GEO DataSets

(Submitter supplied) To dissect the molecular function of mbd5 in zebrafish embryonic development, we carried out transcriptomic analyses at those two developmental stages.

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23085

14 Samples

Download data: TXT

(Submitter supplied) The cortico-basal ganglia circuit mediates decision-making. Here, we generated transgenic tools for adult zebrafish targeting specific subpopulations of the components of this circuit and utilized them to identify evolutionary homologs of the mammalian direct- and indirect-pathway striatal neurons which respectively project to the homologs of the internal and external segment of the globus pallidus (dEN and Vl) as in mammals. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23085

1 Sample

Download data: HTML, MTX, TSV

(Submitter supplied) This study provides a multi-omics approach to determine the effect on the transcriptome and proteome gut profiles of zebrafish inoculated with tick saliva followed by mammalian meat consumption. With bioinformatics analysis using the R software, we sought for significant biological and metabolic pathway changes, in order to fill up some of the current knowledge gaps associated with the alpha-Gal syndrome (AGS). more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23085

6 Samples

Download data: XLSX

(Submitter supplied) Ionizing radiation (IR) affects brain development in vertebrates at early developmental stages, but its effects of IR on other developing tissues have not yet been clarified. To investigate the IR effects on the developing organs, single-cell RNA sequencing was conducted using zebrafish embryos at 24hpf.

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23085

2 Samples

Download data: MTX, TSV

(Submitter supplied) In this research, we found mcm5 mutation lead to T cell deficiency and apoptosis in zebrafish. To reveal the molecular mechanism of mcm5 mutation in regulating T cell maturation, we performed RNA-Seq to discover the signal pathways regulated by mcm5.

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23085

6 Samples

Download data: TXT

(Submitter supplied) The evolution of nervous systems hinges on cell type diversification and specialization. Neural glia, also called macroglia, make up a large percentage of the total cell numbers in the brain of several species including humans and perform critical functions related to producing, maintaining and assiting neurons. Despite their importance, glial cells have been much less studied than neurons. Here, in order to investigate the heterogeneity of adult radial glial cells in zebrafish and to study the evolution of macroglia and the adult neurogenesis process they support, we generated a single cell RNAseq dataset of the adult zebrafish telencephalon enriched for radial glial cells using a sox2:gfp transgenic line.

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23085

3 Samples

Download data: TAR

(Submitter supplied) The accumulation of senescent cells behaves as a key driver of several age-related cancers and degenerative diseases of the general population. Whether cellular senescence also contributes to psychiatric diseases is still elusive. We report here the characterization of a zebrafish model of psychiatric disorder resulting from the invalidation of the ppp2r2c gene known to be involved in various psychiatric pathologies in human and encoding a neural specific regulatory subunit of the Protein Phosphatase 2A (PP2A). more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23085

10 Samples

Download data: TXT

(Submitter supplied) we characterized the zebrafish innate immune response to pneumococcus through a whole-genome level transcriptome analysis. The analysis revealed the induction of genes coding for pro-inflammatory cytokines, chemokines, acute phase proteins, and antimicrobial peptides, indicating a well-conserved innate immune response to the human pathogen pneumococcus in zebrafish embryos. To gain understanding of the genetic factors associated with the increased risk for severe pneumococcal infection in humans, we carried out a medium-scale forward genetic screen in zebrafish. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23085

9 Samples

Download data: TSV

(Submitter supplied) Glucagon receptor (GCGR) is a potential target for diabetes therapy. Several emerging GCGR antagonism-based therapies are under pre-clinical and clinical development. However, the GCGR antagonism as well as GCGR deficient animal accompanied with α-cell hyperplasia and hyperglucagonemia, which may limit the application of GCGR antagonism. To better understand the physiological changes in the α cells during the GCGR disruption, we performed the single cell sequencing of α cells isolated from control and gcgr-/- zebrafish. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23085

2 Samples

Download data: CSV

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

Organism:

Danio rerio

Type:

Methylation profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platforms:

GPL30560 GPL23085

12 Samples

Download data: TXT

(Submitter supplied) Here, we describe environmental Cu2+ in promoting zebrafish (Danio rerio) developmental abnormalities in subsequent generation. This study for the first time demonstrated that: 1. Cu2+ induced alterations in sperm methylome could be passed down to offspring and cause developmental defects in the nervous and digestive system, even the Cu2+ concentration is at 10 μg/L, the National Quality Standards of fishery water (GB11607-89); 2. more...

Organism:

Danio rerio

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL23085

6 Samples

Download data: TXT

(Submitter supplied) The aquatic environment is an important site for perfluorooctanoic acid (PFOA) deposit and induced a high risk for aquatic organisms. Nevertheless, the current toxicity assessment was rarely reported the heart effect of PFOA. The exact mode of action and its resulting heterogeneity toxicological effects in aquatic organisms also remain largely unknown. In this study, the heart effects were investigated with a series of assays. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23085

2 Samples

Download data: MTX, TSV

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

Organism:

Drosophila melanogaster; Eisenia andrei; Danio rerio

Type:

Expression profiling by high throughput sequencing

5 related Platforms

151 Samples

Download data: TXT

(Submitter supplied) Single-cell mRNA sequencing (scRNA-seq) technologies are reshaping the current cell-type classification system. In previous studies, we built the mouse cell atlas (MCA) and human cell landscape (HCL) to catalog all cell types by collecting scRNA-seq data. However, systematically study for zebrafish (Danio rerio) and fruit fly (Drosophila melanogaster) are still lacking. Here, we construct the zebrafish and Drosophila cell atlas with Microwell-seq protocols, which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila, and studying difference between vertebrates and Invertebrates at single cell level.

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL23085 GPL30277

106 Samples

Download data: TXT

(Submitter supplied) To identify key genes in the early sex development of zebrafish, we generated zebrafish (AB strain) feminized by sex hormone 17β-estradiol (E2, CAS: 50-28-2, 100 ng/L) and masculinized by aromatase inhibitor exemestane (EM, CAS: 107868-30-4, 10 μg/L), and detected their transcriptomes by RNA-seq.

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23085

56 Samples

Download data: TXT

(Submitter supplied) Transcriptome sequencing (RNA-seq) analysis uncovered that 1238 genes were upregulated, 923 genes were downregulated in sinhcaf mutant FG follicles, compared to wild type FG follicles. Loss of sinhcaf in mature eggs resulted in upregulation of 904 genes, and downregulation of 911 genes. Downregulated genes in sinhcaf mutant FG follicles and eggs were classified by gene ontology (GO) analysis, then the top 30 GO terms with highest -log10P values were screened out, and at least two downregulated genes were included in each biological processes, cellular components or molecular function term. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23085

18 Samples

Download data: TXT

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

Organism:

Macaca mulatta; Homo sapiens; Canis lupus familiaris; Gallus gallus; Sus scrofa; Oryctolagus cuniculus; Danio rerio; Felis catus; Bos taurus; Ovis aries; Mus musculus; Rattus norvegicus

Type:

Expression profiling by high throughput sequencing; Other

12 related Platforms

54 Samples

Download data: BED, HDF5, XLS

(Submitter supplied) Three-dimensional genome architecture influences the regulation of essential nuclear processes, such as gene transcription. However, how 3D genome architecture is affected by evolutionary forces within major lineages remains unclear. Here, we report a comprehensive comparison of 3D genomes, using high resolution Hi-C data in fibroblast cells of fish, chickens, and 10 mammalian species. This analysis shows a correlation between genome size and chromosome length that affects chromosomal territory (CT) organization in the upper hierarchy of genome architecture, whereas lower hierarchical features, including local transcriptional availability of DNA, are selected through vertebrate’s evolution. more...

Organism:

Felis catus; Bos taurus; Ovis aries; Rattus norvegicus; Gallus gallus; Sus scrofa; Oryctolagus cuniculus; Mus musculus; Danio rerio; Macaca mulatta; Homo sapiens; Canis lupus familiaris

Type:

Expression profiling by high throughput sequencing

12 related Platforms

29 Samples

Download data: TXT

(Submitter supplied) Three-dimensional genome architecture influences the regulation of essential nuclear processes, such as gene transcription. However, how 3D genome architecture is affected by evolutionary forces within major lineages remains unclear. Here, we report a comprehensive comparison of 3D genomes, using high resolution Hi-C data in fibroblast cells of fish, chickens, and 10 mammalian species. This analysis shows a correlation between genome size and chromosome length that affects chromosomal territory (CT) organization in the upper hierarchy of genome architecture, whereas lower hierarchical features, including local transcriptional availability of DNA, are selected through vertebrate’s evolution. more...

Organism:

Danio rerio; Gallus gallus; Macaca mulatta; Homo sapiens; Mus musculus; Canis lupus familiaris; Felis catus; Bos taurus; Ovis aries; Oryctolagus cuniculus; Rattus norvegicus

Type:

Other

11 related Platforms

25 Samples

Download data: BED, HDF5, XLS

(Submitter supplied) A reliable animal model that can mimic the GBM intracranial infiltration and Blood-brain barrier (BBB) interaction is necessary for effective therapeutics development. Here, we report a zebrafish-based orthotopic GBM xenograft model, in which GBM cells from different species and even patients, can robustly propagate and faithfully reproduce their histological characteristics. Single-cell RNA-seq indicates a transcriptomic adaption of GBM xenografts to infiltrative phenotype within the zebrafish brains. more...

Organism:

Homo sapiens; Danio rerio

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL20795 GPL23085

34 Samples

Download data: CSV