GEO DataSets

(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) 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) The optic vesicle comprises a pool of bi-potential progenitor cells from which the retinal pigment epithelium (RPE) and neural retina fates segregate during ocular morphogenesis. Several transcription factors and signaling pathways have been shown to be important for RPE maintenance and differentiation, but an understanding of the initial fate specification and determination of this ocular cell type is lacking. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL14875

6 Samples

Download data: TXT

(Submitter supplied) The developmental pathway of the neural retina (NR) and retinal pigment epithelium (RPE) has been revealed by extensive research in mice. However, the molecular mechanisms underlying the development of the human NR and RPE, as well as the interactions between these two tissues, have not been well defined. Here, we analyzed 2,421 individual cells from human fetal NR and RPE using single-cell RNA sequencing (RNA-seq) technique and revealed the tightly regulated spatiotemporal gene expression network of human retinal cells. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

64 Samples

Download data: CSV

(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) 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) 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 high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL20828

38 Samples

Download data: TAB, XLS

(Submitter supplied) Retinoic acid (RA) is a key signal for the specification of the pancreas. Still, the gene regulatory cascade triggered by RA in the endoderm remains poorly characterized. In this study, we investigated this regulatory network in zebrafish by combining RNA-seq, RAR ChIP-seq and ATAC-seq assays. By analysing the effect of RA and of the RA receptor (RAR) antagonist BMS439 on the transcriptome and on the chromatin accessibility of endodermal cells, we identified a large set of genes and regulatory regions regulated by RA signalling. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20828

24 Samples

Download data: TAB

(Submitter supplied) Retinoic acid (RA) is a key signal for the specification of the pancreas. Still, the gene regulatory cascade triggered by RA in the endoderm remains poorly characterized. In this study, we investigated this regulatory network in zebrafish by combining RNA-seq, RAR ChIP-seq and ATAC-seq assays. By analysing the effect of RA and of the RA receptor (RAR) antagonist BMS439 on the transcriptome and on the chromatin accessibility of endodermal cells, we identified a large set of genes and regulatory regions regulated by RA signalling. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20828

2 Samples

Download data: XLS

(Submitter supplied) Retinoic acid (RA) is a key signal for the specification of the pancreas. Still, the gene regulatory cascade triggered by RA in the endoderm remains poorly characterized. In this study, we investigated this regulatory network in zebrafish by combining RNA-seq, RAR ChIP-seq and ATAC-seq assays. By analysing the effect of RA and of the RA receptor (RAR) antagonist BMS439 on the transcriptome and on the chromatin accessibility of endodermal cells, we identified a large set of genes and regulatory regions regulated by RA signalling. more...

Organism:

Danio rerio

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL20828

12 Samples

Download data: XLS

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

Organism:

Mus musculus; synthetic construct

Type:

Expression profiling by array; Non-coding RNA profiling by array

Platforms:

GPL10740 GPL14613

14 Samples

Download data: CEL

(Submitter supplied) Dysfunction of the retinal pigmented epithelium (RPE) results in degeneration of photoreceptors and vision loss and is correlated with common blinding disorders in humans. Although many protein-coding genes are known to be expressed in RPEs and important for their development and maintenance, virtually nothing is known about the in vivo roles of non-protein coding transcripts in RPEs. The expression patterns of microRNAs (miRNAs) have been analyzed in a variety of ocular tissues, and few were implicated to play role in RPE based on studies in cell lines. more...

Organism:

Mus musculus; synthetic construct

Type:

Non-coding RNA profiling by array

Platform:

GPL14613

7 Samples

Download data: CEL

(Submitter supplied) Dysfunction of the retinal pigmented epithelium (RPE) results in degeneration of photoreceptors and vision loss and is correlated with common blinding disorders in humans. Although many protein-coding genes are known to be expressed in RPEs and important for their development and maintenance, virtually nothing is known about the in vivo roles of non-protein coding transcripts in RPEs. The expression patterns of microRNAs (miRNAs) have been analyzed in a variety of ocular tissues, and few were implicated to play role in RPE based on studies in cell lines. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL10740

7 Samples

Download data: CEL

(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 pigment epithelium (RPE) cells can be obtained through in vitro differentiation of both embryonic stem cell (ESC) and induced pluripotent stem cells (iPSC) for cell replacement therapy. We have previously identified 87 signature genes relevant to RPE cell differentiation and function through transcriptome analysis of both human ESC- and iPSC-derived RPE as well as normal fetal RPE. Here, we profiled miRNA expression through small RNA-seq in human ESCs and their RPE derivatives. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL11154

10 Samples

Download data: TXT

(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) During embryonic development, tissue-specific transcription factors and chromatin remodelers function together to assure the gradual, coordinated differentiation of multiple lineages. Here, we study this regulatory interplay in the developing retinal pigmented epithelium (RPE), a neuroectodermal lineage essential for the development, function, and maintenance of the adjacent retina. We present a high-resolution spatial transcriptomic atlas of the developing mouse RPE and the adjacent ocular mesenchyme, obtained by geographic positional sequencing (Geo-Seq) of a single development stage of the eye, encompassing young and more mature ocular progenitors. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

112 Samples

Download data: TXT

(Submitter supplied) Retinal Pigment Epithelium (RPE) derived from two human embryonic stem cell lines, H1 and H9, were compared with human fetal RPE (hfRPE) using RNA-seq. Nominally, the transcriptome of H1-derived RPE showed greater overlap with hfRPE. For cells maintained in the medium used to differentiate RPE, 6.2% (H1-RPE) and 4.2% (H9-RPE) of the transcripts were expressed in amounts that were statistically different from hfRPE (false discovery rate: 5%). more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL9115 GPL11154

12 Samples

Download data: TXT

(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