|
| Status |
Public on Nov 27, 2007 |
| Title |
Liver cholesterol pool1 Affy |
| Sample type |
RNA |
| |
|
| Source name |
liver, high cholesterol diet
|
| Organism |
Mus musculus |
| Characteristics |
Strain: C57BL/6
Gender: male
Age: 9 - 12 weeks
Tissue: liver
Treatment: vehicle only (5% DMSO in corn oil)
Diet: 1% cholesterol diet
|
| Biomaterial provider |
Adrian Roth
|
| Treatment protocol |
Animals were injected i.p. vehicle (5% DMSO in corn oil). After 10 h they were sacrificed.
|
| Growth protocol |
Animals had free acess to food (standard laboratory chow) and drinking water. They were mantained in 12-hour light/12-hour dark cycle. Seven days prior treatment they were on 1% (w/w) cholesterol diet (Provimi Kliba SA, Kaiseraugst, CH).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using TRIzol reagent (Invitrogen) according to the manufacturer protocol and purified by RNeasy Mini Kit (Qiagen). The total RNAs of two animals were pooled in equal amounts.
|
| Label |
biotin
|
| Label protocol |
All was done according to the Affymetrix recommendations. Briefly, double-stranded cDNA was synthesised using 10μg of total RNA with a (dT)24-T7 primer and amplified with T7 RNA polymerase in the presence of biotinylated nucleotides to cRNA.
|
| |
|
| Hybridization protocol |
After fragmentation, the cRNA was hybridised to the Gene Chips for 16 hours, followed by a standard amplification with biotin/streptavidin/phycoerythrin.
|
| Scan protocol |
Microarrays were scanned using a laser scanner (Affymetrix).
|
| Description |
No additional data.
|
| Data processing |
Raw data were first normalized using log2-transformed expression measure summaries of the probe sets which were computed and normalized using the Robust Multichip Average (RMA) algorithm as described. After transformation to non-logarithmic data, the expression estimates were scaled to the average expression levels in the control group and transcript levels further analyzed using Gene Spring Software (Silicon Genetics, Redwood, USA).
|
| |
|
| Submission date |
Jan 10, 2007 |
| Last update date |
Jan 30, 2007 |
| Contact name |
Peter Juvan |
| Phone |
+386 1 543 7595
|
| Organization name |
Faculty of Medicine, University of Ljubljana
|
| Department |
Institute of Biochemistry
|
| Lab |
Center for Functional Genomics and Bio-Chips
|
| Street address |
Zaloska 4
|
| City |
Ljubljana |
| ZIP/Postal code |
SI-1000 |
| Country |
Slovenia |
| |
|
| Platform ID |
GPL339 |
| Series (1) |
| GSE6721 |
High cholesterol diet and phenobarbital affect cholesterol homeostasis and drug metabolism |
|
