GEO DataSets

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

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25922

3 Samples

Download data: MTX, TSV

(Submitter supplied) As cardiac regeneration requires new coronary vessels, exploring the underlying mechanisms behind revascularization will facilitate the development of regenerative therapies for heart failure. Although multiple tissues and chemokines likely orchestrate coronary formation, the interaction between coronary growth and guidance cues remains unclear. Here, by applying single-cell RNA-sequencing (scRNA-seq) analysis, we examined gene expression in zebrafish epicardial cells during coronary vascularization and identified hapln1a-expressing epicardial cells enriched with vascular-regulating genes. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25922

1 Sample

Download data: MTX, TSV

(Submitter supplied) As cardiac regeneration requires new coronary vessels, exploring the underlying mechanisms behind revascularization will facilitate the development of regenerative therapies for heart failure. Although multiple tissues and chemokines likely orchestrate coronary formation, the interaction between coronary growth and guidance cues remains unclear. Here, by applying single-cell RNA-sequencing (scRNA-seq) analysis, we examined gene expression in zebrafish epicardial cells during coronary vascularization and identified hapln1a-expressing epicardial cells enriched with vascular-regulating genes. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25922

1 Sample

Download data: MTX, TSV

(Submitter supplied) As cardiac regeneration requires new coronary vessels, exploring the underlying mechanisms behind revascularization will facilitate the development of regenerative therapies for heart failure. Although multiple tissues and chemokines likely orchestrate coronary formation, the interaction between coronary growth and guidance cues remains unclear. Here, by applying single-cell RNA-sequencing (scRNA-seq) analysis, we examined gene expression in zebrafish epicardial cells during coronary vascularization and identified hapln1a-expressing epicardial cells enriched with vascular-regulating genes. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25922

1 Sample

Download data: MTX, TSV

(Submitter supplied) In previous studies, we identified and demonstrated that a 1.2kb cebpd downstream element (CEN) is capable and neccessary for the induction of cebpd in the kidney after cardiac injury. The goal of this study is to unveal the Cebpd regulated responses of kidney to cardiac regeneration in zebrafish. we profiled responses by kidney in cebpd mutant and enhancer (CEN) mutant fish zebrafish to massive injuries of the heart.

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29008

12 Samples

Download data: TXT

(Submitter supplied) The goal of this study is to unveal the responses of uninjured tissue to distant tissue injury and the structures required for long-range responses to tissue injuries. we profiled responses by the brain and kidney in zebrafish to massive injuries of the heart and identified cebpd transcript induction in both tissue. We also identified and demonstrated that a 1.2kb cebpd downstream element is capable and neccessary for the induction of cebpd in the brain after cardiac injury.

Organism:

Danio rerio

Type:

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

Platform:

GPL21741

24 Samples

Download data: BW, TXT

(Submitter supplied) The epicardium is a mesothelial tissue layer that envelops the heart. Cardiac injury activates dynamic gene expression programs in epicardial tissue, which in the case of zebrafish enables subsequent regeneration through paracrine and vascularizing effects. To identify tissue regeneration enhancer elements (TREEs) that control injury-induced epicardial gene expression during heart regeneration, we profiled transcriptomes and chromatin accessibility in epicardial cells purified from regenerating zebrafish hearts. more...

Organism:

Danio rerio

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL14875 GPL21741

18 Samples

Download data: BIGWIG, TXT

(Submitter supplied) Here we used RNAsequencing to characterize the transcriptional profile of the kidney of runx1 knock out zebrafish adult compared to wild type.

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18413

5 Samples

Download data: TXT

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

Organism:

Danio rerio; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL17021 GPL25922 GPL18413

26 Samples

Download data: MTX, TSV, TXT

(Submitter supplied) We used single cell-RNA sequencing to investigate the expression and the heterogeneity of wild type and runx1-mutant cd41-GFPLow cd41GFP hematopoietic stem and progenitor cells at embryonic (2.5 days post fertilization, dpf) and larval stages (6, 10 16 dpf).

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25922

9 Samples

Download data: MTX, TSV

(Submitter supplied) Here we used RNA sequencing to characterize the transcriptional profile of the kidney of runx1 knock out zebrafish adult compared to wild type.

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18413

6 Samples

Download data: TXT

(Submitter supplied) The goal of this RNA-seq experiment was to compare gene expression profiles of two different intestinal cell populations (Intestinal epithelial cells that mostly reside in the anterior gut and Lysosome rich enterocytes that reside in mid-intestine) in zebrafish to better understand the characteristics of LREs and uncover the molecular players mediating the function of LREs. Two populations were FACS isolated from 6 days post fertilization (dpf) TgBAC(cldn15la-GFPpd1034) transgenic fish gavaged with Alexa Fluor 568 Dextran 24 hours prior to FACS. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL14875

6 Samples

Download data: TXT

(Submitter supplied) Notochord sheath cells were FACS isolated from 13 days post fertilization (dpf) transgenic zebrafish. Three biological replicates were used for each population, and expression profiles were determined using Illumina HiSeq. Comparison of the sample groups allowed for identification of unique candidates. The sequence reads that passed quality filters were analyzed using HISAT2, and gene counts were analyzed using HTSeq.

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21741

9 Samples

Download data: TXT

(Submitter supplied) Methylmercury (MeHg) is an environmental neurotoxicant known to cause adverse effects in fish, such as locomotor abnormalities, visual deficits or teratogenesis. However, very few studies have investigated the effects of environmentally realistic MeHg exposures on the gene expression of fish embryos. Since the primary source of MeHg exposure in wild fish is through the diet, this study analyzed differential gene expression in zebrafish embryos from parents that had been subjected to environmentally relevant dietary MeHg exposures (0, 1, 3, and 10ppm) throughout their whole life cycle.

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL14875

12 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:

GPL14875

24 Samples

Download data

(Submitter supplied) Methylmercury (MeHg) is a ubiquitous environmental toxicant that is often detected in the tissues of fish-eating species. It has been well established that prenatal exposure to MeHg can lead to widespread brain damage and impaired neurological development resulting in defects ranging from severe cerebral palsy and cognitive deficits to impaired motor and sensory function. A wide range of environmental toxicants have been shown to induce transgenerational inheritance of diseases via changes in DNA methylation—a well-known epigenetic modification. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL14875

12 Samples

Download data: TXT

(Submitter supplied) Methylmercury (MeHg) is a ubiquitous environmental toxicant that is often detected in the tissues of fish-eating species. It has been well established that prenatal exposure to MeHg can lead to widespread brain damage and impaired neurological development resulting in defects ranging from severe cerebral palsy and cognitive deficits to impaired motor and sensory function. A wide range of environmental toxicants have been shown to induce transgenerational inheritance of diseases via changes in DNA methylation—a well-known epigenetic modification. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL14875

12 Samples

Download data: TXT

(Submitter supplied) This study sought to evaluate the effects of dietary MeHg exposure on adult female yellow perch (Perca flavescens) and zebrafish (Danio rerio) reproduction by relating controlled exposures with subsequent reproductive effects. Yellow perch were used in the study for their socioeconomic and ecological importance within the Great Lakes basin, and the use of zebrafish allowed for a detailed analysis of the molecular effects of MeHg. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL14875

12 Samples

Download data: DIFF, FPKM_TRACKING, PDF, TXT

(Submitter supplied) Purpose: RNA seq analysis from isolated zebrafish HSPCs at 48 hpf from control morpholino and dnmt3bb.1 morpholino injected embryos

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL14875

4 Samples

Download data: TXT

(Submitter supplied) We compared transcriptional profiles of regenerating zebrafish caudal fins following fin amputation with profiles from uninjured zebrafish caudal fins

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9319

4 Samples

Download data: TXT