GEO DataSets

(Submitter supplied) The cone-rod homeobox gene (Crx) encodes Crx, a transcription factor selectively expressed in two cell types, retinal photoreceptors and the melatonin secreting pinealocytes of the pineal gland. In this report the role of Crx in regulating gene expression in the mammalian pineal gland was extended using Affymetrix GeneChip technology. Deletion of Crx results in broad modulation of the mouse pineal transcriptome, including a >2-fold downregulation of 543 genes and a >2-fold upregulation of 745 genes. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

12 Samples

Download data: CEL, TXT

(Submitter supplied) NeuroD1 encodes a basic helix-loop-helix transcription factor involved in the development of neural and endocrine structures. NeuroD1 mRNA is highly abundant in the adult mammalian pineal gland and exhibits a developmental expression pattern similar to the retina. This is consistent with the common evolutionary origin of pinealocytes and retinal photoreceptors. Pinealocytes and retinal photoreceptors express a shared set of phototransduction genes and submammalian pinealocytes are photosensitive. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

24 Samples

Download data: CEL

(Submitter supplied) Chick pinealocytes exhibit all the characteristics of a complete circadian system, comprising photoreceptive inputs, molecular clockworks and an easily measured rhythmic output, melatonin biosynthesis. We used microarray analysis to investigate the expression of approximately 8000 genes within cultured pinealocytes subjected to both LD and DD cycles. We report that a reduced subset of genes were rhythmically expressed in vitro compared to those previously published in vivo, and that gene expression rhythms were lower in amplitude, although the functional distribution of the rhythmic transcriptome was largely similar. more...

Organism:

Gallus gallus

Type:

Expression profiling by array

Platform:

GPL3731

196 Samples

Download data

(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) 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) Pineal function follows a 24-hour schedule, dedicated to the conversion of night and day into a hormonal signal, melatonin. In mammals, 24-hour changes in pineal activity are controlled by a neural pathway that includes the central circadian oscillator in the suprachiasmatic nucleus and the superior cervical ganglia (SCG), which innervate the pineal gland. In this study, we have generated the first next-generation RNA sequencing evidence of neural control of the daily changes in the pineal transcriptome. more...

Organism:

Rattus norvegicus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL14844

36 Samples

Download data: TXT, XLSX

(Submitter supplied) This study determines pineal gland gene expression levels in the NeuroD1 knockout mouse at postnatal day zero. Comparison was performed against pineal gland gene expression levels in 129 wildtype mice also disected at P0. Keywords: Comparison of wildtype versus transgenic pineal gland gene expression

Organism:

Mus musculus

Type:

Expression profiling by array

Dataset:

GDS3000

Platform:

GPL1261

6 Samples

Download data: CEL

Analysis of pineal glands of neonates lacking neurogenic differentiation factor 1 (NeuroD1, also referred to as BETA2). NeuroD1 is a member of the bHLH transcription factor family. Results provide insight into the role of NeuroD1 in the pineal gland.

Organism:

Mus musculus

Type:

Expression profiling by array, count, 2 genotype/variation sets

Platform:

GPL1261

Series:

GSE6030

6 Samples

Download data: CEL

(Submitter supplied) The zebrafish pineal gland (epiphysis) is an autonomous clock organ. In addition to being a site of melatonin production, it contains photoreceptor cells and functions as a circadian clock pace maker, making zebrafish a useful model system to study the developmental control of expression of genes associated with melatonin synthesis and photodetection, and the circadian clock. Here we have used DNA microarray technology to study the zebrafish pineal transcriptome. more...

Organism:

Danio rerio

Type:

Expression profiling by array

Dataset:

GDS3824

Platform:

GPL1319

69 Samples

Download data: CEL

Analysis of pineal gland across 5 developmental stages (3 larval, 2 adult) during the day and night. Pineal gland is a site of melatonin production, contains photoreceptor cells, and acts as a circadian clock pace maker. Results provide insight into the molecular basis of pineal gland development.

Organism:

Danio rerio

Type:

Expression profiling by array, count, 5 age, 2 development stage, 2 time, 2 tissue sets

Platform:

GPL1319

Series:

GSE13371

69 Samples

Download data: CEL

(Submitter supplied) We have ectopically expressed two V5-tagged homeobox genes and a control plasmid in mouse embryonic fibroblasts. Following ectopic expression and chemical selection we used whole transcriptome sequencing to reveal any effect of forced missed expression on the MEF transcriptome.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

9 Samples

Download data: TXT

(Submitter supplied) The transcriptome of the rat pineal gland is highly dynamic, with many hundreds of genes changing more than two-fold on a 24-hr daily rhythm, as revealed earlier using Affymetrix GeneChip analysis. Several key transcription factors and enzymes are known to change dramatically during development of the pineal gland. Studies on a small number of genes indicate that the onset of rhythmic expression generally occurs later in development. more...

Organism:

Rattus norvegicus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL14844

8 Samples

Download data: TXT