GEO DataSets

(Submitter supplied) Leber congenital amaurosis (LCA) includes congenital or early-onset blinding diseases, characterized by vision loss together with nystagmus and nonrecordable electroretinogram (ERG). At least 19 genes are associated with LCA. While most LCA is recessive, mutations in the homeodomain transcription factor gene CRX lead to autosomal dominant LCA. The mechanism of CRX-LCA is not understood. Here, we report a new spontaneous mouse mutant carrying a frameshift mutation in Crx (CrxRip). more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11002

20 Samples

Download data: TXT

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

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24676 GPL16791

43 Samples

Download data: H5

(Submitter supplied) Mutations in the cone-rod homeobox (CRX) transcription factor lead to distinct retinopathy phenotypes, including early-onset vision impairment in dominant Leber congenital amaurosis (LCA). Using induced pluripotent stem cells (iPSCs) from a patient with CRX-I138fs mutation, we established an in vitro model of CRX-LCA in retinal organoids that exhibit defective photoreceptor maturation by histology and gene profiling including diminished expression of visual opsins. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

5 Samples

Download data: H5

(Submitter supplied) Mutations in the cone-rod homeobox (CRX) transcription factor lead to distinct retinopathy phenotypes, including early-onset vision impairment in dominant Leber congenital amaurosis (LCA). Using induced pluripotent stem cells (iPSCs) from a patient with CRX-I138fs mutation, we established an in vitro model of CRX-LCA in retinal organoids that exhibit defective photoreceptor maturation by histology and gene profiling including diminished expression of visual opsins. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

38 Samples

Download data: TXT

(Submitter supplied) P10 retinal gene expression analysis of the homozygous Crx Knock-OUT or Knock-IN mice carrying the mutation E168d2 or R90W. Results provide important information about the retinal genes affected by mutations in the transcription factor Crx, which have been implicated in human retinopathies.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6887

12 Samples

Download data: TXT

(Submitter supplied) Otx2 has been shown to be non cell autonomously required for photoreceptor cell survival in the adult mouse RPE. This study aims to identify Otx2 DNA binding profile in both RPE and neural retina to i) identify direct targets of Otx2 in the RPE ii) compare Otx2 binding profile in neural retina and RPE to unveil hidden functions in the neural retina.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11002

7 Samples

Download data: BED

(Submitter supplied) To analyze the expression profile in the Otx2 knock-in (a knock-in mouse line expressing Otx2 from the Crx locus on chromosome 7) and Crx knockout retina, we performed a microarray analysis using wild-type (Crx +/+), Otx2 KI (Crx Otx2/Otx2) and Crx KO (Crx -/-) retina at P12.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL13912

3 Samples

Download data: TXT

(Submitter supplied) Background: Mutations in the cone-rod-homeobox protein CRX are typically associated with dominant blinding retinopathies with variable age of onset and severity. Five well-characterized mouse models carrying different Crx mutations show a wide range of disease phenotypes. To determine if the phenotype variability correlates with distinct changes in CRX target gene expression, we perform RNA-seq analyses on three of these models and compare the results with published data. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

30 Samples

Download data: TXT

(Submitter supplied) Rod and cone photoreceptors in mammalian retina are generated from common pool(s) of neuroepithelial progenitors. NRL, CRX and NR2E3 are key transcriptional regulators that control photoreceptor differentiation. Mutations in NR2E3, a rod-specific orphan nuclear receptor, lead to loss of rods, increased density of S-cones, and supernormal S-cone-mediated vision in humans. To better understand its in vivo function, NR2E3 was expressed ectopically in the Nrl-/- retina, where post-mitotic precursors fated to be rods develop into functional S-cones similar to the human NR2E3 disease. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Dataset:

GDS2455

Platform:

GPL1261

8 Samples

Download data: CEL

Analysis of 4 week-old neural retinal leucine zipper (NRL) null retinas expressing photoreceptor-specific nuclear receptor (NR2E3) from the cone-rod homeobox (CRX) promoter. NRL, NR2E3, and CRX control photoreceptor differentiation. Results provide insight into the molecular function of NR2E3.

Organism:

Mus musculus

Type:

Expression profiling by array, transformed count, 2 strain sets

Platform:

GPL1261

Series:

GSE5338

8 Samples

Download data: CEL

(Submitter supplied) CRX is a key transcript factor for photoreceptor development and homeostasis. We have characterized the CRX-dependent cis-regulatory network by ChIP-chip analysis of 2 month old BL/6 mouse retinas using Affymetrix Mouse Promoter 1.0 arrays

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL5811

1 Sample

Download data: BED, CEL, TXT

(Submitter supplied) In order to define the genomic targets of Crx, we carried out Crx chromatin-immunoprecipitation followed by massively parallel sequencing (ChIP-seq) of eight-week-old mouse retinas using the Solexa platform. Sequence reads were mapped to the genome and 'peaks' were identified. These data were subjected to extensive bioinformatic analysis. In addition, selected peaks were experimentally tested for cis-regulatory activity by electroporation as promoter-reporter fusions into living mouse retinas. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9185

7 Samples

Download data: BED

(Submitter supplied) Mutation of rod photoreceptor-enriched transcription factors is a major cause of inherited blindness. We identified the orphan nuclear hormone receptor ERRβ as selectively expressed in rod photoreceptors. Overexpression of ERRβ induces expression of rod-specific genes in retinas of both wildtype and in Nrl-/- mice, which lack rod photoreceptors. Mutation of ERRβ results in dysfunction and degeneration of rods, while inverse agonists of ERRβ trigger rapid rod degeneration, which is rescued by constitutively active mutants of ERRβ. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

6 Samples

Download data: CEL, CHP

(Submitter supplied) Photoreceptor disorders are collectively known as retinal degeneration (RD), and include retinitis pigmentosa (RP), cone-rod dystrophy and age related macular degeneration (AMD). These disorders are largely genetic in origin; individual mutations in any one of >200 genes cause RD, making mutation specific therapies prohibitively expensive. A better treatment plan, particularly for late stage disease, may involve stem cell transplants into the photoreceptor or ganglion cell layers of the retina. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL8321

20 Samples

Download data: CEL

(Submitter supplied) To comprehensively capture changes in retinal transcriptome for the LCA7 organoids compared to control, we performed single cell RNA-sequencing (scRNAseq) using the 10X Genomics platform. Retinal organoids at D150 of differentiation were dissociated for scRNAseq analysis. scRNAseq data revealed significant dysregulation of specific photoreceptor genes between control and LCA7 organoids, as well as mutation-specific differences in various genes, including CRX, RCVRN, ARR3, and AIPL1.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

3 Samples

Download data: TAR

(Submitter supplied) To define molecular mechanisms underlying rod and cone differentiation, we generated H9 human embryonic stem cell line carrying a GFP reporter that is controlled by the promoter of cone-rod homeobox (CRX) gene, the first known marker of post-mitotic photoreceptor precursors. CRXp-GFP reporter in H9 line replicates endogenous CRX expression when induced to form self-organizing 3-D retina-like tissue. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL10999

23 Samples

Download data: CSV, XLS

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

Organism:

Mus musculus

Type:

Non-coding RNA profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platforms:

GPL21103 GPL17021

22 Samples

Download data

(Submitter supplied) We performed mRNA transcriptional profiling of mouse retina in the wild-type and Nrl-null context to determine Nrl-dependent gene expression We sequenced cDNA libraries made from polyA+ selected RNA from retinas of litter-matched WT and Nrl-/- adult mice at postnatal day 21 (P21) (WT vs Nrl-/-, n=5 and n= 6 resp.)

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

11 Samples

Download data: XLSX

(Submitter supplied) We performed non-coding transcriptional profiling to identify Nrl-dependent ncRNAs by deep sequencing non-polyadenylated RNA from the same control and Nrl-/- retinal samples. non-coding RNA profiling is a robust method for the identification of cell-type specific functional enhancer elements in the mouse retina

Organism:

Mus musculus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL21103

11 Samples

Download data: BW, TXT

(Submitter supplied) In the vertebrate retina, the Otx2 transcription factor plays a crucial role in the cell fate determination of both rod and cone photoreceptors. Otx2 conditional knockout (CKO) mice exhibited a total absence of rods and cones in the retina due to their cell fate conversion to amacrine-like cells. In order to investigate the entire transcriptome regulated by Otx2 in the developing retina, we performed microarray analysis on the Otx2 CKO retina.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

12 Samples

Download data: CEL