Similar Datasets
Project description:Lens epithelial cells transcriptome analysis
| PRJNA764592 | ENA
Project description:Total RNA was isolated from three separate populations of human lens epithelial cells and three matching populations of lens cortical fiber cells. All samples were analyzed on separate microarrays. Keywords: repeat sample
2005-02-15 | GSE2256 | GEO
Project description:Total RNA was isolated from three separate populations of human lens epithelial cells and three matching populations of lens cortical fiber cells. All samples were analyzed on separate microarrays.
2007-08-25 | E-GEOD-2256 | biostudies-arrayexpress
Project description:Lens epithelial explants consist of lens epithelial cells (P8 FVB/N mice) grown in vitro on their native basement membrane, the lens capsule. For decades, biologists have used lens epithelial explants to study lens fiber cell differentiation. However, the global change in the accessibility of the chromatin and transcriptome during the process of explanting and culture is unknown. Therefore, P8 FVB/N lens epithelial explants cultured in either unsupplemented media or media containing 50% bovine vitreous humor for one or five days were collected. Chromatin and RNA was collected for ATAC-sequencing and RNA-sequencing respectively. Differentially accessible regions and differentially expressed genes were identified for each condition to provide a genome wide view of chromatin architecture and gene expression during fiber cell differentiation in vitro. Vitreous humor generally increased chromatin accessibility in promoter regions of genes associated with fiber differentiation and immune response, and this was associated with increased transcript levels for these genes. In contrast, vitreous had relatively little effect on the accessibility of most of the genes highly expressed in the lens epithelium despite dramatic reductions in the transcript levels of these genes.
2023-02-15 | GSE215952 | GEO
Project description:Lens epithelial explants consist of lens epithelial cells (P8 FVB/N mice) grown in vitro on their native basement membrane, the lens capsule. For decades, biologists have used lens epithelial explants to study lens fiber cell differentiation. However, the global change in the accessibility of the chromatin and transcriptome during the process of explanting and culture is unknown. Therefore, P8 FVB/N lens epithelial explants cultured in either unsupplemented media or media containing 50% bovine vitreous humor for one or five days were collected. Chromatin and RNA was collected for ATAC-sequencing and RNA-sequencing respectively. Differentially accessible regions and differentially expressed genes were identified for each condition to provide a genome wide view of chromatin architecture and gene expression during fiber cell differentiation in vitro. Vitreous humor generally increased chromatin accessibility in promoter regions of genes associated with fiber differentiation and immune response, and this was associated with increased transcript levels for these genes. In contrast, vitreous had relatively little effect on the accessibility of most of the genes highly expressed in the lens epithelium despite dramatic reductions in the transcript levels of these genes.
2023-02-15 | GSE215950 | GEO
Project description:Epithelial cells and differentiated fiber cells represent distinct compartments in the ocular lens. While previous studies have revealed proteins that are preferentially expressed in epithelial vs. fiber cells, a comprehensive proteomics library comparing the molecular composition of epithelial vs. fiber cells is essential for understanding lens formation, function, disease and regenerative potential, and for efficient differentiation of pluripotent stem cells for modeling of lens development and pathology in vitro. To compare protein composition between the lens epithelium and fibers, we employed tandem mass spectrometry (2DLC/ MS) analysis of micro-dissected mouse P0.5 lenses. Functional classifications of the top 525 identified proteins into gene ontology categories by molecular process and subcellular localization, were adapted for lens. Expression levels of both epithelial and fiber proteomes were compared with their temporal and spatial mRNA levels using E14.5, E16.5, E18.5, and P0.5 RNA-Seq data sets. During this developmental time window, multiple complex biosynthetic and catabolic processes generate the molecular and structural foundation for lens transparency. As expected, crystallins showed a high correlation between their mRNA and protein levels. Comprehensive data analysis confirmed and/or predicted roles for transcription factors (TFs), RNA-binding proteins, translational apparatus including ribosomal heterogeneity and initiation factors, microtubules, cytoskeletal and membrane proteins in lens formation and maturation. Our data highlighted many proteins with unknown function in the lens that were preferentially enriched in epithelium or fibers, setting the stage for future studies to further dissect the roles of these proteins in fiber cell differentiation vs. epithelial cell maintenance. In conclusion, the present proteomic datasets established reference mouse lens epithelium and fiber cell proteomes, provided quantitative analyses of protein and RNA-Seq data, and probed the major proteome remodeling required to form the mature lens fiber cells.
2019-03-05 | PXD009639 | Pride
Project description:This trancriptome analysis reveals the first detailed analysis on how the remnant lens epithelial cells (LECs) greatly reprogram their transcriptome towards inflammation/fibrosis by 24 hours post cataract surgery (PCS).
2018-10-18 | GSE111430 | GEO
Project description:The lens is comprised of the anterior lens epithelium and posterior lens fibers, which form the bulk of the lens. The RNAseq data enables identification of lens epithelium and fiber differentially expressed genes and temporally differentially expressed genes which were also validated by qRTPCR. The present RNA-seq data serves as a comprehensive reference resource for deciphering molecular principles of normal mammalian lens differentiation, mapping a full spectrum of signaling pathways and DNA-binding transcription factors operating in both lens compartments, and predicting novel pathways required to establish lens transparency.
2018-10-02 | GSE113887 | GEO
Project description:The epithelial-mesenchymal transition (EMT) of lens epithelial cells (LECs) has been proposed as a major cause of posterior capsule opacification (PCO) after cataract surgery. Molecular mechanism of PCO progression is still unclear. Using a microarray-based approach, herein we studied the changes in gene expression pattern during rat PCO formation in vivo as a model.
2020-09-30 | GSE152593 | GEO
Project description:Analysis of Tdrd7 deficiency in mouse lens epithelial-derived cell line at gene expression level. The hypothesis tested was that Tdrd7 is involved in post-transcriptional control of gene expression in the lens. Results provide evidence for differential regulation of genes involved in lens homeostasis and cataract formation in the absence of Tdrd7. In eukaryotic cells, cytoplasmic RNA granules (RGs) function in the post-transcriptional control of gene expression. However, the involvement of RGs and their component proteins in vertebrate organogenesis is unknown. We report two independent cases of pediatric cataract with loss-of-function mutations in TDRD7, which encodes a Tudor domain RNA binding protein. TDRD7 deficiency in chick lens produces cataracts, and Tdrd7 null mouse mutants develop cataracts, as well as features of glaucoma and male sterility due to azoospermia. In lens fiber cells, TDRD7 is necessary for the RG-mediated post-transcriptional control of critical lens mRNAs, while in the testis it functions as a component of a specialized RG, the chromatoid body. These findings define a new role for RGs in vertebrate organogenesis, and a novel mechanism for cataractogenesis. Total RNA obtained from Tdrd7 knockdown cells compared to lentiviral GFP control in 21EM15 lens epithelial-derived cell line
2012-02-21 | E-GEOD-25774 | biostudies-arrayexpress