GEO DataSets

(Submitter supplied) Zebrafish (Danio rerio) gutGFP transgenic embryos [Tg(XlEef1a1:GFP)s854] were collected at 4 time points: 2 days post fertilization (dpf), 3, dpf, 4 dpf, 6 dpf. Embryos were dissociated into single cells and sorted by FACS based on GFP expression. RNA was extracted from the different cell populations (Stratagene), amplified (NuGEN Ovation), and hybridized to Affymetrix Zebrafish GeneChips. Keywords: Time course.

Organism:

Danio rerio

Type:

Expression profiling by array

Platform:

GPL1319

24 Samples

Download data: CEL

(Submitter supplied) Vertebrates are colonized at birth by complex microbial communities (microbiota) that influence diverse aspects of host biology. We have used a functional genomics approach to identify zebrafish genes that are differentially expressed in response to the microbiota. We assessed RNA expression profiles from zebrafish larvae at 6 days post-fertilization (dpf) that were either raised continuously in the absence of any microorganism (germ-free or GF), or raised GF through 3dpf then colonized with a normal zebrafish microbiota (conventionalized or CONVD). more...

Organism:

Danio rerio

Type:

Expression profiling by array

Platform:

GPL1319

6 Samples

Download data: CEL

(Submitter supplied) Estrogen signaling is important for vertebrate embryonic development. Here we have used zebrafish (Danio rerio) as a vertebrate model to identify estrogen regulated genes during the first 4 days of development. Zebrafish embryos were exposed to 1 µM 17β-estradiol from 3 hours post fertilization to 4 days post fertilization, harvested daily and subjected to RNA extraction for transcriptome analysis using microarrays. more...

Organism:

Danio rerio

Type:

Expression profiling by array

Platform:

GPL6457

28 Samples

Download data: TXT

(Submitter supplied) In this report, we describe a successful protocol for isolating and expression-profiling live fluorescent- protein-labelled neurons from zebrafish embryos. As a proof-of-principle for this method, we FAC-sorted and RNA-profiled GFP-labelled spinal CiA interneurons and compared the expression profile of these cells to those of post-mitotic spinal neurons in general and to all trunk cells. We show that RNA of sufficient quality and quantity to uncover both expected and novel transcription profiles via Affymetrix microarray analysis can be extracted from 5,700 to 20,000 FAC-sorted cells. more...

Organism:

Danio rerio

Type:

Expression profiling by array

Platform:

GPL1319

15 Samples

Download data: CEL

(Submitter supplied) The Spi1/ Pu.1 transcription factor plays a crucial role in myeloid cell development across many species. Several Spi1 target genes have been identified so far, yet the Spi1-dependent gene group remains largely unknown. To identify novel genes downstream of Spi1 we employed a microarray strategy using zebrafish embryos. We established the gene group down-regulated upon spi1 knockdown while simultaneously enriched in FACS-sorted embryonic myeloid cells of a spi1:GFP transgenic line, thus representing putative myeloid-specific Spi1 target genes. more...

Organism:

Danio rerio

Type:

Expression profiling by array

Platform:

GPL7735

8 Samples

Download data: TXT

(Submitter supplied) In this study, developing zebrafish were exposed to 500-4500 µg/L BPA for 7 days from 3 hours post-fertilization for a microarray experiment to obtain molecular insights into BPA early-life exposure toxicity.

Organism:

Danio rerio

Type:

Expression profiling by array

Platform:

GPL10182

18 Samples

Download data: TXT

(Submitter supplied) We describe a method for isolating RNA suitable for high-throughput RNA sequencing (RNA-seq) from small numbers of fluorescently labeled cells isolated from live zebrafish (Danio rerio) embryos without using costly, commercially available columns. This method ensures high cell viability after dissociation and suspension of cells and gives a very high yield of intact RNA. We demonstrate the utility of our new protocol by isolating RNA from fluorescence activated cell sorted (FAC sorted) pineal complex neurons in wild-type and tbx2b knockdown embryos at 24 hours post fertilization. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL14875

8 Samples

Download data: TXT

(Submitter supplied) We examined the transcriptional effect of preventing cardiac contraction in zebrafish embryos which can be deprived of circulation without experiencing hypoxia since the fish obtain sufficient oxygen via diffusion. Morpholino antisense knockdown of cardiac troponin T2 (tnnt2) prevented cardiac contraction without affecting vascular development. We concluded that absence of hemodynamic force induces endothelial CXCR4a up-regulation and promotes recovery of blood flow. more...

Organism:

Danio rerio

Type:

Expression profiling by array

Platform:

GPL1319

18 Samples

Download data: CEL, TXT, XLS

(Submitter supplied) We performed microarray experiment on zebrafish exposed to estrogen (17β-estradiol; a classified carcinogen) and an anti-estrogen (ICI 182,780). Our transcriptome analysis captured multiple estrogen-responsive genes and signaling pathways that increased cell proliferation, promoted DNA damage and genome instability, and decreased tumor suppressing effects, suggesting a common mechanism for estrogen-induced carcinogenesis. more...

Organism:

Danio rerio

Type:

Expression profiling by array

Platform:

GPL2715

10 Samples

Download data: GPR, TXT

(Submitter supplied) Purpose: The purpose of this study was to develop a framework for analyzing RPE expression profiles from zebrafish eye mutants. Methods: The fish model we used was smarca4 (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4), a retinal dystrophic mutant that the retinal phenotype and expression profiles were previously characterized. Histological and Affymetrix GeneChip analyses were conducted to define the RPE defects and underlying differential expression respectively. more...

Organism:

Danio rerio

Type:

Expression profiling by array

Platform:

GPL1319

18 Samples

Download data: CEL

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

Organism:

Danio rerio

Type:

Expression profiling by array

Platforms:

GPL1319 GPL7302

96 Samples

Download data: CEL, TXT

(Submitter supplied) Pou5f1 and Sox2 overexpression experiments with and without protein synthesis inhibitor were performed to investigate direct transcriptional targets of Pou5f1 and Sox2

Organism:

Danio rerio

Type:

Expression profiling by array

Platform:

GPL7302

18 Samples

Download data: TXT

(Submitter supplied) Zebrafish embryo were analyzed at 30 and 60 % epiboly for changes in transcriptome of wild-type and MTspg mutant embryos The Data are used as an independent experimental validation of data obtained for the same stages by Agilent arrays in the main experiments (especially Exp. 1)

Organism:

Danio rerio

Type:

Expression profiling by array

Platform:

GPL1319

8 Samples

Download data: CEL

(Submitter supplied) Comparison of Mspg and MZspg mutants at two stages, zebrafish

Organism:

Danio rerio

Type:

Expression profiling by array

Platform:

GPL7302

12 Samples

Download data: TXT

(Submitter supplied) Developmental curve of zebrafish MZ spg mutants compared to WT, 10 timepoints from 0 to 8 hours post fertilization transcriptome changes by microarray analysis at ten distinct time-points during development, from ovaries to late gastrulation, in MZ spg and WT zebrafish

Organism:

Danio rerio

Type:

Expression profiling by array

Platform:

GPL7302

58 Samples

Download data: TXT

(Submitter supplied) Zinc deficiency is detrimental to organisms highlighting its role as an essential micronutrient contributing to numerous biological processes. To investigate the underlying molecular events invoked by zinc depletion we performed a temporal analysis of transcriptome changes observed within zebrafish gill. This tissue represents a model system for studying ion absorption across polarised cells as it provides a major pathway for fish to acquire zinc directly from water whilst sharing a conserved zinc transporting system with mammals. more...

Organism:

Danio rerio

Type:

Expression profiling by array

Platform:

GPL10429

49 Samples

Download data: TXT

(Submitter supplied) The Notch signaling is an evolutionarily conserved signal transduction cascade that plays essential roles in a variety of developmental processes. In this study, we examined the mib mutants for defects in pancreas development using in situ hybridization and GFP expression analysis of pancreas-specific GFP lines, and carried out the global gene expression profile analysis of three different mib mutantalleles. more...

Organism:

Danio rerio

Type:

Expression profiling by array

Platform:

GPL2715

42 Samples

Download data

(Submitter supplied) To adapt to its changing dietary environment, the digestive tract is extensively remodeled from the embryo to the adult during vertebrate development. Xenopus laevis metamorphosis is an excellent model system for studying mammalian gastrointestinal development and is used to determine the genes and signaling programs essential for intestinal development and maturation. The metamorphosing intestine can be divided into four distinct developmental time points and these were analyzed with X. more...

Organism:

Xenopus laevis

Type:

Expression profiling by array

Platform:

GPL10302

11 Samples

Download data: TXT

(Submitter supplied) The goal was to identify genes targeted by miR-30a. Keywords: Transfection of cultured cells with antisense oligonucleotide

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

10 Samples

Download data: CEL

(Submitter supplied) Transcriptional profiling of miRNA in embryonic and newborn mouse liver Keywords: miRNA, liver, newborn, embryonic

Organism:

Mus musculus

Type:

Non-coding RNA profiling by array

Platform:

GPL6512

12 Samples

Download data: TXT