Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

48 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Whole genome methylation profiling of the retinal pigment epithelium of individuals with age-related macular degeneration

ABSTRACT: Illumina Infinium HumanMethylation450 BeadChip data from genomic DNA of retinal pigment epithelium from Age-related Macular Degeneration patients or age-matched controls.

ORGANISM(S): Homo sapiens

SUBMITTER: Yongxiang Fang

PROVIDER: E-MTAB-7183 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Transcriptomic analysis of human retinal detachment (RD) reveals both inflammation and photoreceptor death

Project description:We have used surgical specimens to perform a differential analysis of the transcriptome of human retinal tissues following detachment. Data analysis reveals major involvement of the immune response in the disease and interindividual variation was monitored to unravel a second crucial aspect of the pathological process, the death of photoreceptor cells. In total 38 surgical specimens (samples) were analyzed, 19 represent biopsies from patients with retinal detachment (RD) and 19 represent contral samples without retinal detachment.

2012-03-06 | E-GEOD-28133 | biostudies-arrayexpress

Transcription profiling of mouse Nxnl1-/- retina

Project description:Rod-derived Cone Viability Factor (RdCVF, alias nxnl1) is a retina-specific protein identified for its therapeutic potential in supporting cone survival during retinal degeneration. A nxnl1 knockout mouse model was created and the transcriptome used to demonstrate that the retina is compromised by the absence of nxnl1. Experiment Overall Design: In total 9 samples were analyzed, they represent three different genotypes (wt/wt, ko/wt, ko/ko) that were tested in triplicate each.

2010-02-17 | E-GEOD-13869 | biostudies-arrayexpress

Pigment Epithelium Derived Factor (PEDF) secreted from iPSC derived-RPE facilitates apoptotic causes cell death, not the differentiation, of iPSCs

Project description:We show that Retinal pigment epithelium (RPE) secreted-factor, pigment epithelium derived factor (PEDF) secreted/derived from primary or iPSC-derived retinal pigment epithelium (RPE)RPE, dramatically inhibitsed the cell growth of iPSCs. PEDF was detected abundantly in culture supernatant media of primary and iPSC-derived RPE. We examined the gene expression in primary RPE and iPS-derived RPE. Two samples: RPE derived from 253G1 iPSC, Primary RPE.

2013-01-03 | E-GEOD-43257 | biostudies-arrayexpress

cryo-EM study of bovine retinal pigment epithelium cell lysate

Project description:This is the proteomic analysis data of bovine retinal pigment epithelium cell lysate subjected to cryo-EM study.

2023-01-02 | PXD037186 | Pride

Transcriptome of the Nxnl2-/- mouse retina

Project description:A nxnl2 knockout mouse model was created and the transcriptome used to demonstrate that the retina is compromised by the absence of nxnl2. For the mouse lacking Nxnl2, the gene encoding RdCVF2, the progressive decline of the visual performance of the cones in parallel with their degeneration arises due to loss of trophic support from RdCVF2 Keywords: genetic modification, transcription-profile, retina In total 6 samples were analyzed, they represent the genotypes wt/wt and ko/ko that were tested in triplicate each.

2011-09-11 | E-GEOD-21863 | biostudies-arrayexpress

DNA methylation analysis of phaeochromocytoma, paraganglioma and normal adrenal medulla samples

Project description:Illumina Infinium MethylationEPIC BeadChip array files from phaeochromocytoma, paraganglioma tumours of different genotypes and normal adrenal medulla control samples. This is the first study using high-resolution MethylationEPIC arrays and also includes a large number of Cluster 1 tumours (n=16) which exhibit extensive epigenetic deregulation.

2023-12-21 | E-MTAB-13433 | biostudies-arrayexpress

Proteomics reveals ablation of PlGF down-regulate the insulin resistance pathway, increase antioxidant and neuroprotective proteins in the diabetic mice retina

Project description:PGF (Placental growth factor) is a member of the vascular endothelial growth factor (VEGF) sub-family a crucial factor in angiogenesis and vasculogenesis. Mechanisms by which PlGF expression is regulated remain to be investigated in diabetic retinopathy DR. However, the underlying molecular mechanisms that PlGF, mediates in the early complications at non-proliferative DR remain mostly elusive. Here we have applied an LC-MS/MS-based label-free quantification proteomic approach to PlGF ablation in the retinal tissues from mouse strains (Akita, PlGF-/- and Akita.PlGF-/-). The proteomes of retinal tissues were extracted, digested by the Trypsin/LysC enzyme and subsequently analyzed by a Q-Exactive hybrid Quadrupole-Orbitrap mass spectrometer. We have performed normalization by the Z-score method, correlation by Pearson correlation coefficient and identified differentially expressed proteins in four comparisons. The gene ontology, functional pathways, and protein-protein network interaction analysis suggested that Gnb1, Gnb2, Gnb4, Gnai2, Gnao1, Snap2 and Gngt1 proteins are involved in insulin resistance pathways, which are down-regulated/ no significant in PlGF ablation in Akita diabetics (Akita.PlGF-/- vs. Akita), up-regulated in Akita vs. C57, PlGF-/- vs. C57. Prdx6, Map2 are involved in antioxidant activity and neural protection pathways respectively, which are up-regulated in Akita.PlGF-/- vs. Akita. Our proteomics outcomes anticipated that down-regulated of insulin resistance pathways, up-regulation of antioxidant and neuroprotection proteins might epitomize the potential mechanisms of anti-PlGF therapies in the treatment of DR.

2019-03-13 | PXD010757 | Pride

RNA-seq of retinal pigment epithelium (RPE) derived from human induced pluripotent stem cells (iPSCs): healthy control and USH1B patient iPSCs

Project description:Compare transcriptomes of control and USH1B patient iPSC-derived retinal pigment epithelium (RPE) to elucidate disease mechanisms of Usher syndrome type IB (USH1B). USH1B patient fibroblasts were collected at Great Ormond Street Hospital (GOSH) and reprogrammed to iPSCs. Control and patient iPSCs differentiated in vitro to generate retinal pigment epithelium (RPE) and collected for RNA-seq at 24 week. Sequencing was performed at University College London (UCL) Genomics on a NovaSeq 6000 system. Data aligned to the human genome UCSC hg38 using RNA-STAR 2.5.2b.

2023-08-22 | E-MTAB-12165 | biostudies-arrayexpress

BLUEPRINT WP4: Methylation study of germinal-center derived B-cell lymphoma cell lines as part of whole epigenomes

Project description:INFINIUM HUMAN METHYLATION 450 BEAD CHIP ANALYSIS OF germinal-center derived B-cell lymphoma cell line DNA (cell lines: BL2, DG75, JVM2, Karpas422, SUDHL5, U266, Z138)

2014-12-25 | E-MTAB-3184 | biostudies-arrayexpress

DNA methylation analysis in infants with low and high body fatness

Project description:We combined genome-wide DNA methylation profiling of buccal cells from 47 full-term one-week old infants with accurate measurements of infant fat mass and fat-free mass using air-displacement plethysmography and found no significant a between DNA methylation and infant body composition

2020-11-11 | E-MTAB-9596 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data