|
| Status |
Public on Sep 25, 2008 |
| Title |
5 days post infarction, array 3 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Mouse left ventricle, sham operated
|
| Organism |
Mus musculus |
| Characteristics |
Mouse C57BL6,male, 8 weeks, heart, sham operated
|
| Extracted molecule |
total RNA |
| Extraction protocol |
SV total RNA isolation system, Promega
|
| Label |
Cy5
|
| Label protocol |
Agilent Low RNA input fluorescent linear amplification kit
|
| |
|
| Channel 2 |
| Source name |
Mouse left ventricle, non-infarcted tissue, 5 days post infarction
|
| Organism |
Mus musculus |
| Characteristics |
Mouse C57BL6,male, 8 weeks, heart, myocardial infarction
|
| Extracted molecule |
total RNA |
| Extraction protocol |
SV total RNA isolation system, Promega
|
| Label |
cy3
|
| Label protocol |
Agilent Low RNA input fluorescent linear amplification kit
|
| |
|
| |
| Hybridization protocol |
Agilent oligo microarray kit hybridization protocol
|
| Scan protocol |
The arrays were controlled for spatial and intensity dependent effects by visual inspections of the array images and of ratio/intensity (RI) plots. To retain saturated spots (with more than half of the pixels in saturation) we performed additional lower scans of the arrays and modified the saturated intensities according to the algorithm described in Lyng, Badiee et al (2004). As measures of the spot intensities we used the median of the foreground pixel intensities, and log-transformed them to obtain approximate normality. No further normalisation was done because this is taken care of in our model-based analysis described below
|
| Description |
Gene expression was examined in non-infarcted left ventricle at 3, 5, 7 and 14 days after myocardial infarction. Left ventricle from sham operated mice were used as controls.
|
| Data processing |
Our model is based on a log-linear mixed effect model according to Kerr et al (2000). The base2 logarithm of each of the measured fluorescent intensity was modelled as a sum of dye, gene and array effects plus effects of the interaction terms array*gene (i.e. spot effects), dye*gene and time*variety*gene (the time-dependent effect of the specific variety – here myocardial infarction or control - on each gene). The latter is the parameter of main concern, and we note that the difference here for a given gene between myocardial infarction and control is the log2 ratio (normalised for experimental noise) in gene expression between the two types. Parameter estimates were obtained using the MicroArray ANOVA (MAANOVA) package by Wu et al (2002), for the statistical language R. We sat the threshold of significance of 30% change and p<0.05.
|
| |
|
| Submission date |
Dec 13, 2006 |
| Last update date |
Sep 25, 2008 |
| Contact name |
Cathrine Husberg |
| E-mail(s) |
cathrine.husberg@biotek.uio.no
|
| Organization name |
Institute for experimental medical research
|
| Street address |
Kirkeveien 166
|
| City |
Oslo |
| ZIP/Postal code |
0407 |
| Country |
Norway |
| |
|
| Platform ID |
GPL891 |
| Series (1) |
| GSE6580 |
Molecular alterations following myocardial infarction in mice |
|
