Ontology highlight
ABSTRACT:
PROVIDER: PRJNA912096 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR22745700.fastq.gz | Fastqsanger.gz | |||
| SRR22745701.fastq.gz | Fastqsanger.gz | |||
| SRR22745702.fastq.gz | Fastqsanger.gz | |||
| SRR22745703.fastq.gz | Fastqsanger.gz | |||
| SRR22745704.fastq.gz | Fastqsanger.gz |
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Project description:We collected some vitreous humors from rat eyes through a photolabile paper based chip which experienced different natural recovery processes at day 0, 0.25, 1, 3, 7 day after eye stroke by laser induced in rat. These mirs samples were collected from extracelluar vesicles of vitreous humor in rat. We used microarray to find some new miRNAs that may participate in the natural recovery process after experience eye stroke.
2023-06-30 | GSE154312 | 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 | GSE215952 | GEO
Project description:Purpose: To study the proteome of the subretinal fluid (SRF) from rhegmatogenous retinal detachment (RRD) in search for novel markers for improved diagnosis and prognosis of RRD. Methods: Human undiluted SRF obtained during vitrectomy for primary RRD using a 41G needle (n = 24) was analyzed and compared to vitreous humor from 2-days post-mortem eyes (n = 20). Sample preparation underwent nanoflow liquid chromatography-tandem mass spectrometry (LC-MS/MS). Label-free quantification (LFQ) using MaxQuant was used to determine differential expressed proteins between SRF and vitreous humor. The intensity-based absolute quantification (iBAQ) was used to rank proteins according to their molar fractions within groups. Identification of proteins beyond the quantitative level was performed using the Mascot search engine. Results: The protein concentration of the control vitreous humor was lower and more consistent (1.2 ± 0.4 mg) than that of the SRF (17.9 ± 22 mg). The iBAQ analysis showed high resemblance between SRF and vitreous humor, except for crystallins solely identified in vitreous humor. The LFQ analysis found 37 protein misregulations between SRF and vitreous humor of which the blood coagulation pathway was found to be enriched using the PANTHER Classification System. Combined, the iBAQ, LFQ and Mascot analysis found an overlap only in chitinase-3-like protein 1 and galectin-3-binding protein unique to the SRF. Conclusions: The proteome of the SRF was highly represented by proteins involved in proteolysis. Such proteins can possibly serve as targets in modulating the effects of SRF in RD.
2020-10-20 | PXD019159 | Pride
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:The addition of 50% vitreous humor to the media bathing lens epithelial explants results in the induction of both lens fiber cell differentiation and a significant immune/inflammatory response. Although Fgfr loss blocks differentiation in lens epithelial explants, this loss can be partially rescued by deleting Pten, demonstrating an epistatic relationship between FGFR-signaling and PTEN. To investigate the functions of Fgfrs and Pten during lens fiber cell differentiation, we utilized a lens epithelial explant system and conducted RNA sequencing on vitreous humor-exposed explants lacking Fgfrs, or Pten or both Fgfrs and Pten. We found that Fgfr loss impairs both vitreous-induced differentiation and inflammation while the additional loss of Pten restores these responses. Additionally, vitreous exposure triggers a less pronounced immune response in explants lacking both Fgfrs and Pten than in wildtype explants, but a stronger immune response than in explants lacking only Fgfrs. Furthermore, transcriptomic analysis suggested that PDGFR-signaling in FGFR-deficient explants might be required to mediate the rescue of vitreous-induced fiber cell differentiation in explants lacking both Fgfrs and Pten. The blockage of β- crystallin induction in explants lacking both Fgfrs and Pten in the presence of a PDGFR-inhibitor supports this hypothesis. Our findings demonstrate that a wide array of genes associated with fiber cell differentiation are downstream of FGFR-signaling and that the vitreous-induced immune responses also depend on FGFR-signaling. Our data also demonstrates that many of the vitreous-induced gene expression changes Fgfr-deficient explants can be rescued in explants lacking both Fgfrs and Pten.
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Project description:In this study, we investigated the proteome of normal human vitreous humor using high resolution Fourier transform mass spectrometry. We identified 1269 proteins. This largest catalog of vitreous proteins to date should facilitate biomedical research into pathological conditions of the eye including diabetic retinopathy, retinal detachment and cataract.
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Project description:PURPOSE: To investigate the circulatory microRNA (miRNA) profiles of aqueous, vitreous, and plasma in order to identify biomarkers in aqueous humor or plasma that are reflecting changes in vitreous of patients with diabetes. METHODS: Aqueous, vitreous and plasma samples were collected from a total of 27 patients - 11 controls (macular pucker or macular hole patients) and 16 patients with diabetes mellitus (DM) undergoing vitreoretinal surgery: DM-Type I with proliferative diabetic retinopathy (PDR) (DMI-PDR), DM Type II with PDR (DMII-PDR) and DM Type II with nonproliferative DR (DMII-NPDR). MiRNAs were isolated using Qiagen microRNeasy kit, quantified on BioAnalyzer, labeled with FlashTag kit, and profiled on Affymetrix GeneChip miRNA 3.0 microarrays. Data analysis was done using Expression Console (EC), Transcriptome Analysis Console (TAC), and Ingenuity Pathway Analysis (IPA) software. RESULTS: Our comparison of circulatory miRNA population of aqueous and vitreous humor and plasma showed that out of total of 847 human miRNA probes on the Affymetrix GeneChip miRNA 3.0 we found common miRNAs for both aqueous and vitreous samples, as well as larger number of unique miRNA, dependent on the DM type and presence of retinopathy. Most of the dysregulated miRNAs in aqueous and vitreous of DM patients were upregulated, while in plasma, most of the DM-specific miRNAs were downregulated. Dysregulation of miRNAs in aqueous generally do not appear to be a good representative of the miRNA abundance in vitreous, or plasma, although we did identify a few candidates for common biomarkers: let-7b, miR-320b, miR-762 and miR-4488. Additionally, each of the DR subtypes showed a set of miRNA that is uniquely dysregulated in each fluid, for example in aqueous samples for DMII-NPDR it was miR-455-3p, for DMII-PDR was miR-296, and for DMI-PDR it was miR-3202. Pathway analysis identified TGF-beta and VEGF pathways as the common targets for miRNAs dysregulated in DR aqueous and vitreous. CONCLUSIONS: The comparative profiling of circulatory miRNAs in aqueous, vitreous, and plasma showed that a small number of circulatory miRNAs displayed differential presence in controls vs. diabetic retinopathy. A pattern is emerging of sets of miRNA that are common or uniquely dysregulated in the blood plasma or ocular fluids of DR subtypes, offering promise for the use of ocular fluids and plasma for identifying diagnostic and therapeutic targets.
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Project description:To characterize vitreous humor (VH) exosomes and to explore their role in the development of proliferative vitreoretinopathy (PVR) using mass-spectrometry based proteome profiling.
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Project description:To study the differences in protein profiles before and after intravitreal ranibizumab (IVR) treatment, 12 vitreous humor (VH) samples were collected from 6 proliferative diabetic retinopathy (PDR) patients before (pre group) and after IVR treatment (post group). LC–MS/MS and bioinformatics analysis were performed to identify differentially expressed proteins.Targeted proteins were validated by parallel reaction monitoring (PRM).
2022-08-12 | PXD027592 | Pride