Use of microarray analyses to determine the effect of hyperoxia and hypoxia on gene expression in early oxygen-induced retinopathy (OIR).
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ABSTRACT:
ORGANISM(S): Rattus norvegicus
PROVIDER: GSE36037 | GEO | 2012/02/24
SECONDARY ACCESSION(S): PRJNA151759
REPOSITORIES: GEO
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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.
2009-11-13 | GSE18998 | GEO
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
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
Project description:Femoral neck bone mineral density and structure candidate gene analysis in Fischer 344 (F344) and Lewis (LEW) rats Hip fracture is the most devastating osteoporotic fracture type with significant morbidity and mortality. Previously, we identified that the region of 4q21-q41 on chromosome (Chr) 4 uniquely harbors multiple femoral neck quantitative trait loci (QTLs) in inbred Fischer 344 (F344) and Lewis (LEW) rats. In this study we identified the candidate genes for femoral neck density and structure by correlating gene expression in the proximal femur with the femoral neck phenotypes linked to the QTLs on Chr 4. Microarray analysis was performed using RNA extracted from proximal femora of 4-week-old rats from F344, LEW and two other strains. A total of 104 genes in the 4q21-q41 region were differentially expressed (p<0.05) among all strains of rats with a false discovery rate (FDR) less than 10%. These 104 genes were then ranked based on the proportion of variation in femoral neck phenotypes in F2 animals homozygous for a particular strain’s allele at the Chr 4 QTL explained by the expression level of the gene in that strain. A total of 37 genes, including 21 candidate genes and 16 predicted genes, were strongly correlated (r2>0.50) with different femoral neck phenotypes and prioritized for further analysis. Ingenuity pathway analysis revealed several direct or indirect relationships among the candidate genes related to bone metabolism including pathways related to beta-estradiol, interleukin 6, insulin growth factor 2, androgen receptor and tumor necrosis factor. Keywords: Comparison of gene expression profiles between F344, LEW, COP and DA rats
2009-03-31 | GSE11180 | GEO
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
Project description:Femoral neck bone mineral density and structure candidate gene analysis in Fischer 344 (F344) and Lewis (LEW) rats; Hip fracture is the most devastating osteoporotic fracture type with significant morbidity and mortality. Previously, we identified that the region of 4q21-q41 on chromosome (Chr) 4 uniquely harbors multiple femoral neck quantitative trait loci (QTLs) in inbred Fischer 344 (F344) and Lewis (LEW) rats. In this study we identified the candidate genes for femoral neck density and structure by correlating gene expression in the proximal femur with the femoral neck phenotypes linked to the QTLs on Chr 4. Microarray analysis was performed using RNA extracted from proximal femora of 4-week-old rats from F344, LEW and two other strains. A total of 104 genes in the 4q21-q41 region were differentially expressed (p<0.05) among all strains of rats with a false discovery rate (FDR) less than 10%. These 104 genes were then ranked based on the proportion of variation in femoral neck phenotypes in F2 animals homozygous for a particular strainâ??s allele at the Chr 4 QTL explained by the expression level of the gene in that strain. A total of 37 genes, including 21 candidate genes and 16 predicted genes, were strongly correlated (r2>0.50) with different femoral neck phenotypes and prioritized for further analysis. Ingenuity pathway analysis revealed several direct or indirect relationships among the candidate genes related to bone metabolism including pathways related to beta-estradiol, interleukin 6, insulin growth factor 2, androgen receptor and tumor necrosis factor. Experiment Overall Design: Comparison of differentially expressed genes at the chromosome 4 QTL identified in F344 and LEW F2 rats.
2009-04-04 | E-GEOD-11180 | biostudies-arrayexpress
Project description:We profiled hepatic transcriptional responses of 6 strains of rats with varying sensitivity to a dioxin, TCDD, at 19 hours following exposure. The resistant rats exhibited significantly reduced transcriptional responses in comparison to the sensitive strains. We hypothesize that genes which show differential changes between the resistant and sensitive rats may potentially explain sensitivity. Rats with varying sensitivities (Long-Evans, L-E; Han/Wistar, H/W; Fischer 344, F344; Wistar, Wis; Line-A, Ln-A; and Line-C, Ln-C) were treated with 100 ug/kg TCDD or corn oil vehicle and euthanized 19 hours post-treatment. Each treatment group contains four or six animals (biological replicates), each of which was assayed on an individual microarray.
2011-08-16 | E-GEOD-31411 | biostudies-arrayexpress
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
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
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