GEO DataSets

(Submitter supplied) To gain mechanistic insight into how Hand2 regulates cardiac fusion, we performed transcriptomic analyses of hand2 loss- and gain-of-function 20 hpf cardiomyocytes.

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30614

12 Samples

Download data: TXT

(Submitter supplied) RNA splicing and protein degradation systems allow the functional adaptation of the proteome in response to changing cellular contexts. However, the regulatory mechanisms connecting these processes remain poorly understood. Here, we show that impaired spliceosome assembly caused by USP39 deficiency leads to a pathogenic splicing profile characterized by the use of cryptic 5′ splice sites. Importantly, disruptive cryptic variants evade mRNA surveillance pathways and are translated into misfolded proteins. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30614

8 Samples

Download data: TXT

(Submitter supplied) We used single-cell RNA expression to uncover the cellular and molecular heterogeneity of isolated endocardial cells in the heart. From this study, we uncovered the presence of an endocardial-hematopoietic cluster, along with other significant clusters including valve endocardial and interstitial cells, and non-valve cells.

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30614

2 Samples

Download data: MTX, TSV

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

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30614

14 Samples

Download data: TAR

(Submitter supplied) The innate immune system is triggered rapidly after injury and its spatiotemporal dynamics are critical for successful regeneration. MyD88 is a key component of the innate immune response; however, its role during regeneration remains unclear. Here we show that MyD88 controls not only the inflammatory but also the fibrotic response during zebrafish cardiac regeneration. Our data reveal a significant reduction in pro-inflammatory neutrophil and macrophage populations, as well as the expansion of a collagen-rich endocardial population in cryoinjured myd88-/- ventricles. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30614

2 Samples

Download data: TAR

(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:

GPL30614

12 Samples

Download data: TXT

(Submitter supplied) Atrial cardiomyocytes undergo complex cellular behaviours after 72 hours post fertilization to build muscle structures. We aimed to identify the genes involved during this process, and therefore we seqeunced the RNA from 48 and 72 hpf atrial cardiomyocytes to uncover changes in the transcirptome that might regulate or trigger atrial morphogenesis after 72 hpf.

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30614

6 Samples

Download data: TXT

(Submitter supplied) Melanocytes of the skin have traditionally been viewed as a homogeneous population, however, recent findings suggest the existence of distinct cell states within the melanocyte population. To investigate this further, we employed the zebrafish as a valuable model system for studying melanocyte biology. The zebrafish offers advantages such as its transparent nature and the availability of transgenic lines that allow specific labeling of melanocytes. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30614

2 Samples

Download data: CSV, MTX, TSV

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

Organism:

Homo sapiens; Danio rerio; Mus musculus

Type:

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

Platforms:

GPL30173 GPL30614 GPL30172

20 Samples

Download data: BED, BW, MTX, NARROWPEAK, TBI, TSV

(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 identify suitable experimental designsfor toxicology experiments (i.e., sample size, pool size, number of biological replicates, and number of doses), we exposed zebrafish embryos to 0.1% dimethyl sulfoxide for 4-120 hours post fertilization. We then created 96 samples to examine the impact of pool size comprised of 1, 5, 10, and 20 zebrafish embryos each (n = 24). From these, total RNA extraction was extracted and transcriptomic analyses were done using the TempO-Seq S1500+ Surrogate Assay platform. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30614

96 Samples

Download data: CSV

(Submitter supplied) To screen for Egr3 targets mediating cardiac valve development we assessed gene expression on dissected hearts of egr3 mutants and wild-type siblings.

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30614

4 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:

GPL30614

8 Samples

Download data: MTX, TSV

(Submitter supplied) scRNA-seq was used to investigate neurovascular cross-talk in zebrafish trunk.

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30614

4 Samples

Download data: MTX, TSV

(Submitter supplied) scRNA-seq was used to investigate the different endothelial cell population and differential gene expression between arterial and venous cells.

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30614

4 Samples

Download data: MTX, TSV

(Submitter supplied) The oxidative phosphorylation (OXPHOS) system is dynamic and the respiratory complexes (RCs) coexist with super-assembled quaternary structures called supercomplexes (SCs). How assembly occurs and the physiological role of supercomplex assembly is still under intensive investigation. The Cox7a family member Cox7a2l, also known as Scaf1, promotes CIII-CIV super assembly and energetic efficiency in zebrafish, mice, and humans. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30614

8 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

Platforms:

GPL20828 GPL30614

3 Samples

Download data: MTX, TSV

(Submitter supplied) In contrast to adult mammals, adult zebrafish are able to fully regenerate injured cardiac tissue, and this regeneration process requires an adequate and tightly controlled immune response. However, which immune aspects drive particular aspects of the regenerative response are unclear. Here, we report the participation and requirement of the antigen presentation-adaptive immunity axis during zebrafish cardiac regeneration. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30614

2 Samples

Download data: MTX, TSV

(Submitter supplied) In contrast to adult mammals, adult zebrafish are able to fully regenerate injured cardiac tissue, and this regeneration process requires an adequate and tightly controlled immune response. However, which immune aspects drive particular aspects of the regenerative response are unclear. Here, we report the participation and requirement of the antigen presentation-adaptive immunity axis during zebrafish cardiac regeneration. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30614

4 Samples

Download data: TXT

(Submitter supplied) Seeking to identify additional transcription factors required for cardiac valve formation, we determined and explored the transcriptional landscape of endocardial cells at the time when key morphogenetic events underlying valve development take place.

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30614

2 Samples

Download data: TAR