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Links from GEO DataSets

Items: 20

1.
Full record GDS2455

Photoreceptor-specific nuclear receptor NR2E3 ectopic expression effect on NRL null retinas

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
2.

In vivo function of NR2E3 in establishing photoreceptor identity during mammalian retinal development

(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
Series
Accession:
GSE5338
ID:
200005338
3.

Expression profiling of the developing and mature Nrl -/- mouse retina (Yoshida et al. 2004, HMG)

(Submitter supplied) The rod photoreceptor-specific neural retina leucine zipper protein Nrl is essential for rod differentiation and plays a critical role in regulating gene expression. In the mouse retina, rods account for 97% of the photoreceptors; however, in the absence of Nrl (Nrl-/-), no rods are present and a concomitant increase in cones is observed. Using mouse GeneChips (Affymetrix), we have generated expression profiles of the wild-type and Nrl-/- retina at three time-points representing distinct stages of photoreceptor differentiation. more...
Organism:
Mus musculus
Type:
Expression profiling by array
Dataset:
GDS2936
Platform:
GPL81
24 Samples
Download data: CEL
Series
Accession:
GSE8972
ID:
200008972
4.
Full record GDS2936

Neural retina leucine zipper deficiency effect on retinas: time course

Analysis of retinas of mutants lacking the rod photoreceptor-specific neural retina leucine zipper protein (Nrl), at up to 2 months of age. In the absence of Nrl, rods are missing and cones increase in number. Results provide insight into the differences between the two photoreceptor subtypes.
Organism:
Mus musculus
Type:
Expression profiling by array, count, 3 age, 2 genotype/variation sets
Platform:
GPL81
Series:
GSE8972
24 Samples
Download data: CEL
DataSet
Accession:
GDS2936
ID:
2936
5.

Targeting of GFP to new-born rods by Nrl promoter and temporal expression profiling of flow-sorted photoreceptors

(Submitter supplied) Purpose: To investigate the gene regulatory networks during photoreceptor differentiation. Special aims: To generate gene expression profiles of purified photoreceptors at distinct developmental stages and from different genetic backgrounds. Background: Rod photoreceptor genesis spans a broad temporal window during retinal development. It starts as early as E12.5 and peaks at P0-P2. At E16.5, there are some early born rods but the peak of rod genesis does not occur. more...
Organism:
Mus musculus
Type:
Expression profiling by array
Dataset:
GDS1693
Platform:
GPL1261
39 Samples
Download data: CEL, TXT
Series
Accession:
GSE4051
ID:
200004051
6.
Full record GDS1693

Transcription factor Nrl deficiency effect on photoreceptor development

Analysis of photoreceptors (PRs) from wild type and Nrl deficient retinas at various developmental stages. PRs isolated based on transgene GFP expression from an Nrl promoter. Nrl ablation leads to cones at the expense of rods. Results provide insight into the regulation of PR development.
Organism:
Mus musculus
Type:
Expression profiling by array, count, 5 development stage, 2 genotype/variation sets
Platform:
GPL1261
Series:
GSE4051
39 Samples
Download data: CEL
7.

Gene expression changes during retinal development and rod specification.

(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
Series
Accession:
GSE59201
ID:
200059201
8.

Transcriptome dynamics of developing photoreceptors in 3-D retina cultures recapitulates temporal sequence of human cone and rod differentiation revealing cell surface markers and gene networks

(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
Series
Accession:
GSE67645
ID:
200067645
9.

The orphan nuclear hormone receptor ERRβ controls rod photoreceptor survival.

(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
Series
Accession:
GSE21944
ID:
200021944
10.

Expression profiling of P14 and P28 mouse retina from 4 genotypes: +/+, Rorb-/- , +/+;CrxpNrl and Rorb-/-;CrxpNrl

(Submitter supplied) Rorb is essential for rod photoreceptor development in the mouse retina. Using Affymetrix mouse GeneChips, we have generated expression profiles of the +/+, Rorb-/- , +/+;CrxpNrl and Rorb-/-;CrxpNrl retina at P14 and P28. In this dataset, we include the expression data obtained from retina of wt and mutants. These data are used to obtain 1189 genes that are differentially expressed in Rorb-/- vs wt.
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL1261
31 Samples
Download data: CEL
Series
Accession:
GSE16585
ID:
200016585
11.

Genome-Wide CRX Binding Sites in adult mouse photoreceptors

(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
Series
Accession:
GSE23567
ID:
200023567
12.

Deciphering the cis-regulatory architecture of mammalian photoreceptors

(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
Series
Accession:
GSE20012
ID:
200020012
13.

Enhancer transcription identifies cis-regulatory elements for photoreceptor cell types

(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:
GPL17021 GPL21103
22 Samples
Download data
Series
Accession:
GSE136565
ID:
200136565
14.

Transcriptional profiling of the adult mouse retina in wild-type and Nrl deficient mice

(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
Series
Accession:
GSE136564
ID:
200136564
15.

Non-coding Transcriptional profiling of the adult mouse retina in wild-type and Nrl deficient mice

(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
Series
Accession:
GSE136563
ID:
200136563
16.

Preservation of cone photoreceptors after a rapid yet transient degeneration and remodeling in cone-only Nrl-/- mouse retina

(Submitter supplied) Cone photoreceptors are the primary initiator of visual transduction in the human retina. Dysfunction or death of rod photoreceptors precedes cone loss in many retinal and macular degenerative diseases, suggesting a rod-dependent trophic support for cone survival. Rod differentiation and homeostasis are dependent on the basic motif leucine zipper transcription factor NRL. The loss of Nrl in mice (Nrl-/-) results in a retina with predominantly S-opsin containing cones that exhibit molecular and functional characteristics of WT cones. more...
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL6193
20 Samples
Download data: CEL
Series
Accession:
GSE33674
ID:
200033674
17.

OTX2 loss causes rod differentiation defect in CRX-associated congenital blindness

(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
Series
Accession:
GSE52006
ID:
200052006
18.

Sall3 controls cone photoreceptor and horizontal cell differentiation

(Submitter supplied) Transcription factors have been implicated in the specification and differentiation of all cells in the mammalian retina with several transcription factors controlling the development of multiple neuronal subclasses. Horizontal cells and cone photoreceptors share a particularly intimate functional relationship but have been previously thought to develop through separate and distinct intrinsic molecular processes. more...
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL6096
6 Samples
Download data: CEL, CHP
Series
Accession:
GSE24083
ID:
200024083
19.

Temporal ChIP-on-Chip of RNA-Polymerase-II to detect novel gene activation events during photoreceptor maturation

(Submitter supplied) RNA Polymerase-II active regions were mapped comparing mouse neural retina tissue at age P25 and P2 to find novel gene activation predictions during maturation of photoreceptors. Over 800 predictions of increased activation were novel compared to previous mRNA expression array studies.
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by genome tiling array
Platform:
GPL5811
3 Samples
Download data: BED, CEL
Series
Accession:
GSE19999
ID:
200019999
20.

Epigenomic Landscapes of Retinal Rods and Cones

(Submitter supplied) Both rod and cone photoreceptors are critical for mammalian vision yet they have important functional differences. In this study, we investigate patterns of DNA methylation and chromatin accessibility in mouse rods and cones. Unexpectedly, we find that a substantial fraction of hypo-methylated regions in the rod methylome are in inaccessible chromatin. These regions show marks of active regulatory regions earlier in neuronal development and could remain undermethylated in adult rods due to their highly compact chromatin. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Methylation profiling by high throughput sequencing
Platforms:
GPL13112 GPL17021
33 Samples
Download data: BW, TAR, TXT
Series
Accession:
GSE72550
ID:
200072550
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