Dataset features

Specifications


Application: Gene expression microarray analysis
Number of samples: 9
Release date: Oct 25 2018
Last update date: Oct 25 2018
Access: Public
Diseases: Heart Failure, Cardiomyopathies, Myocardial Infarction
Dataset link Acute Mechanical Unloading Prior to Reperfusion is Cardioprotective and Limits the Development of Heart Failure After Myocardial Infarction

Experimental Protocol


To explore the optimal duration of mechanical unloading prior to reperfusion, adult, male Yorkshire swine were divided into 4 groups (n=4/group; Figure 1A). All groups underwent 90 minutes of LAD occlusion. In Group 1, LAD occlusion followed by 120 minutes of reperfusion served as the control group (Primary Reperfusion). In Groups 2 and 3, LAD occlusion was followed by insertion and activation of a TV-Pump (Impella CP; Abiomed Inc; Danvers, MA) via a 14Fr sheath in the left femoral artery and maintained at maximal support (44,000 rotations per minute). This was followed by an additional 15 (Group 2) or 30 (Group 3; Primary Unloading) minutes of occlusion respectively, then 120 minutes of reperfusion. In Group 4, LAD occlusion was followed by reperfusion, and after 30 minutes of reperfusion, a TVP was inserted and activated for the remaining 90 minutes of reperfusion (Post Reperfusion Unloading). At the end of each study, animals were euthanized for determination of myocardial infarct size. Three sham-operated animals were intubated, anesthetized, and mechanically ventilated without myocardial infarction or mechanical unloading. LV tissue samples obtained from sham controls were used for tissue analysis. RNA was collected from the center of the infarct zone of group 1 (Primary Reperfusion), group 3 (Primary Unloading) animals, or from the same region of the left ventricle in sham operated animals. RNA was processed and hybridized to Affymetrix Porcine Gene 1.0 ST expression microarrays (3 to 4 arrays per condition), using the standard Affymetrix workflow. Gene level expression values were determined using the Robust Multiarray Average (RMA) method (1) as part of the affy package (version 1.36.1) (2) in the Bioconductor R suite (version 2.12) (3), together with Entrez Gene-specific probeset maping (17.0.0) from the Molecular and Behavioral Neuroscience Institute (Brainarray) at the University of Michigan (4)). Array quality was measured by computing Relative Log Expression (RLE) and Normalized Unscaled Standard Error (NUSE) using the affyPLM package (version 1.34.0) (5). The three best samples from each group, by RLE value, were selected for further analysis. Data was quantile normalized using normalize.quantiles in the R preprocessCore package (version 1.32.0), and differential expression was determined using Limma (6) (version 3.26.9) for three contrasts: Primary Reperfusion vs Sham, Primary Unloading vs. Sham, and Primary Unloading vs. Primary Reperfusion. Genes showing at least a 2.0 fold change in expression and a raw p.value of less than 0.01.

Repositories


GEO

GSE108644

BioProject

PRJNA428019

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Contact


Gavin Schnitzler