multiple mechanisms. Viral infection elicits various pathophysiological responses in the host. However, whether viral infection can affect the hypoxia response is still largely unknown. In this study, we found that Spring viraemia of carp virus (SVCV) infection in zebrafish caused symptoms similar to those in zebrafish under hypoxic conditions. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24995

6 Samples

Download data: TXT

(Submitter supplied) We found that il11a induction in adult zebrafish hearts can initiate regeneration programs, including cardiomyocyte (CM) prolifeartion and vascularization, even in the absence of injury. However, we also found that chronic il11a induction results in collagen deposition in the cortical layer of the ventricle. In conclusion, our studies unveil the regenerative roles of Il11 signaling and provide a potential strategy of dual treatment to improve heart repair.

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24995

14 Samples

Download data: TXT

(Submitter supplied) Integrin alpha–V (ITGAV) forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor β (TGF-β) signaling. We examined three unrelated families with common disease features including two children born with congenital brain anomalies and later development of immune dysregulation, atopy, and colitis, and three fetuses with brain and developmental defects. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24995

18 Samples

Download data: TSV

(Submitter supplied) Development of the vertebrate jaw apparatus depends on highly conserved signaling pathways. Patterning of the lower jaw is driven by Endothelin receptor type A (Ednra) and secreted ligand Endothelin 1 (Edn1). The Ednra signaling pathway establishes the identity of lower jaw progenitors by regulating expression of numerous patterning genes, but the intracellular signaling mechanisms linking receptor activation to gene regulation remains poorly understood. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24995

2 Samples

Download data: MTX, TSV

(Submitter supplied) Ribosome small subunit (SSU) is assembled by the SSU processome which contains approximately 70 non-ribosomal protein factors. The biochemical mechanism for the SSU processome in 18S rRNA processing and maturation has been extensively studied, however, how the SSU processome components enter to the nucleolus has not been systematically investigated. Here we checked the nucleolar localization of 50 human SSU processome components and find that UTP3 and other 24 proteins enter to the nucleolus autonomously. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24995

4 Samples

Download data: TXT

(Submitter supplied) In yeast, Upt3 overexpression caused a de-repression of the silenced genes at different loci, suggesting Utp3 might be involved in regulating gene expression. To this end, we extracted total RNA from the WT and sas10 (zebrafish homolg of yeast utp3) embryos, three biological repeats each, at 5dpf and carried out an RNA-seq analysis. Comparing the gene expression between the WT and sas10 using DESeq2 identified a total of 8574 differentially expressed genes (DEGs), including 4457 downregulated and 4117 upregulated DEGs in the sas10 mutant (criteria adopted: TPM>5 in at least one replicate, fold-change more than 1.5, p-adjust <0.05). more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24995

6 Samples

Download data: CSV, TXT

(Submitter supplied) Wnt signaling plays a fundamental role in the initial patterning and development of the embryo, including in the regulation of convergent extension during gastrulation and the establishment of the dorsal axis. Further, Wnt signaling is a crucial regulator of craniofacial morphogenesis. The relationship between early embryo patterning and craniofacial outcomes warrants further study. The adapter proteins Dact1 and Dact2 modulate the Wnt signaling pathway through binding to Disheveled, however, the distinct roles of Dact1 and Dact2 during embryogenesis remain to be fully elucidated. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24995

10 Samples

Download data: MTX, TSV

(Submitter supplied) 3,3’,5.5’-Tetrabromobisphenol A (TBBPA) is a widely used brominated flame-retardant utilized in the production of electronic devices and plastic paints. The objective of this study is to use zebrafish as a model and determine the effects of TBBPA exposure on early embryogenesis. We initiated TBBPA exposures (0, 10, 20 and 40μM) at 0.75 h post fertilization (hpf) and monitored early developmental events such as cleavage, blastula and epiboly that encompass maternal-to-zygotic transition (MZT) and zygotic genome activation (ZGA). more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24995

24 Samples

Download data: TXT

(Submitter supplied) The per-and polyfluoroalkyl substances (PFAS) are of significant global concern due to their highly ubiquitous and persistent nature, bioaccumulation in organisms, and potential toxicity. The aquatic environment is known as an important sink for PFAS resulting in high concentrations in aquatic organisms. However, little is known about the developmental windows of sensitivity in which the PFAS chemicals are biologically active, in addition to the toxicity endpoints that best reflect chemical hazard. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24995

1006 Samples

Download data: TXT