Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Gene expression microarray analysis of early oxygen-induced retinopathy (OIR)

ABSTRACT: Different inbred strains of rats differ in their susceptibility to OIR, an animal model of human retinopathy of prematurity. We examined gene expression profiles in Fischer 344 (F344, resistant to OIR) and Sprague Dawley (SD, susceptible to OIR) rats at the early time point of day 3 to identifying gene pathways related to the underlying genetic cause of phenotypic differences between strains.

ORGANISM(S): Rattus norvegicus

PROVIDER: GSE18998 | GEO | 2009/11/13

SECONDARY ACCESSION(S): PRJNA120427

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Gene expression microarray analysis of early oxygen-induced retinopathy (OIR)

Project description:Different inbred strains of rats differ in their susceptibility to OIR, an animal model of human retinopathy of prematurity. We examined gene expression profiles in Fischer 344 (F344, resistant to OIR) and Sprague Dawley (SD, susceptible to OIR) rats at the early time point of day 3 to identifying gene pathways related to the underlying genetic cause of phenotypic differences between strains. To examine gene expression changes in rats strains which are resistant and susceptible to OIR, four different experimental conditions were analysed: F344 cyclic hyperoxia (O2) exposed, F344 room air (RA) exposed, SD O2 exposed and SD RA exposed. A minimum of two samples of pooled RNA, comprising of 3 individual rats from 2 separate litters, was used for each experimental condition. Pooled RNA from different rats were used as biological replicates. An additional sample for F344 O2 and SD RA rats was included on the basis of the principal components analysis from the initial 8 samples. Pooled RNA from age-matched room air-exposed rats were used as controls.

2009-11-12 | E-GEOD-18998 | biostudies-arrayexpress

Use of microarray analyses to determine the effect of hyperoxia and hypoxia on gene expression in early oxygen-induced retinopathy (OIR).

2012-02-24 | GSE36037 | GEO

Use of microarray analyses to determine the effect of hyperoxia and hypoxia on gene expression in early oxygen-induced retinopathy (OIR).

Project description:Different inbred strains of rats differ in their susceptibility to OIR, an animal model of human retinopathy of prematurity. We examined gene expression profiles in Fischer 344 (F344, resistant to OIR) and Sprague Dawley (SD, susceptible to OIR) rats at the early time points of day 5 (in response to hyperoxia) and day 6 (in response to relative hypoxia) to identify gene pathways related to the underlying genetic cause of the phenotypic differences observed between strains. To examine gene expression changes in rat strains which are resistant and susceptible to OIR, four different experimental conditions were analysed: F344 cyclic hyperoxia (O2) exposed, F344 room air (RA) exposed, SD O2 exposed and SD RA exposed. Two samples of pooled RNA, comprising of 3 individual rats from 2 separate litters, was used for each experimental condition, for each time point of interest. Pooled RNA from age-matched room air-exposed rats were used as controls.

2012-02-24 | E-GEOD-36037 | biostudies-arrayexpress

Impact of phlebotomy induced anemia on whole retinal transcriptome at P15 and P20 in the rat 50/10 OIR model

Project description:Phlebotomy-induced-anemia (PIA), which induces tissue hypoxia and angiogenesis, occurs universally among infants at risk for severe retinopathy of prematurity (ROP). We hypothesized that PIA exacerbates pathologic retinal neovascularization in ROP. Methods: We induced PIA to a hematocrit of 18% among rats undergoing the established 50/10 oxygen-induced retinopathy (OIR) model. Rats were euthanized at P15 and P20, during the avascular and neovascular phases of OIR, respectively. Whole retinal transcriptomes were compared to non-PIA controls. Results: RNA sequencing showed dampened pathways of angiogenesis, inflammation, and neural development in anemic OIR females at P20. Conclusion: PIA dampened transcriptomic pathways central to retinal vascular and neural development in neonatal rats. These data suggest PIA provides a protective effect from ROP.

2024-09-04 | GSE272252 | GEO

Single-cell RNAseq of Normoxic and OIR mouse retina by Drop-seq

Project description:Proliferative retinopathy is associated with abnormal vascular development (neovascularisation) of the retina. In mouse, the oxygen-induced retinopathy (OIR) model mimics the proliferative retinopathy found in extreme premature babies (Retinopathy of Prematurity) and in patients suffering from diabetic retinopathy. Using Drop-seq, we performed single-cell RNAseq analysis of mouse retina under physiological, normoxic (NORM) condition and retina under OIR condition, at postnatal day 14 and day 17, periods associated with a peak of neovascularisation. We used both whole retina cells or rod (CD73) depleted retina cells. Sorting conditions (whole vs. rod-depleted) derived count matrices were aligned with Seurat CCA and processed for dimensionality reduction and clustering.

2020-08-20 | GSE150703 | GEO

RNA-sequencing of the oxygen induced retinopathy (OIR) model in C57BL/6 mice

Project description:Pathological retinal angiogenesis is one of the major causes of vision loss worldwide. The breakdown of blood vessels and aberrant vessels growth usually lead to hemorrhage, macular edema, fibrotic scar, and retinal detachment. OIR model serves as a proxy for human pathological retinal neovascularization such as proliferative diabetic retinopathy, retinal vein occlusion and retinopathy of prematurity. C57BL/6 mice were exposed to 75% O2 in a hyperoxic chamber from postnatal day P7 to P12 and then returned to room air. The greatest neovascular response occurred at postnatal 17 days (P17) when the mice are put back to room air condition for 5 days. In order to reveal potential genes that involve in pathological neovascularization, we performed transcriptomic analyses of retina of P17.

2024-08-20 | GSE241239 | GEO

Profiling the retinal microRNA (miRNA) transcriptomes in a rat model of oxygen-induced retinopathy (OIR) by next-generation sequencing

Project description:Purpose: The study aimed to determine the transcriptome profile of retinal miRNA in a Sprague Dawley (SD) rat model of oxygen-induced retinopathy Methods: The newborn rats in OIR group were subjected to daily cycles of 80% oxygen for 21 hours and room air for 3 hours in a customised chamber for 14 days (postnatal day 14, P14), then return to room air for 15 days (postnatal day 29, P29). The newborn rats in sham group were housed in room air for 14 days. Retinal miRNA expression profiles of OIR or sham rats at P14 or OIR rats at P29 were generated by deep sequencing, in triplicate, using Illumina Hiseq-2500 RNA-seq platform. Briefly, the sequence reads from all samples were analysed for overall quality, screened for the presence of any contaminants and trimmed accordingly. The cleaned sequence reads were then processed through the quantification modules miRDEEP2 ver2.0.0.7 pipeline for known miRNA expression profiling. Rat miRNAs from miRBASE release21 were used for mapping and quantification. Differential miRNA expression analysis was undertaken using voom bioconductor package (https://www.bioconductor.org/packages/release/bioc/vignettes/limma/inst/doc/usersguide.pdf). Results: A total of 465 miRNAs were identified in the rat retina. The miRNAs with significantly altered levels (P<0.05) were identified in OIR rats at P14 compared with the sham controls or OIR rats at P29. Among those altered miRNAs, seven miRNAs were down-regulated in OIR rats at P14 with Log2 (Fold Change) < -1 fold, and no miRNAs were up-regulated. Additionally, the expression of these down-regulated miRNAs in OIR rats at P14 was restored at P29 after they were exposed to room air. Conclusion: Our study represents the first detailed analysis of retinal miRNA expression profile in rat model of OIR by miRNA-NGS technology.

2022-10-01 | GSE104620 | GEO

Transcriptome analysis of the oxygen induced retinopathy (OIR) model at 5 different timepoints

Project description:High-throughput sequencing of murine retina of the oxygen induced retinopathy (OIR) model compared to control mice at 5 consecutive days (P12-P16)

2022-11-11 | GSE200195 | GEO

Systems level analysis of lipid metabolism in oxygen-induced retinopathy [retina_RNAseq]

Project description:Activation of anaplerosis takes away glutamine from the biosynthetic pathway to the energy-producing TCA cycle. Especially, induction of hyperoxia driven anaplerosis in neurovascular tissues such as the retina during early stages of development could deplete biosynthetic precursors from newly proliferating endothelial cells impeding physiological angiogenesis and leading to vasoobliteration. Using an oxygen-induced retinopathy (OIR) mouse model, we investigated the metabolic differences between OIR-resistant BALB/cByJ and OIR susceptible C57BL/6J strains at system levels to understand the molecular underpinnings that potentially contribute to hyperoxia-induced vascular abnormalities in the neural retina. Our systems level in vivo RNA-seq, proteomic, and lipidomic profiling and ex-vivo explant studies show that the medium-chain fatty acids serves as an alternative source to feed the TCA cycle. Our findings strongly implicate that medium-chain fatty acids could suppress glutamine-fueled anaplerosis and ameliorate hyperoxia-induced vascular abnormalities in conditions such as retinopathy of prematurity.

2024-11-15 | GSE281855 | GEO

Progenitor cell combination normalizes retinal vascular development by enhancing pericyte ensheathment in the oxygen-induced retinopathy (OIR) model

Project description:Retinopathy of prematurity (ROP) is a disorder of the developing retina of preterm infants. ROP can lead to blindness due to abnormal angiogenesis that is the result of suspended vascular development and vaso-obliteration leading to severe retinal stress and hypoxia. We tested the hypothesis that a combined treatment with two human progenitor populations, the CD34+ cells, bone marrow-derived, and the endothelial colony-forming cells (ECFCs) synergistically protected the developing retinal vasculature in a murine model of ROP, the oxygen-induced retinopathy (OIR)., CD34+ cells alone, ECFCs alone, or a combination thereof were injected intravitreally at either P5 or P12 and pups were euthanized at P17. Retinas from OIR mice injected with ECFCs or the combined treatment revealed formation of the deep vascular plexus (DVP) while still in hyperoxia, with normal appearing connections between the superficial vascular plexus (SVP) and the DVP. The combination therapy prevented aberrant retinal neovascularization and was more effective anatomically and functionally at rescuing the ischemia phenotype than either cell type alone. The beneficial effect of the cell combination was the result of their ability to orchestrate an acceleration of vascular development and more rapid ensheathment of pericytes on the developing vessels.

2019-12-31 | GSE135844 | GEO

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