GEO DataSets

(Submitter supplied) Corneal epithelial RCE1(5T5) cells follow a sequential process that leads to the formation of a 4-5 layered stratified epithelium with a gene expression pattern similar to that shown in primary cultures of corneal epithelial cells. We have identified three different developmental stages during the differentiation of the rabbit corneal epithelial cell line RCE1(5T5), and thus, analyzed the transcriptome of such different stages in order to understand the regulation of the corneal epithelial cell differentiation. more...

Organism:

Oryctolagus cuniculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16405

3 Samples

Download data: TXT

(Submitter supplied) PAX6-related Aniridia is a sight-threatening disease due to progression of secondary glaucoma and aniridia associated keratopathy (AAK). Changes or loss of limbal epithelial progenitors causes the epithelial surfaces defects. We analyzed how PAX6 contribute to this with a two-step approach. 1) mRNA Sequencing of limbal epithelial cells isolated from controls and aniridia patients. 2) confirming the bioinformatical and literature-based result list on a siRNA based primary aniridia cell model (PAX6- knockdown). more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

4 Samples

Download data: BW

(Submitter supplied) Ability of CTCF binding on various gene promoters is essential to regulate their expression. It's been demonstrated that cornea-specific Pax6 expression is regulated conversely by CTCF (Li et al.). circular chromosome conformation capture (4C) and ChIP-chip profiling have been performed using HTCE cells. This approach is to elicit the epigenetic mechanism involving CTCF-mediated chromatin remodeling that regulates Pax6 and some target gene interactions.

Organism:

Homo sapiens

Type:

Other

Platform:

GPL22144

1 Sample

Download data: GFF, PAIR

(Submitter supplied) The specialized corneal epithelium requires differentiated properties, specific for its role at the anterior surface of the eye, thus tight maintenance of the differentiated qualities of the corneal epithelial is essential. Our studies have focused on pinin (PNN), an exon junction component (EJC) that has dramatic implications on corneal epithelial cell differentiation and may act as a stabilizer of the corneal epithelial cell phenotype. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

32 Samples

Download data: XLSX

(Submitter supplied) Corneal epithelial stem cells reside in the limbus that is the transitional zone between the cornea and conjunctiva, and are essential to maintain the homeostasis of corneal epithelium. However, their characterization is poorly understood. Therefore, we constructed gene expression profiles of limbal epithelial SP and non-SP cell using RNA-sequencing. As a result, limbal epithelial SP cells have immature cell phenotypes with endothelial/mesenchymal cell markers, while limbal epithelial non-SP cells have epithelial progenitor cell markers.

Organism:

Oryctolagus cuniculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21655

8 Samples

Download data: TXT

(Submitter supplied) Microarray was used to study global gene expression of a cell culture model based on SV40-immortalized human corneal epithelial (iHCE) cells. The gene expression profile of the cell line was compared to the normal human corneal epithelium. Affymetrix HG-U133A GeneChips® were used for microarray experiments and results were validated by performing RT-qPCR for selected genes. iHCE was found to over- and under-express 22 % and 14 % of the annotated genes, respectively. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL96

3 Samples

Download data: CEL

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

Organism:

Homo sapiens

Type:

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

Platform:

GPL20795

44 Samples

Download data: XLSX

(Submitter supplied) Adult stem cell identity, plasticity, and homeostasis are precisely orchestrated by lineage-restricted epigenetic and transcriptional regulatory networks. Here, by integrating super-enhancer and chromatin accessibility landscapes, we delineate core transcription regulatory circuitries (CRCs) of limbal stem/progenitor cells (LSCs) and find that RUNX1 and SMAD3 are required for maintenance of the corneal epithelial identity and homeostasis. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL20795

32 Samples

Download data: XLSX

(Submitter supplied) Adult stem cell identity, plasticity, and homeostasis are precisely orchestrated by lineage-restricted epigenetic and transcriptional regulatory networks. Here, by integrating super-enhancer and chromatin accessibility landscapes, we delineate core transcription regulatory circuitries (CRCs) of limbal stem/progenitor cells (LSCs) and find that RUNX1 and SMAD3 are required for maintenance of the corneal epithelial identity and homeostasis. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20795

12 Samples

Download data: XLSX

(Submitter supplied) Limbal vs. corneal epithelial basal cell gene expression patterns were identified and compared Keywords: repeat

Organism:

Mus musculus

Type:

Expression profiling by array

Dataset:

GDS2433

Platform:

GPL1261

16 Samples

Download data: CEL, EXP

Analysis of microdissected resting limbal epithelial basal cells (LE) and central corneal epithelial (CE) basal cells of the eye. LE are enriched in corneal epithelial stem cells, CE in transient amplifying cells. Results provide insight into the molecular nature of the two basal cell populations.

Organism:

Mus musculus

Type:

Expression profiling by array, count, 8 individual, 2 tissue sets

Platform:

GPL1261

Series:

GSE4098

16 Samples

Download data: CEL, EXP

(Submitter supplied) Forkhead box C1 (FOXC1) is required for neural crest and ocular development, and mutations in FOXC1 lead to inherited Axenfeld–Rieger syndrome. Here, we find that FOXC1 and paired box 6 (PAX6) are co-expressed in the human limbus and central corneal epithelium. Deficiency of FOXC1 and alternation in epithelial features occur in patients with corneal ulcers. FOXC1 governs the fate of the corneal epithelium by directly binding to lineage-specific open promoters or enhancers marked by H3K4me2. more...

Organism:

Homo sapiens

Type:

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

Platform:

GPL20795

18 Samples

Download data: BED, XLSX

(Submitter supplied) Corneal epithelial cells derived from hPSCs provides an important cells source for the construction of the in vitro preclinical models aimed for ophthalmic drugs tests. However, the recent differentiation protocols lack the optimal culturing conditions that hinder the robustness and the quality of cells as well as the scale-up application of cells production. Here we introduce a simplified, yet efficient small molecules-based corneal induction method (SSM-CI) for the generation of corneal epithelial cells from hPSCs. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

12 Samples

Download data: TAB, XLSX

(Submitter supplied) Single-cell expression profiling by RNA-Seq promises to exploit cell-to-cell variation in gene expression to reveal regulatory circuitry governing cell differentiation and other biological processes. Here, we describe Monocle, a novel unsupervised algorithm for ordering cells by progress through differentiation that dramatically increases temporal resolution of expression measurements. This reordering unmasks switch-like changes in expression of key regulatory factors, reveals sequentially organized waves of gene regulation, and exposes regulators of cell differentiation. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL11154 GPL16791

384 Samples

Download data: TXT