GEO DataSets

(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) Retinal cells are specified in a zebrafish recessive mutant called young (yng) but they fail to terminally differentiate; i.e. extend neurites and make synaptic contacts. A point mutation in a brahma-related gene 1 (brg1) is responsible for this phenotype. In this microarray study, a three-factor factorial design was utilized to investigate the effects of 1) mutation, 2) change in time (36 vs. 52hpf), and 3) change in tissue (retina vs. more...

Organism:

Danio rerio

Type:

Expression profiling by array

Platform:

GPL1319

24 Samples

Download data: CEL, EXP

(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) 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) Purpose: The retinal pigment epithelium (RPE) forms the outer blood-retinal barrier. Primary cultures of RPE can model the barrier, but are very sensitive to culture conditions. We examined how the neural retina regulates the RPE transcriptome in a culture model of embryonic development. Attention focused on the tight junctional genes essential for barrier function. Methods: Chick RPE from embryonic day 7 (E7) or embryonic day 14 (E14) was cultured on filters in a serum free medium. more...

Organism:

Gallus gallus

Type:

Expression profiling by array

Platform:

GPL3213

24 Samples

Download data: CEL, CHP

(Submitter supplied) The retinal pigment epithelium (RPE) is a polarized cell layer that is critical for photoreceptor function and survival. It’s unique relationship to the photoreceptors and its specific physiology makes the RPE a critical determinant of human vision. Therefore we performed global expression profiling of native and cultured human fetal and adult RPE and determined a unique set of highly-expressed genes (called the “signature” set) by comparing the observed RPE gene profiles to the Novartis expression database (SymAtlas: http://wombat.gnf.org/index.html) of 78 tissues.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

31 Samples

Download data: CEL

(Submitter supplied) We characterize transcriptomic landscape using RNA-seq in isolated NR and RPE populations in zebrafish.

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18413

15 Samples

Download data: TXT

(Submitter supplied) We captured chromatin accessibility branching using ATAC-seq in isolated NR and RPE populations in zebrafish. We identify differentially active cis-regulatory modules and classify them as activating or repressing elements.

Organism:

Danio rerio

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18413

4 Samples

Download data: BED

(Submitter supplied) The microarray technique was used to investigate gene expression level changes in human retinal pigment epithelium (RPE) microdissected from fetal eyes (13 and 16 weeks of gestation) and adult eyes (40-60 years old). The gene expression analysis of human fetal RPE during development were performed and compared to human native RPE. Of the 45,033 probe sets on the microarray, 30,736 were detected. 3498 differentially expressed genes could be clustered into 8 patterns of expression that were statistically significant. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL10191 GPL16025

6 Samples

Download data: CALLS, PAIR, TXT

(Submitter supplied) Mesoderm differentiation in zebrafish relies on a complex interaction between transcription factors and signaling pathways. Tbx16 is a t-box transcription factor involved in this interaction. Here, we examine downstream targets of tbx16 in the intermediate mesoderm at the 4/5-somite stage and tail mesoderm at the 21-somite stage by comparing wild-type tissues with tissues from the tbx16 mutant, spadetail (spt).

Organism:

Danio rerio

Type:

Expression profiling by array

Platform:

GPL1319

11 Samples

Download data: CEL

(Submitter supplied) Uveal coloboma is a congenital eye malformation caused by failure of the optic fissure to close in early human development.  Despite significant progress in identifying genes whose regulation is important for executing this closure, mutations are detected in a minority of cases using known gene panels, implying additional genetic complexity.  We show that the mouse Zfp503/Nlz2 gene is dynamically regulated in developing mouse eyes and that loss of its expression results in uveal coloboma. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

12 Samples

Download data: TXT

(Submitter supplied) The retinal pigment epithelial (RPE) cell line ARPE-19 provides a widely-used alternative to native RPE. However, retention of the native RPE phenotype becomes problematic after multiple passages. We wished to determine if suitable culture conditions and differentiation could restore RPE-appropriate gene expression to ARPE-19. ARPE-19 cells at passages p9 to p12, grown in DMEM containing high glucose and pyruvate with 1% fetal bovine serum, were differentiated for up to 4 months. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

6 Samples

Download data: TXT

(Submitter supplied) Age-related macular degeneration is a progressive disease resulting in impaired central vision. Degeneration of the retinal pigmented epithelial (RPE) monolayer is associated with the progression of the disease. To date no treatment is able to stop this progression, however new cell replacement studies using human embryonic stem cells (hESC) to generate RPE show a promising prospective. To improve cell replacement strategies a better understanding about the development of RPE cells is necessary. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL4133

12 Samples

Download data: TXT

(Submitter supplied) Retinal degeneration often affects the whole retina even though the disease-causing gene is specifically expressed in the light-sensitive photoreceptors. These retinal defects can potentially be determined by gene-expression profiling of the whole retina. In this study, we measured the gene-expression profile of retinas microdissected from a zebrafish pde6cw59 (pde6c) mutant. Its retinas display not only photoreceptor degeneration but also issues in other cell types starting from 4 days postfertilization (dpf). more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL14875

6 Samples

Download data: TXT

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

Organism:

Homo sapiens

Type:

Other; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL24676 GPL23227

53 Samples

Download data: BEDGRAPH

(Submitter supplied) Vision depends on the functional interplay between the photoreceptor cells of the neural retina and the supporting cells of the underlying retinal pigment epithelium (RPE). Many genes involved in inherited retinal diseases (IRD) display highly specific spatiotemporal expression within these interconnected retinal components through the local recruitment of cis-regulatory elements (CREs) in 3D nuclear space. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL23227

4 Samples

Download data: HIC

(Submitter supplied) Vision depends on the functional interplay between the photoreceptor cells of the neural retina and the supporting cells of the underlying retinal pigment epithelium (RPE). Many genes involved in inherited retinal diseases (IRD) display highly specific spatiotemporal expression within these interconnected retinal components through the local recruitment of cis-regulatory elements (CREs) in 3D nuclear space. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL24676

41 Samples

Download data: BEDGRAPH