GEO DataSets

(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

Platforms:

GPL9319 GPL18413

12 Samples

Download data: BED, TXT

(Submitter supplied) We report the distribution of human SATB2 in a primary zebrafish melanoma that overexpresses human SATB2, and H3K27Ac histone marks in zebrafish melanomas overexpressing either EGFP (control) or human SATB2.

Organism:

Danio rerio

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL9319 GPL18413

6 Samples

Download data: BED, 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

(Submitter supplied) We compared transcriptional and chromatin profiles of regenerating zebrafish hearts following genetic ablation with profiles from uninjured zebrafish hearts.

Organism:

Danio rerio

Type:

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

Platforms:

GPL9319 GPL14875

8 Samples

Download data: TXT, WIG

(Submitter supplied) The precise positioning of organ progenitor cells constitutes an essential, yet poorly understood step in organ development and function. Using primordial germ cells and the process of gonadogenesis as an in vivo model, we present the developmental mechanisms facilitating the maintenance of a motile progenitor cell population at the site where the organ develops. We find that the action of repulsive cues coupled with the generation of physical barriers confine the cells to the correct bilateral positions within the embryo. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9319

4 Samples

Download data: XLS

(Submitter supplied) The mammalian heart has poor regenerative capacity following injury. In contrast, certain lower vertebrates such as zebrafish retain a robust capacity for regeneration into adult life. Here we use an integrated approach to identify evolutionary conserved regenerative miRNA-dependant regulatory circuits in the heart. We identified novel miRNA-dependant networks involved in critical biological pathways, which are differentially utilized between the infarcted mouse heart and the regenerating zebrafish heart.

Organism:

Danio rerio

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9319

8 Samples

Download data: TXT

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

Organism:

Danio rerio; Mus musculus

Type:

Expression profiling by array; Non-coding RNA profiling by high throughput sequencing

4 related Platforms

34 Samples

Download data: CEL

(Submitter supplied) We sequenced mRNA from two preparations of isolated Notch-responsive ductal pancreas cells and compared transcript expression to all other non-Notch-responsive cells from each sample to charactarize zebrafish centroacinar cells.

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9319

4 Samples

Download data: TXT

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

Organism:

Danio rerio

Type:

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

Platforms:

GPL6457 GPL14875 GPL9319

16 Samples

Download data: GPR

(Submitter supplied) Study of Smad2 and Eomesa genomic binding in zebrafish blastulas, their relationship to eachother and the relaptionship between genomic binding and Ndr1 and Eomesa responsive genes as identified by microarray and RNA-seq.

Organism:

Danio rerio

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9319

6 Samples

Download data: TXT

(Submitter supplied) To identify genes regulated by Rx3 during optic vesicle morphogenesis, adult zebrafish carriers of a null rx3 mutation were mated. Before 13 hours post fertilization (hpf), the earliest time point at which optic vesicle evagination phenotypes could be reliably detected, offspring were phenotypically separated into pools comprising of mutants with an absence of optic vesicles or siblings exhibiting a wild-type phenotype. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9319

7 Samples

Download data: TXT

(Submitter supplied) Background: Adult zebrafish spontaneously regenerate their retinas after damage. Although a number of genes and signaling pathways involved in regeneration have been identified, the extent of mechanisms regulating regeneration is unclear. Small non-coding RNAs, microRNAs (miRNAs), that regulate regeneration of various tissues in lower vertebrates were examined for their potential roles in regulating zebrafish retinal regeneration. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9319

3 Samples

Download data: TXT

(Submitter supplied) The Gata4 transcription factor is essential for normal heart development, but the molecular basis for its function remain poorly understood. We profiled at the whole genome level transcript changes in cardiomyocytes when Gata4 is depleted from zebrafish embryos. Our objective was to elucidate the cardiomyocyte-specific molecular program functioning downstream of Gata4 in order to better understand the role of Gata4 in cardiac morphogenesis.

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL14875 GPL9319

6 Samples

Download data: TXT, WIG

(Submitter supplied) Poly(A) tails enhance the stability and translation of most eukaryotic messenger RNAs, but difficulties in globally measuring poly(A)-tail lengths have impeded greater understanding of poly(A)-tail function. Here we describe poly(A)-tail length profiling by sequencing (PAL-seq) and apply it to measure tail lengths of millions of individual RNAs isolated from yeasts, cell lines, Arabidopsis thaliana leaves, mouse liver, and zebrafish and frog embryos. more...

Organism:

Homo sapiens; Schizosaccharomyces pombe; Danio rerio; Saccharomyces cerevisiae; Arabidopsis thaliana; Drosophila melanogaster; Xenopus laevis; Mus musculus

Type:

Expression profiling by high throughput sequencing

13 related Platforms

64 Samples

Download data: TXT

(Submitter supplied) Deletion of caudal/cdx genes alters hox gene expression and causes defects in posterior tissues and hematopoiesis. Yet, the defects in hox gene expression only partially explain these phenotypes. To gain deeper insight into Cdx4 function, we performed ChIP-seq combined with gene expression profiling in zebrafish, and identified the transcription factor spalt-like 4 (sall4) as a Cdx4 target. ChIP-seq revealed that Sall4 bound to its own gene locus and the cdx4 locus. more...

Organism:

Danio rerio

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL14875 GPL9319

7 Samples

Download data: BED, BW

(Submitter supplied) Silver nanoparticles cause toxicity in exposed organisms and are an environmental health concern. The mechanisms of silver nanoparticle toxicity, however, remain unclear. We examined the effects of exposure to silver in nano-, bulk- and ionic forms on zebrafish embryos (Danio rerio) using a Next Generation Sequencing approach in an Illumina platform (High-Throughput SuperSAGE). Significant alterations in gene expression were found for all treatments and many of the gene pathways affected, most notably those associated with oxidative phosphorylation and protein synthesis, overlapped strongly between the three treatments indicating similar mechanisms of toxicity for the three forms of silver studied. more...

Organism:

Danio rerio

Type:

Other

Platform:

GPL9319

8 Samples

Download data: TXT

(Submitter supplied) The post-transcriptional fate of messenger RNAs (mRNAs) is largely dictated by their 3' untranslated regions (3'UTRs), which are defined by cleavage and polyadenylation (CPA) of pre-mRNAs. We used poly(A)-position profiling by sequencing (3P-Seq) to map poly(A) sites at eight developmental stages and tissues in the zebrafish. Analysis of over 60 million 3P-Seq reads substantially increased and improved existing 3'UTR annotations, resulting in confidently identified 3'UTRs for more than 78.79% of the annotated protein-coding genes in zebrafish. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL14875 GPL9319

14 Samples

Download data: BED, BW, TXT

(Submitter supplied) MicroRNAs regulate gene expression through deadenylation, repression and mRNA decay. However, the contribution of each mechanism in non-steady-state situations remains unclear. We monitored the impact of miR-430 on ribosome occupancy of endogenous mRNAs in wild type and dicer mutants lacking mature miR-430. Our results indicate that miR-430 reduces the number of ribosomes on target mRNAs before causing mRNA decay. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9319

22 Samples

Download data: BED

(Submitter supplied) During early vertebrate development, a large number of noncoding RNAs are maternally inherited or expressed upon activation of zygotic transcription. The exact identity, expression levels, and function during early vertebrate development for most of these noncoding RNAs remains largely unknown. miRNAs (microRNAs) and piRNAs (piwi-interacting RNAs) are two classes of small non-coding RNAs that play important roles in gene regulation during early embryonic development. more...

Organism:

Danio rerio

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9319

5 Samples

Download data: FA, TXT

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

Organism:

Danio rerio

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9319

6 Samples

Download data: WIG