GEO DataSets

(Submitter supplied) Loss of the retinal pigment epithelium (RPE) due to dysfunction or disease can lead to blindness in humans. Harnessing the intrinsic ability of the RPE to self-repair is an attractive therapeutic strategy; however, mammalian RPE is limited in its regenerative capacity. Zebrafish possess tremendous intrinsic regenerative potential in ocular tissues, including the RPE, but little is known about the mechanisms that drive RPE regeneration. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20828

18 Samples

Download data: TXT

(Submitter supplied) Loss of the retinal pigment epithelium (RPE) due to dysfunction or disease can lead to blindness in humans. Harnessing the intrinsic ability of the RPE to self-repair is an attractive therapeutic strategy; however, mammalian RPE is limited in its regenerative capacity. Zebrafish possess tremendous intrinsic regenerative potential in ocular tissues, including the RPE, but little is known about the mechanisms that drive RPE regeneration. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20828

12 Samples

Download data: TXT

(Submitter supplied) Zebrafish is capable of endogenously regenerating functional retina pigment epithelium (RPE) after widespread genetic ablation which involves a series of cellular and molecular events that remain to be defined. Here, using the RPE genetic ablation model in zebrafish, we observed that mTOR signaling was activated in the RPE cells post-ablation. Pharmacological and genetic inhibition of mTOR signaling impaired RPE regeneration, while activation of mTOR signaling benefited RPE recovery, suggesting mTOR signaling was required and sufficient for RPE regeneration post-ablation in zebrafish. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20828

24 Samples

Download data: 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) Eye development and photoreceptor maintenance requires the retinal pigment epithelium (RPE), a thin layer of cells that underlies the neural retina. Despite its importance, RPE development has not been studied by a genomic approach. A microarray expression profiling methodology was established in this study for studying RPE development. The intact retina with RPE attached was dissected from developing embryos, and differentially expressed genes in RPE were inferred by comparing the dissected tissues with retinas without RPE using microarray and statistical analyses. more...

Organism:

Danio rerio

Type:

Expression profiling by array

Dataset:

GDS2556

Platform:

GPL1319

6 Samples

Download data: CEL, DAT

Analysis of microdissected embryonic retinas with or without the retinal pigment epithelium (RPE). The RPE is a thin layer of cells that underlies the neural retina and supports the function and development of photoreceptors. Results provide insight into the development of the RPE.

Organism:

Danio rerio

Type:

Expression profiling by array, count, 2 tissue sets

Platform:

GPL1319

Series:

GSE5048

6 Samples

Download data: CEL, DAT

(Submitter supplied) Adult zebrafish are able to regenerate many organs such as their caudal fin in only few days post amputation. To explore the landscape and dynamic of the genes involed in regeneration, we performed a global transcriptomic analysis using RNA-seq during zebrafish caudal fin regeneration.

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24788

12 Samples

Download data: XLSX

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

Organism:

Mus musculus

Type:

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

Platforms:

GPL21493 GPL21103 GPL25621

15 Samples

Download data: BED, BEDGRAPH, TXT

(Submitter supplied) We investigated the epigenetic plasticity of adult murine RPE using whole-genome bisulfite sequencing (WGBS)

Organism:

Mus musculus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL21493

2 Samples

Download data: BEDGRAPH

(Submitter supplied) We investigated the epigenetic plasticity of adult murine RPE using ChIP-seq analysis.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21103

10 Samples

Download data: BED

(Submitter supplied) To characterize RPE isolated from adult mice, we studied gene expression in these cells using MEEBO microarrays.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL25621

3 Samples

Download data: TXT

(Submitter supplied) To explore the epigenetic contribution to retinal development, we generated conditional knockout alleles of DNA methytransferase-1 (Dnmt1) mediated by Rx-Cre in mice. The results demonstrate a unique function of DNMT1-mediated DNA methylation in controlling RPE apicobasal polarity and neural retina differentiation.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6096

32 Samples

Download data: CEL

(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:

GPL18413 GPL14664

16 Samples

Download data: TXT

(Submitter supplied) Zebrafish can regenerate their hearts. As a first response to injury, the epicardium reacts by upregulalion of developmental marker genes. Here we compared in an unbiased manner the expression of the epicardium from uninjured zebrafish hearts and hearts at 3 days postcryoinjury. To label epicardial cells of uninjured hearts we usd pard3:GFP (POon et al 2010) and to label epicardium of the injured heart wt1b:eGFP (Perner et al 2007)

Organism:

Danio rerio

Type:

Expression profiling by array

Platform:

GPL14664

8 Samples

Download data: TXT, XLS

(Submitter supplied) Little is known about zebrafish macrophage subtypes and their contribution to organ regeneration. Using the transgenic line wt1b:eGFP we identified a subtype of macrophages in the regenerating heart that is transcriptionally different from the rest of macrophages.

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18413

8 Samples

Download data: XLS

(Submitter supplied) Primary neonatal rat cardiac myocytes or fibroblasts were isolated and subjected to siRNA mediated Yap knockdown

Organism:

Rattus norvegicus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24782

12 Samples

Download data: XLSX

(Submitter supplied) A Yap knockout zebrafish line was used to observe how loss of Yap affects cardiac regeneration.

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24776

12 Samples

Download data: XLSX

(Submitter supplied) Zebrafish have the remarkable ability to regenerate body parts including the heart, spinal cord and fins by a process referred to as epimorphic regeneration. Recent studies have illustrated that similar to adult zebrafish, early life stage-larvae also possess the ability to regenerate the caudal fin. A comparative genomic analysis was used to determine the degree of conservation in gene expression among the regenerating adult caudal fin, adult heart and larval fin. more...

Organism:

Danio rerio

Type:

Expression profiling by array

Platform:

GPL1319

24 Samples

Download data: CEL, CHP

(Submitter supplied) To determine mouse retinal pigment epithelium (RPE) specific gene expression, we compared the gene expression profile of the RPE to the gene expression of its adjacent layers: the choroid (CH) and photoreceptors (PR). We collected the tissues using the meticulous laser dissection microscopy. Next, we performed RNA isolation, amplification, labeling and hybridization against 44k Agilent microarrays. Compared RPE gene expression with CH gene expression, and with PR gene expression

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL10333

9 Samples

Download data: TXT