Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12329669_1.fastq.gz | Fastqsanger.gz | |||
| SRR12329669_2.fastq.gz | Fastqsanger.gz | |||
| SRR12329670_1.fastq.gz | Fastqsanger.gz | |||
| SRR12329670_2.fastq.gz | Fastqsanger.gz | |||
| SRR12329671_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Hydrotalea sp. AMD isolate:AMD Genome sequencing and assembly
| PRJNA513256 | ENA
Project description:Purpose: Age-related degeneration (AMD) is a major cause of blindness in developed countries. The molecular pathogenesis of early events in AMD is poorly understood. We investigated differential gene expression in samples of human retinal pigment epithelium (RPE)/choroid from early AMD and control maculas using exon-based arrays. Methods: Gene expression levels in nine early AMD and nine control human donor eyes were assessed using Affymetrix Human Exon ST 1.0 arrays. Two controls did not pass quality control and were removed. Differentially expressed genes were annotated using DAVID, and gene set enrichment analysis (GSEA) was performed on RPE-specific and endothelium-associated gene sets. CFH genotype was also assessed and differential expression was analyzed with respect to high AMD risk (YH/HH) and low AMD risk (YY) genotypes. Results: Seventy-five genes were identified as differentially expressed (raw p-value < 0.01; >50% fold change, mean log2 expression level in AMD or control M-bM-^IM-% median of all average gene expression values); however, no genes were significant (adj. p-value < 0.01) after correction for multiple hypothesis testing. Of 52 genes with decreased expression in AMD (fold change < 0.5; raw p-value < 0.01), 18 genes were identified by DAVID analysis as associated with vision or neurological processes. GSEA of RPE-associated and endothelium-associated genes revealed a significant decrease in genes typically expressed by endothelial cells in the early AMD group compared to controls, consistent with previous histologic and proteomic studies. Analysis with respect to CFH genotype indicated decreased expression of ADAMTS9 in eyes with high-risk genotypes (fold change = -2.61; raw p-value = 0.0008). Conclusions: GSEA results suggest that RPE transcripts are preserved or elevated in early AMD, concomitant with loss of endothelial cell marker expression. These results are consistent with the notion that choroidal endothelial cell dropout occurs early in the pathogenesis of AMD. Using AltAnalyze (ver. 2.0.7 beta), we analyzed nine early AMD and nine control eyes using Affymetrix Human Exon ST 1.0 arrays. Following initial processing in AltAnalyze, two control arrays were identified as potential outliers by tests implement in arrayQualityMetrics, a package for R.
2013-12-23 | E-GEOD-50195 | biostudies-arrayexpress
Project description:Comparing fibroblasts and derived -iPSC and - RPE cells from human AMD and non-AMD donors Retinal pigment epithelium (RPE) generated from skin biopsies of donors with age-related macular degeneration (AMD) exhibit a disease phenotype and a distinct transcriptome compared to age-matched controls. We investigated whether similar differences existed in the skin fibroblasts and induced pluripotent stem cells (iPSCs) derived from them. Hierarchical cluster and principal component analyses revealed significant overlap in the transcriptome of fibroblasts of AMD and non-AMD donors. After reprogramming, iPSCs exhibited slight differences. In contrast, the transcriptome of RPE derived from AMD and normal donors segregated into two distinct clusters. Differences in the expression of specific genes that were evident between normal and AMD-derived RPE were not observed in fibroblasts or iPSCs. Mitochondrial respiration was reduced in RPE from AMD patients but not in fibroblast or iPSCs. RPE derived from AMD patients have a distinct transcriptome and phenotype compared to controls that is not observed in their corresponding skin fibroblasts or iPSCs.
2024-04-23 | GSE149202 | GEO
Project description:Purpose: Age-related degeneration (AMD) is a major cause of blindness in developed countries. The molecular pathogenesis of early events in AMD is poorly understood. We investigated differential gene expression in samples of human retinal pigment epithelium (RPE)/choroid from early AMD and control maculas using exon-based arrays. Methods: Gene expression levels in nine early AMD and nine control human donor eyes were assessed using Affymetrix Human Exon ST 1.0 arrays. Two controls did not pass quality control and were removed. Differentially expressed genes were annotated using DAVID, and gene set enrichment analysis (GSEA) was performed on RPE-specific and endothelium-associated gene sets. CFH genotype was also assessed and differential expression was analyzed with respect to high AMD risk (YH/HH) and low AMD risk (YY) genotypes. Results: Seventy-five genes were identified as differentially expressed (raw p-value < 0.01; >50% fold change, mean log2 expression level in AMD or control ≥ median of all average gene expression values); however, no genes were significant (adj. p-value < 0.01) after correction for multiple hypothesis testing. Of 52 genes with decreased expression in AMD (fold change < 0.5; raw p-value < 0.01), 18 genes were identified by DAVID analysis as associated with vision or neurological processes. GSEA of RPE-associated and endothelium-associated genes revealed a significant decrease in genes typically expressed by endothelial cells in the early AMD group compared to controls, consistent with previous histologic and proteomic studies. Analysis with respect to CFH genotype indicated decreased expression of ADAMTS9 in eyes with high-risk genotypes (fold change = -2.61; raw p-value = 0.0008). Conclusions: GSEA results suggest that RPE transcripts are preserved or elevated in early AMD, concomitant with loss of endothelial cell marker expression. These results are consistent with the notion that choroidal endothelial cell dropout occurs early in the pathogenesis of AMD.
2013-12-23 | GSE50195 | GEO
Project description:Comparing iPS derived RPE cells from human AMD and non-AMD donors It has been a challenge to model retinal disorders such as geographic atrophy (GA) in in vivo animals, primarily because several factors, including genetics and aging itself, contribute to disease phenotype of age-related macular degeneration (AMD). We generated retinal pigment epithelial (RPE) cells from patients with advanced AMD and assessed their ability to model disease. We observed alterations in the transcriptome of AMD patients compared to non-diseased controls. RPE cells from AMD patients displayed decreases in mitochondrial function (basal respiration and adenosine triphosphate (ATP) production) compared with non-diseased controls. Using a system of mimicing AMD diseased ECM, we showed RPE cells derived from patients with AMD have a reduced ability to survive and proliferate on nitrite-modified extracellular matrix (ECM) when compared to non-diseased controls. These results demonstrate changes in the cell biology and phenotype of RPE cells from patients with advanced AMD, providing a platform for disease modeling to understand AMD pathophysiology.
2020-02-26 | GSE125564 | GEO
Project description:Age-related macular degeneration (AMD) is a major cause of blindness in the western world. While genetic studies have linked both common and rare variants in genes involved in regulation of the complement system to increased risk of development of AMD, environmental factors, such as smoking and nutrition, can also significantly affect the risk of developing the disease and the rate of disease progression. Since epigenetics has been implicated in mediating, in part, the disease risk associated with some environmental factors, we investigated a possible epigenetic contribution to AMD. We performed genome-wide DNA methylation profiling of blood from AMD patients and controls. No differential methylation site reached genome-wide significance; however, when epigenetic changes in and around known GWASdefined AMD risk loci were explored, we found small but significant DNA methylation differences in the blood of neovascular AMD patients near age-related maculopathy susceptibility 2 (ARMS2), a top-ranked GWAS locus preferentially associated with neovascular AMD. The methylation level of one of the CpG sites significantly correlated with the genotype of the risk SNP rs10490924, suggesting a possible epigenetic mechanism of risk. Integrating genome-wide DNA methylation analysis of retina samples with and without AMD together with blood samples, we further identified a consistent, replicable change in DNA methylation in the promoter region of protease serine 50 (PRSS50). These methylation changes may identify sites in novel genes that are susceptible to non-genetic factors known to contribute to AMD development and progression.
2017-08-23 | GSE102952 | GEO
Project description:Wet age-related macular degeneration (AMD), characterized by leaky neovessels emanating from the choroid, is a main cause of blindness. As current treatments for wet AMD require regular intravitreal injections of anti-VEGF biologics, there is a need for the novel development of less invasive treatments. Here, we developed a novel inhibitor of microtubule-associated End Binding 3 protein (EB3), herein termed EBIN, which blocked pathological Ca2+ signaling in activated endothelial cells and suppressed leakage of choroidal neovessels. Delivery of EBIN via eye drops in mouse and non-human primate (NHP) models of AMD prevented neovascular leakage and neovascularization as effectively as intravitreal injection of anti-VEGF therapy. EBIN activated Meis2-Pax6 regenerative pathways in metabolic-active endothelial cells comprising neovessels and promoted tissue regeneration. Furthermore, single nuclei assay for transposase-accessible chromatin sequencing (sn-ATAC-seq) analysis demonstrated that in metabolic-active endothelial cells, the RPE, and photoreceptors, EBIN induced global increases in chromatin accessibility, the biological process progressively inhibited in AMD patients. These results suggest the unique therapeutic mode of action of this novel drug candidate, which can potentially promote regeneration of eye tissue by reversing the degenerative processes underlying both the neovascular and atrophic forms of AMD.
2023-08-30 | GSE228270 | GEO
Project description:Age related macular degeneration (AMD) is one of the leading causes of irreversible central vision loss in the elderly population. According to the WHO estimates, AMD globally ranks third in causing vision impairment with a blindness prevalence of 8.7%.There is no cure for AMD; however,if it is diagnosed at an early stage, its progression can be slowed down by maintaining a healthy life style. Studies have been carried out to identify biomarkers in the plasma or serum of AMD patients. However, a consensus has not been reached with respect to an ideal biomarker which can predict and prognosticate the disease at an earlier stage. This can be attributed to the differences in the ethnicity and other geographical differences, which makes it important to conduct the study in specific regions.The current study aims to findnon-invasive prognostic biomarkers in the urine specimens of the AMD patients. Comparative proteomic analysis of urine samples from Early AMD, Choroidalneovascular membrane(CNVM) , Geographic atrophy(GA) and healthy controls was performed using Tandem mass tags (TMT) followed by mass spectrometry. Out of 751 proteins identified 383 proteins were found to be differentially expressed in various groups of AMD patients. Gene ontology classification of differentially expressed proteins revealed majority of them were involved in catalytic functions and binding activities. Pathway analysis showed, cell adhesion molecule pathways (CAMs), Complement and coagulation cascades, to be significantly deregulated in AMD. Upon validation by ELISA, SERPINA-1, TIMP-1, APOA-1 were significantly over expressed in AMD patients compared to the controls. A logistic model of APOA-1 in combination with CFH and C3 polymorphisms predicted the risk of developing AMD with 82% accuracy. This study gives us a preliminary data on non invasive biomarkers for AMD, which can be further validated in a large cohort and translated for diagnostic use.
2022-03-02 | PXD007531 | Pride
Project description:Single Cell RNA-Seq of normal and AMD eyes
2022-05-25 | GSE188280 | GEO