|
| Status |
Public on Jan 14, 2014 |
| Title |
aorta-6m-rep4 |
| Sample type |
RNA |
| |
|
| Source name |
aorta, 6 months
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: aorta
gender: male
age: 6 months
|
| Treatment protocol |
Male C57BL/6 mice were obtained from Janvier (Saint Berthevin, France) and kept one week in the local animal house for acclimatization. Mice were aged 6 months and 20 months and water and standard rodent chow were fed ad libitum.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The descending aorta was flushed thoroughly with ice-cold phosphate-buffered saline (PBS), through the left ventricle of the heart, cleaned of periadventitial fat and connective tissues, and snap-frozen in liquid nitrogen and stored at -80 °C. Extraction of total RNA from the tissue was followed with Qiagen RNeasy Mini Kit (Qiagen, Hilden, Germany). Total RNA from 6 individual mice of each group was treated with DNase I to remove residual genomic DNA. Total RNA preparations were checked for RNA integrity by Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA). All samples showed common high quality RNA Integrity Numbers (RIN 9.0-9.6) and RNA was quantified by photometric Nanodrop measurement.
|
| Label |
Cy3
|
| Label protocol |
Synthesis of cDNA and subsequent fluorescent labelling of cRNA was performed on six replicates of each experimental condition (adult and old mice) according to the manufacturers protocol (One-Color Microarray-Based Gene Expression Analysis / Low Input Quick Amp Labeling; Agilent Technologies). Briefly, 100 ng of total RNA were converted to cDNA, followed by in vitro transcription and incorporation of Cy3-CTP into nascent cRNA.
|
| |
|
| Hybridization protocol |
After fragmentation labelled cRNA was hybridized to Agilent SurePrint G3 Mouse GE 8x60k Microarrays for 17 h at 65 °C
|
| Scan protocol |
Samples were scanned as described in the manufacturers protocol. Signal intensities on 20 bit tiff images were calculated by Feature Extraction software (FE, Vers. 10.7.1.1; Agilent Technologies).
|
| Data processing |
Data analyses were conducted with GeneSpring GX software (Vers. 12.5; Agilent Technologies). Probe signal intensities were quantile normalized across all samples to reduce inter-array variability (Bolstad et al., 2003). Input data pre-processing was concluded by baseline transformation to the median of all samples.
|
| |
|
| Submission date |
Sep 12, 2013 |
| Last update date |
Jan 14, 2014 |
| Contact name |
Karl Koehrer |
| E-mail(s) |
rene.deenen@hhu.de
|
| Organization name |
University of Duesseldorf
|
| Department |
BMFZ
|
| Lab |
GTL
|
| Street address |
Universitaetsstr. 1
|
| City |
Duesseldorf |
| ZIP/Postal code |
40225 |
| Country |
Germany |
| |
|
| Platform ID |
GPL10787 |
| Series (1) |
| GSE50833 |
Analysis of age-related vascular gene expression in mice |
|
