|
| Status |
Public on Jun 30, 2014 |
| Title |
HF_Pio_Apex_285 |
| Sample type |
RNA |
| |
|
| Source name |
mouse heart
|
| Organism |
Mus musculus |
| Characteristics |
strain: LDL-/-
gender: male
treatment: high fat + pioglitazone
tissue: heart
genetic background: C57BL/6
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from individual hearts (n=8 hearts per group, 48 samples in total) using glass beads and RNAzol (Campro Scientific, Veenendaal, The Netherlands).
|
| Label |
Biotin
|
| Label protocol |
The Illumina® TotalPrep™ RNA Amplification Kit (Ambion, art. No. AM-IL1791) was used to synthesize biotin labeled cRNA starting with 500 ng total RNA. Concentration of the labeled cRNA was measured using the Nanodrop spectrophotometer.
|
| |
|
| Hybridization protocol |
We have used standard Illumina hybridisation protocol. The amount of biotinylated cRNA that was hybridized onto the MouseRef-8 Expression BeadChip was 750 ng
|
| Scan protocol |
Illumina’s Genomestudio v1.1.1 software with the default settings advised by Illumina, was used for Gene Expression analysis. All the quality control data of this BeadChip were within specifications of the microarray service provider (Service XS, Leiden, the Netherlands).
|
| Data processing |
Probe-level, background subtracted expression values were used as input for GeneSpring GX11 software (Agilent), which was used for normalization of data; threshold signals below the value of 5 were set at 5. To be considered expressed, the signal detection p-value of the probe had to be lower than 0.01 in at least 1 of 48 experiments. 15505 probes fulfilled these criteria. Differential expression of probes was assessed using unpaired moderated t-test (LIMMA) via The Remote Analysis Computation for gene Expression data (RACE) suite at http://race.unil.ch
Pipeline for illumina arrays (www.arrayanalysis.org) was used to normalize data. Differential expression of probes was assessed using unpaired moderated t-test (LIMMA) via The Remote Analysis Computation for gene Expression data (RACE) suite at http://race.unil.ch
|
| |
|
| Submission date |
Jul 17, 2013 |
| Last update date |
Jun 30, 2014 |
| Contact name |
Lars Verschuren |
| E-mail(s) |
lars.verschuren@tno.nl
|
| Phone |
+31888666039
|
| Organization name |
TNO
|
| Department |
Microbiology and Systems Biology
|
| Street address |
Utrechtseweg 48
|
| City |
Zeist |
| ZIP/Postal code |
3704HE |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL6885 |
| Series (1) |
| GSE48977 |
A systems biology approach to understand the pathophysiological mechanisms of cardiac pathological hypertrophy associated with rosiglitazone |
|
