GEO DataSets

(Submitter supplied) We determined the accessible genome of postmitotic cone photoreceptors in the central region of the mouse retina on postnatal days P3, P6, and P10. At eachtimepoint we isolated GFP-labeled cells from three different Chrnb4-GFP mice (biological triplicates) using fluorescence-activated cell sorting. We then acquired reads of regions of accessible DNA of the sorted cones using ATAC sequencing. Our data set contained 9 samples.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17021

9 Samples

Download data: BED, CSV

(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

48 Samples

Download data

(Submitter supplied) We determined the transcriptomes of postmitotic cone photoreceptors in the central region of the mouse retina every day between birth (P0) and eye opening (P12). At each postnatal day we isolated GFP-labeled cells from three different Chrnb4-GFP mice (biological triplicates) using fluorescence-activated cell sorting. We then acquired the transcriptomes of the sorted cones using next generation RNA sequencing. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

39 Samples

Download data: CSV

(Submitter supplied) To analyze roles of transcription factor Fezf2 in retinal development, knockout mouse of Fezf2 was generated, and gene expression pattern of Fezf2-KO retina and control retina was examined by RNA-seq.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

4 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) 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

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

Organism:

Mus musculus

Type:

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

Platforms:

GPL6246 GPL13112

42 Samples

Download data: CEL, TXT

(Submitter supplied) The outer segments of cones serve as light detectors for daylight color vision, and their dysfunction leads to human blindness conditions. We show that the cone-specific disruption of DiGeorge Syndrome Critical Region Gene 8 (DGCR8) in adult mice led to the loss of miRNAs and the loss of outer segments, resulting in photoreceptors with significantly reduced light responses. Using next-generation sequencing of RNA from isolated wild type P60 cones, we determine the most highly expressed miRNAs as candidates for controlling outer segment maintenance. more...

Organism:

Mus musculus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL13112

2 Samples

Download data: TXT

(Submitter supplied) We have analyzed gene expression in cone photoreceptors isolated from wild type and C-DGCR8 (DiGeorge Syndrome Critical Region Gene 8) KO mice at five different time points to get a mechanistic inside into the altered molecular pathways after microRNAs depletion.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

20 Samples

Download data: TXT

(Submitter supplied) We have analyzed gene expression in cone photoreceptors isolated from wild type and C-DGCR8 (DiGeorge Syndrome Critical Region Gene 8) KO mice at five different time points to get a mechanistic inside into the altered molecular pathways after microRNAs depletion.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6246

20 Samples

Download data: CEL

(Submitter supplied) Purpose: Identify Top2b-dependent genes by comparing retinal transcriptome profiling (RNA-seq) Methods: Retinal mRNA profiles of neonatal (postnatal day 0 and 6) wild-type (WT) and Topoisomerase IIbeta (Top2b) conditional knockout (Top2b−/−, or cKO) mice were generated using the SOLiD System (Applied Biosystems). Data analysis was performed according to published protocols (Trapnell et al., 2012) with minor modifications. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL10010

4 Samples

Download data: DIFF