GEO DataSets

(Submitter supplied) Zebrafish is an important model system for the study of vertebrate embryonic development and adaptive immunese response. Recent years have seen great advancement in the understanding of the regulatory mechanisms during zebrafish embryogenesis and immune processes, yet large gaps still remain in the functional pathways critical for each developmental stage, especially for the late embryonic development. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL10658

9 Samples

Download data: TXT

(Submitter supplied) Study of transcriptome dynamics using a high-resolution gene-expression time course with 180 individual embryos, obtained from nine different spawns that are profiled from late blastula to mid gastrula stage. All individual embryos of genotype ABTL were photographed and an initial developmental time was estimated using percentage epiboly as a metric.

Organism:

Danio rerio

Type:

Expression profiling by array

Platform:

GPL22016

180 Samples

Download data: FTR, TXT

(Submitter supplied) mRNA seq based approach to determine the transcriptome dynamics during early development To study the mechanisms regulating this developmental event in zebrafish, we applied RNA deep sequencing technology and generated comprehensive transcriptome profiles of 6 developmental stages from oocyte to early gastrulation. We determined the expression levels of maternal and zygotic transcripts and clustered them based on expression pattern. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL10658

6 Samples

Download data: BEDGRAPH, GFF

(Submitter supplied) Wild-type and MZoep zebrafish embryos were mechanically dissociated and profiled using 10x Genomics pipeline.

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20828

2 Samples

Download data: MTX, TSV

(Submitter supplied) During embryogenesis, cells acquire distinct fates by transitioning through transcriptional states. To uncover these transcriptional trajectories during zebrafish embryogenesis, we sequenced 38,731 cells and developed URD, a simulated diffusion-based computational reconstruction method. URD identified the trajectories of 25 cell types through early somitogenesis, gene expression along them, and their spatial origin in the blastula. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL18413 GPL20828

446 Samples

Download data: MTX, TSV

(Submitter supplied) Wild-type zebrafish embryos were mechanically dissociated and profiled using Drop-seq

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20828

28 Samples

Download data: TXT

(Submitter supplied) SMART-seq2 was performed on single cells isolated from visually staged zebrafish embryos.

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18413

416 Samples

Download data: TXT

(Submitter supplied) Zic3 regulates early embryonic patterning in vertebrates. Its loss-of-function disrupts gastrulation, left-right patterning, and neurogenesis. We use the zebrafish as a model to study the developmental role of Zic3 in vivo. Using a combination of two genomics approaches – ChIP-seq and microarray, we identified Zic3 targets, which include genes from the Nodal and Wnt pathways, and show for the first time cis-regulation of these genes by Zic3 using in vivo enhancer assay. more...

Organism:

Danio rerio

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL10164

4 Samples

Download data: BED, 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

Platforms:

GPL14875 GPL15180

7 Samples

Download data: TSV, TXT

(Submitter supplied) We compared Agilent custom made expression microarrays with Illumina deep sequencing for RNA analysis of zebrafish embryos 5 days post fertilization, showing as expected a high degree of correlation of expression of a common set of 15,927 genes for untreated fish. The transcriptomes were also compared for fish injected in the yolk with Mycobacterium marinum

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL14875

3 Samples

Download data: TSV

(Submitter supplied) We compared Agilent custom made expression microarrays with Illumina deep sequencing for RNA analysis of zebrafish embryos 5 days post fertilization, showing as expected a high degree of correlation of expression of a common set of 15,927 genes.

Organism:

Danio rerio

Type:

Expression profiling by array

Platform:

GPL15180

4 Samples

Download data: TXT

(Submitter supplied) Atrazine is an herbicide applied to agricultural crops and is indicated to be an endocrine disruptor. Atrazine is frequently found to contaminate potable water supplies above the maximum contaminant level of 3 mg/L as defined by the U.S. Environmental Protection Agency. The developmental origin of adult disease hypothesis suggests that toxicant exposure during development can increase the risk of certain diseases during adulthood. more...

Organism:

Danio rerio

Type:

Expression profiling by array

Platform:

GPL21560

12 Samples

Download data: PAIR

(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) In this study, single cell sequencing technique was utilized to explore the transcriptomes of zebrafish PGCs in three time points: 6hpf (shield stage), 11hpf (3-somite stage) and 24hpf (prim-5 stage).

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18413

9 Samples

Download data: TXT

(Submitter supplied) Purpose: We report the application of NGS for profiling the impacts of BDE47 exposure on the transcriptome of zebrafish larvae. Methods: mRNA profiles of 6-day-old BDE47-treated and control zebrafish larvae were generated by deep sequencing using Illumina Hisq 2000 platform. The sequence reads that passed quality filters were analyzed at the transcript isoform level with TopHat followed by Cufflinks. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL14875

3 Samples

Download data: TXT

(Submitter supplied) In the early zebrafish embryo, the developing genome profile can be interfered with by exposure to pentachlorophenol, and some specific sets of genes are up-regulated or down-regulated. We used microarrays to detail the global program of gene expression underlying cellularisation and identified distinct classes of up-regulated genes during this process.

Organism:

Danio rerio

Type:

Expression profiling by array

Platform:

GPL1319

9 Samples

Download data: CEL

(Submitter supplied) We performed whole transcriptome polyA+ RNA sequencing experiments on 17 stages of embryonic development

Organism:

Ambystoma mexicanum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21473

49 Samples

Download data: TXT

(Submitter supplied) Very little is known on the nature of epigenetic states in developing zebrafish despite its growing importance as a model organism in developmental biology. We report histone modifications on promoters of pluripotency genes in zebrafish embryos at the mid-late blastula transition (MBT+) stage. We identify three classes of expressed genes based on these profiles: (1) those with a promoter occupied by marks of active genes without any repressive marks; (2) those co-occupied by both activating and repressive modifications; of these genes, klf4 was notably found to be mosaically expressed in the embryo, possibly accounting for this epigenetic pattern; (3) those occupied by repressive marks with, surprisingly, little not acetylated H3K9 or H4. more...

Organism:

Danio rerio

Type:

Expression profiling by array

Platform:

GPL9998

7 Samples

Download data: TXT

(Submitter supplied) The Compugen set of zebrafish oligonucleotides was designed by Compugen based on ESTs, mostly from the Washington University Zebrafish Genome Assemblies. Compugen no longer sell or support this product. Sequences are not for commercial use, copyright reserved to Compugen 2002. Protocol: For each gene one 65-mer oligonucleotide probe was designed from the 3' region of the sequence. Each probe was selected from a sequence segment that is common to a maximum number of splice-variants predicted for each gene. more...

Organism:

Danio rerio

1 DataSet

2 Series

15 Samples

Download data

(Submitter supplied) Pitx2c, a homeodomain transcription factor, is classically known for its left-right patterning role. However, an early wave of pitx2 expression occurs at the onset of gastrulation in several species, indicating a possible earlier role that remains relatively unexplored. Here, we show that in zebrafish, maternal-zygotic (MZ) pitx2c mutants exhibit a shortened body axis indicative of convergence and extension (CE) defects. more...

Organism:

Danio rerio

Type:

Expression profiling by array

Platform:

GPL19785

4 Samples

Download data: TXT, XLSX