E-GEOD-35396 - Gene expression profile of retina and pineal gland of NeuroD1 conditional knockout mice

Released on 25 July 2012, last updated on 22 September 2015
Mus musculus
Samples (24)
Array (1)
Protocols (8)
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. In contrast to the retina, the pineal gland is a relatively homogeneous structure, composed 95% of pinealocytes. This makes the pineal gland a particularly useful model for understanding photoreceptor cell biology. The loss of NeuroD1 in the retina results in progressive photoreceptor degeneration and the molecular mechanisms underlying this retinal degeneration phenotype remain unknown. Similarly, the role that NeuroD1 plays in the pineal gland is unknown. To determine the function of NeuroD1 in the pineal gland and retina, a Cre/loxP recombination strategy was used to selectively target a NeuroD1 floxed allele and generate NeuroD1 conditional knockout (cKO) mice. Tissue specificity was conferred using Cre recombinase expressed under the control of the promoter of Crx, a transcription factor selectively expressed in the pineal gland and retina. Pineal and retinal tissues from two-month-old NeuroD1 cKO and control animals were used in microarray studies to identify candidate genes responsible for the photoreceptor degeneration phenotype. The Cre/loxP recombination strategy was used to target a NeuroD1 floxed allele and generate NeuroD1 conditional knockout mice (NeuroD1floxed::Crx-Cre+/-). NeuroD1 floxed mice (NeuroD1floxed::Crx-Cre-/-) served as the controls. Pineal glands and retinas from two-month-old control and conditional knockout mice were collected at ZT6 and ZT20. 3 pools of 6 pineal glands per genotype and respective time of day were collected for each sample. Similarly, 3 pools of 6 retinas each were also collected. RNA from each pool was extracted and hybridized on the Affymetrix Mouse 430 2.0 array.
Experiment type
transcription profiling by array 
Margaret Ochocinska <ochocinm@mail.nih.gov>, David C Klein, Estela M Munoz, Joan L Weller, Klaus A Nave, Margaret J Ochocinska, Nikita V Pozdeyev, P M Iuvone, Sandra Goebbels, Shobi Veleri, Steven L Coon, Takahisa Furukawa
NeuroD1 is required for survival of photoreceptors but not pinealocytes: Results from targeted gene deletion studies. Ochocinska MJ, Muñoz EM, Veleri S, Weller JL, Coon SL, Pozdeyev N, Iuvone PM, Goebbels S, Furukawa T, Klein DC.
Investigation descriptionE-GEOD-35396.idf.txt
Sample and data relationshipE-GEOD-35396.sdrf.txt
Raw data (1)E-GEOD-35396.raw.1.zip
Processed data (1)E-GEOD-35396.processed.1.zip
Array designA-AFFY-45.adf.txt