ScRNA-seq on C57BL/6J mice retina
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE153818 | GEO | 2020/09/29
REPOSITORIES: GEO
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Project description:The iris is a fine structure that controls the amount of light that enters the eye. Iris diseases that result in visual disability and blindness include iritis, primary angle closure glaucoma, and pigment dispersion syndrome. A detailed investigation of the proteome of the normal human iris may provide a foundation for new investigations into the iris biology and pathophysiology. We conducted an in-depth proteomic analysis of five normal irides. Proteins were fractionated using SDS-PAGE. After in-gel digestion, peptides were analyzed using LC-MS/MS on an Orbitrap Elite mass spectrometer. We identified 3,000 non-redundant proteins in the human iris, including 26 unambiguous protein isoforms. The proteins identified in the iris included numerous proteins involved in smooth muscle motility, melanosome development, extracellular matrix, and selenoproteins involved in redox signaling. The MS proteome database of the human iris may serve as a valuable resource for future investigations of the eye in health and disease.
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Project description:The iris is a fine structure that controls the amount of light that enters the eye. The ciliary body controls the shape of the lens and produces aqueous humor. The retinal pigment epithelium and choroid (RPE/choroid) are essential in supporting the retina and absorbing light energy that enters the eye. Proteins were extracted from iris, ciliary body, and RPE/choroid tissues of eyes from five individuals and fractionated using SDS-PAGE. After in-gel digestion, peptides were analyzed using LC-MS/MS on an Orbitrap Elite mass spectrometer. In iris, ciliary body, and RPE/choroid, we identified 2,959, 2,867, and 2,755 non-redundant proteins with protein false positive rate <1%. There were 43 unambiguous protein isoforms identified in iris, ciliary body, and RPE/choroid. Four “missing proteins” were found in ciliary body. The MS proteome database of the human iris, ciliary body, and RPE/choroid may serve as a valuable resource for future investigations of the eye in health and disease. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD001424.
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Project description:The iris is a fine structure that controls the amount of light that enters the eye. Iris diseases that result in visual disability and blindness include iritis, primary angle closure glaucoma, and pigment dispersion syndrome. A detailed investigation of the proteome of the normal human iris may provide a foundation for new investigations into the iris biology and pathophysiology. We conducted an in-depth proteomic analysis of five normal irides. Proteins were fractionated using SDS-PAGE. After in-gel digestion, peptides were analyzed using LC-MS/MS on an Orbitrap Elite mass spectrometer. We identified 3,000 non-redundant proteins in the human iris, including 26 unambiguous protein isoforms. The proteins identified in the iris included numerous proteins involved in smooth muscle motility, melanosome development, extracellular matrix, and selenoproteins involved in redox signaling. The MS proteome database of the human iris may serve as a valuable resource for future investigations of the eye in health and disease.
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Project description:Identification of genes expressed in a preferential manner in the developing ciliary body/iris will provide a starting point for future functional analyses. To identify candidate genes expressed in a variety of ocular tissues during development, we have profiled single cells from the developing eye. Post hoc identification of the origin of these cells showed that they included cells from the periphery of the developing optic cup. By comparing the expression profiles of these cells to many retinal cell types, candidate genes for preferential expression in the periphery were identified. Single retinal cells were isolated in tubes containing lysis buffer, their mRNAs were reverse transcribed, and the resulting cDNAs were PCR amplified for 35 cycles. Labeled cDNA samples were hybridized to Affymetrix 430 2.0 microarrays and the data was normalized using MAS5.0 software. Since the retinal cells isolated during these developmental times had not yet adopted their mature morphologies, a post hoc strategy was employed to classify each cell based upon the expression of clusters of genes (Trimarchi et al., 2008). This classification method allowed for the identification of 21 single cells as developing retinal ganglion (RGC), amacrine (AC) or photoreceptor cells (PR) (Trimarchi et al., 2007) and an additional 42 cells as cycling RPCs (Trimarchi et al., 2008). However, a number of the single cells did not score significantly for any of the retinal cell types. Two cells in particular expressed genes that suggested these cells originated from the developing ciliary body/iris region.
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