{"owner": "ArrayExpress Uploader", "pop_total": 0, "id": 7523, "factors": [{"GSE5338GSM121316": {}}, {"GSE5338GSM121242": {}}, {"GSE5338GSM121249": {}}, {"GSE5338GSM121315": {}}, {"GSE5338GSM92611": {}}, {"GSE5338GSM92612": {}}, {"GSE5338GSM92613": {}}, {"GSE5338GSM92610": {}}], "ownerprofile_id": "arrayexpress_sid", "platform": 6, "summary_wrapped": "Rod and cone photoreceptors in mammalian retina are generated from common pool(s) of neuroepithelial progenitors.  NRL, CRX and NR2E3 are...", "pubmed_id": 16868010, "geo_gse_id": "E-GEOD-5338", "owner_profile": "/profile/8773/arrayexpressuploader", "factor_count": 0, "sample_count": 8, "tags": ["cone", "disease", "photoreceptor", "retina", "rhodopsin"], "lastmodified": "Dec.12, 2014", "is_default": false, "geo_gds_id": "", "slug": "transcription-profiling-of-mouse-retina-with-ectop", "geo_id_plat": "E-GEOD-5338_A-AFFY-45", "name": "Transcription profiling of mouse retina with ectopic expression of NR2E3 in Nrl-/- animals reveals in vivo function of NR2E3 in establishing photoreceptor identity during mammalian retinal development", "created": "Nov.12, 2014", "summary": "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.  Expression of NR2E3 in the Nrl-/- retina completely suppressed cone differentiation and resulted in morphologically rod-like photoreceptors, which were not functional.  Gene profiling of FACS-purified photoreceptors confirmed the role of NR2E3 as a strong suppressor of cone genes and an activator of a subset of rod genes (including rhodopsin) in vivo.  Ectopic expression of NR2E3 in cone precursors and differentiating S-cones of wild type retina also generates rod-like cells.  The dual regulatory function of NR2E3 is not dependent upon the presence of NRL and/or CRX, but on the timing and level of its expression.  Our studies reveal a critical role of NR2E3 in establishing functional specificity of post-mitotic photoreceptor precursors during retinal neurogenesis.   Experiment Overall Design: We mated the Crx::Nr2e3/Nrlko mice with the Nrl::GFP transgenic mice, in which the expression of GFP is driven by an Nrl promoter. Mouse retinas were dissected at 4 wk.  GFP+ photoreceptors were enriched by FACS (FACSAria, BD Biosciences, Franklin Lakes, NJ).  RNA was extracted from 1~5x105 flow-sorted cells using Trizol (Invitrogen).  Total RNA (40-60 ng) was used for linear amplification with Ovation Biotin labeling system (Nugen), and 2.75 ug of biotin-labeled fragmented cDNA was hybridized to mouse GeneChips MOE430.2.0 (Affymetrix) having 45,101 probesets (corresponding to over 39,000 transcripts, and 34,000 annotated mouse genes).   Experiment Overall Design: Four independent samples were used at 4 weeks. We normalized Experiment Overall Design: Crx::Nr2e3/Nrl-ko-Gfp data along with Nrl-ko-Gfp 4 weeks samples ( 4 replicates, refer to Series submission GSE4051). The normalized data was then subjected to two stage analysis based on False Discovery Rate Confidence Interval (FDR-CI) for screening differentially expressed genes (24, 27) with a minimum fold change of 4.", "source": "http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-5338", "species": "mouse", "sample_source": "http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-5338/samples/"}