Unknown,Transcriptomics,Genomics,Proteomics

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Affymetrix GeneChip™ Canine Gene 1.1ST Array of canine heart valves in all stages of Myxomatous mitral valve disease (Normal-4)

ABSTRACT: Whole mitral valves from each Whitney grade of disease; normal (n=6), grade 1 (n=5), grade 2 (n=6), grade 3 (n=6) and grade 4 (n=5). mRNA was extracted using the qiagen RNeasy minikit and assessed by the agilent 2200 bioanalsyser. all samples passed quality control and transcriptomic analysis was performed by edinburgh genomics using the Affymetrix GeneChip™ Canine Gene 1.1ST Array. Results were reported as CEL files and then analysed in Affymetrix expression console (version 1.4.1.46) using the canine 1.1ST library files from Affymetrix. Robust Multi-array Average (RMA) was used to perform gene level normalisation and signal level summarisation.Following this, quality control assessment was performed on the data set. This included assessment of hybridisation (spike in) controls, labelling (poly-A) controls and area under the curve (AUC) control, probe cell intensity boxplots, a signal histogram graph and principle component analysis (PCA) plot. Following this assessment, the datasets were exported with annotation as a text file or as a CHT file. Affymetrix transcriptome analysis console (version 3.1.0.5) was used to perform unpaired one-way analysis of variance (ANOVA).

ORGANISM(S): Canis lupus familiaris

SUBMITTER: Greg Markby

PROVIDER: E-MTAB-8618 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Multiple molecular and cellular mechanisms are associated with the initiation and progression of aortic valve disease. Alterations in ECM remodeling, increased expression of pro-inflammatory cytokines, calcification, lipid deposition and changes in valve cell phenotype have demonstrated roles in development of aortic valve disease. Mechanical stimulation has a significant role in determining the physiological properties of valve tissue and an altered hemodynamic environment may result in pathological changes. We used microarrays to detail the global of gene expression profiles underlying valve remodeling during valve exposure to of two levels of cyclic mechanical pressure (normotensive 0-80mmHg and hypertensive 0-120mmHg ) on porcine valve tissue transcriptome using Sus Scrofa cDNA microarrays from Affymetrix and we identified distinct classes of up-regulated genes during this process. Hybridizations were carried out with RNA isolated from six independetn samples of valve tissue exposed to normotensive and hypertensive pressure for 24 hours at 1hz frecuency. Differentially expressed genes were identified by The t test with the option of unequal variance was used to calculate P values for each gene. The fold change and Q values for each gene were calculated with SAM program with permutation of 500 . Biological modeling of the differentially expressed genes (DE) was carried out based on GO groups and network analysis in ingenuity Pathway Analysis (IPA). Experiment Overall Design: The experimental design included three biological samples of porcine valve leaflets exposed to cyclic pressures of 0-80 or 0-120 mmHg for 24 hours, representing normotensive and hypertensive diastolic transvalvular pressure, respectively. Using Affymetrix porcine microarrays, we compared global gene expression profiles of aortic valve leaflets exposed to elevated and normal physiological pressure conditions . The effects of cyclic pressure on the transcriptome was determined by comparing the quantity and magnitud of change in gene expression levels of valve leflets, as well evaluating the molecular function each gene has in the cell,in the presence of hypertennsive (experimental) and normotensve pressurec (control).

Dataset Information

Affymetrix GeneChip™ Canine Gene 1.1ST Array of canine heart valves in all stages of Myxomatous mitral valve disease (Normal-4)

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