GEO DataSets

(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) 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

(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) 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) 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

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

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

Organism:

Mus musculus

Type:

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

Platform:

GPL17021

21 Samples

Download data: BW

(Submitter supplied) The basic motif-leucine zipper (bZIP) transcription factor NRL determines rod photoreceptor cell fate during retinal development, and its loss leads to cone-only retina in mice. NRL works synergistically with homeodomain protein Cone-Rod Homeobox and other regulatory factors to control the transcription of most genes associated with rod morphogenesis and functional maturation, which span over a period of several weeks in the mammalian retina. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17021

15 Samples

Download data: BW, TSV

(Submitter supplied) The basic motif-leucine zipper (bZIP) transcription factor NRL determines rod photoreceptor cell fate during retinal development, and its loss leads to cone-only retina in mice. NRL works synergistically with homeodomain protein Cone-Rod Homeobox and other regulatory factors to control the transcription of most genes associated with rod morphogenesis and functional maturation, which span over a period of several weeks in the mammalian retina. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

6 Samples

Download data: TSV

(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

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

(Submitter supplied) Gene regulatory networks (GRNs) guiding differentiation of cell types and cell assemblies in the nervous system are poorly understood because of inherent complexities and interdependence of signaling pathways. Here, we report transcriptome dynamics of differentiating rod photoreceptors in the mammalian retina. Given that the transcription factor NRL determines rod cell fate, we performed expression profiling of developing NRL-positive (rods) and NRL-negative (S-cone-like) mouse photoreceptors. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6096

28 Samples

Download data: CEL

(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) Dozens of mutations in the photoreceptor-specific transcription factor CRX are linked with different human blinding diseases that vary in their severity and age of onset. How these mutations in a single TF cause a range of pathological phenotypes is not understood. We deployed massively parallel reporter assays (MPRAs) in live mouse retina to directly measure changes to CRX cis-regulatory function caused by two disease-causing mutations, one in the DNA binding domain (p.R90W) and the other in the activation domain (p.E168d2).

Organism:

Mus musculus; synthetic construct

Type:

Other

Platforms:

GPL19057 GPL19424

38 Samples

Download data: TSV

(Submitter supplied) Vertebrate ancestors had only cone-like photoreceptors. The duplex retina evolved in jawless vertebrates with the advent of highly photosensitive rod-like photoreceptors. Despite cones being the arbiters of high-resolution color vision, rods emerged as the dominant photoreceptor in mammals during a nocturnal phase early in their evolution. We investigated the evolutionary and developmental origins of rods in two divergent vertebrate retinae. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11002

9 Samples

Download data: BED, TXT

(Submitter supplied) Vertebrate ancestors had only cone-like photoreceptors. The duplex retina evolved in jawless vertebrates with the advent of highly photosensitive rod-like photoreceptors. Despite cones being the arbiters of high-resolution color vision, rods emerged as the dominant photoreceptor in mammals during a nocturnal phase early in their evolution. We investigated the evolutionary and developmental origins of rods in two divergent vertebrate retinae. more...

Organism:

Mus musculus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL11002

13 Samples

Download data: TXT

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

Organism:

Mus musculus

Type:

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

Platform:

GPL11002

52 Samples

Download data: BED, TXT

(Submitter supplied) Vertebrate ancestors had only cone-like photoreceptors. The duplex retina evolved in jawless vertebrates with the advent of highly photosensitive rod-like photoreceptors. Despite cones being the arbiters of high-resolution color vision, rods emerged as the dominant photoreceptor in mammals during a nocturnal phase early in their evolution. We investigated the evolutionary and developmental origins of rods in two divergent vertebrate retinae. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11002

30 Samples

Download data: GTF, XLSX

(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