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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Mouse iPS cells-derived 3D-retinas: Vehicle control- vs. 4-hydroxytamoxifen (4-OHT)-treated 3D-retinas w/o supplements

ABSTRACT: Transcriptional profiling of 3D-retinas differentiated from mouse iPS cells comparing vehicle control with 4-OHT-treated w/o supplements. 4-OHT is an inverse agonist of estrogen-related receptor beta (ERRÎ²), a rod-enriched transcription factor responsible for maintenance of rod photoreceptor cells and the treatment induces photoreceptor specific cell death in the 3D-retinas. Goal was to understand the mechanism of protective effects of representative ophthalmic supplements for treating the photoreceptor degeneration. 4-OHT w/o supplements-induced gene expression in the 3D-retinas was measured at DD 25 when the photoreceptor cells started to be degenerated. Four-condition experiment, vehicle control- vs. 5 ÂµM 4-OHT- vs. 5 ÂµM 4-OHT with 400 ÂµM vitamin E- vs. 5 ÂµM 4-OHT with 200 nM lutein-treated 3D-retinas. Biological replicates: each sample has 24 3D-retinas and 1replicate.

ORGANISM(S): Mus musculus

SUBMITTER: Shin-ichiro Ito

PROVIDER: E-GEOD-83984 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Mouse iPS cells-derived 3D-retinas: Vehicle control- vs. 4-hydroxytamoxifen (4-OHT)-treated 3D-retinas

Project description:Transcriptional profiling of 3D-retinas differentiated from mouse iPS cells comparing vehicle control- with 4-OHT-treated. 4-OHT is an inverse agonist of estrogen-related receptor beta (ERRÎ²), a rod-enriched transcription factor responsible for maintenance of rod photoreceptor cells and the treatment induces photoreceptor specific cell death in the 3D-retinas. Goal was to understand the mechanism of 4-OHT-induced degeneration of photoreceptor cells in the 3D-retinas. 4-OHT-induced gene expression in the 3D-retinas was measured at DD 26 when the photoreceptor cells were degenerated. Two-condition experiment, vehicle control- vs. 5 ÂµM 4-OHT-treated 3D-retinas. Biological replicates: each sample has 24 3D-retinas and 1 replicate.

2016-07-05 | E-GEOD-83985 | biostudies-arrayexpress

Mouse iPS cells-derived 3D-retinas: Vehicle control- vs. 4-hydroxytamoxifen (4-OHT)-treated 3D-retinas w/o supplements

Project description:Transcriptional profiling of 3D-retinas differentiated from mouse iPS cells comparing vehicle control with 4-OHT-treated w/o supplements. 4-OHT is an inverse agonist of estrogen-related receptor beta (ERRβ), a rod-enriched transcription factor responsible for maintenance of rod photoreceptor cells and the treatment induces photoreceptor specific cell death in the 3D-retinas. Goal was to understand the mechanism of protective effects of representative ophthalmic supplements for treating the photoreceptor degeneration.

2016-07-05 | GSE83984 | GEO

Mouse iPS cells-derived 3D-retinas: Vehicle control- vs. 4-hydroxytamoxifen (4-OHT)-treated 3D-retinas

2016-07-05 | GSE83985 | GEO

Mouse iPS cells-derived 3D-retinas

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2016-07-05 | E-GEOD-83986 | biostudies-arrayexpress

Mus musculus

Project description:Mouse iPS cells-derived 3D-retinas: Vehicle control- vs. 4-hydroxytamoxifen (4-OHT)-treated 3D-retinas w/o supplements

| PRJNA327748 | ENA

Transcription profiling time series of rat retina after intra-orbital nerve transection, intra-orbital nerve crush or no treatment

Project description:Array experiment: Animals were divided into a control group (naive), which did not undergo any experimental manipulation (n=20) and two experimental groups, one receiving an intra-orbital nerve transection (IONT, n=60) and the other an intra-orbital nerve crush (IONC, n=60) Sterile precautions were maintained for all surgical procedures. The left ON was intraorbitally axotomized according to procedures that are standard in our laboratory. (REF) Briefly, an incision was made in the superior orbital rim, the superoexternal orbital contents were dissected, and the superior and external rectus muscles were removed. When performing IONT, the dura mater was opened longitudinally to spare the blood supply, and the optic nerve was transected 0.5 mm from the optic disc. To perform IONC the optic nerve was crushed 3 mm from the optic disc during 10 seconds using a pair of watchmakers forceps (Vidal-Sanz et al., 1988, 1991; Villegas-Perez et al., 1993). Before and after the procedure, the eye fundus was observed through the operating microscope to assess the integrity of the retinal blood flow. Tissue processing and RNA extraction: Animals were kept the appropriate time post injury (12h, 24h, 48h, 3d 7d and 15d, n=8-12 per time point) and then sacrificed by an intraperitoneal overdose of sodium pentobarbital. Left retinas were fresh dissected and immediately frozen in liquid nitrogen. Four retinas from each time point, animal group and biological replica were pooled and RNA was extracted using Trizol (Invitrogen). RNA was further cleaned through RNAeasy mini kit columns (Quiagen). The RNA integrity was checked using a Bioanalyzer (Agilent Technologies, USA) and concentrations were determined using a NanoDrop (NanoDrop Technologies, Wilmington, DE, USA).

2008-06-14 | E-MEXP-1387 | biostudies-arrayexpress

Mouse iPS cells-derived 3D-retinas

Project description:Mouse iPS cells-derived 3D-retinas

| PRJNA327746 | ENA

Comparison of wild-type and Mfsd2a KO eye cups

Project description:Eye photoreceptor membrane discs in outer rod segments are highly enriched in the visual pigment rhodopsin and the omega-3 fatty acid docosahexaenote (DHA). The eye acquires DHA from blood, but transporters for DHA uptake across the blood-retinal barrier (BRB) or retinal pigment epithelium have not been identified. Mfsd2a is a newly described sodium-dependent lysophosphatidylcholine symporter expressed at the BRB. Microarrays were used to determine difference in gene expression between wild-type and Mfsd2a KO eye cups. RNA was extracted from eye cups from postnatal day 13 wild-type and Mfsd2a KO mice. Equal amounts of RNA from 6 wild-type eye cups were pooled for the wild-type sample, or 6 Mfsd2a KO eye cups were pooled for the Mfsd2a KO sample. Microarray profiling was done on pooled samples with a RIN cut-off of 7.0 using Mouse 430 2.0 arrays (Affymetrix).

2016-03-23 | E-GEOD-77403 | biostudies-arrayexpress

Mus musculus

Project description:Mouse iPS cells-derived 3D-retinas: Vehicle control- vs. 4-hydroxytamoxifen (4-OHT)-treated 3D-retinas

| PRJNA327747 | ENA

Combined analysis of single cell RNA-Seq and ATAC-Seq data reveals regulatory toggles operating in native and iPS-derived retina

Project description:To improve the comparison of the developmental trajectories of native retina (NaR) and iPSC-derived 3D retinal aggregates(3D-RA) , we performed scRNA-Seq of murine NaR and 3D-RA at four matched stages of development: embryonic day (E)13 vs differentiation day (DD)13, postnatal day (P)0 vs DD21, P5 vs DD25 and P9 vs DD29. NaR were dissected from two to 11 C57Bl6 mice (of both sexes) per stage. Mouse 3D-RA were generated from the iPSC Nrl-GFP line. Cells from NaR and OV were dissociated and subjected to droplet-based scRNA-Seq using a 10X Genomics Chromium platform. We obtained sequence information for 21,249 cells from NaR and 16,842 cells from 3D-RA, distributed evenly amongst developmental stages. We generated an average of 74,808 reads per cell, corresponding to 5,940 unique molecular identifiers (UMIs) and 2,471 genes per cell.

2021-06-30 | E-MTAB-9395 | biostudies-arrayexpress

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