|
| Status |
Public on Jul 23, 2008 |
| Title |
Liver 3 |
| Sample type |
RNA |
| |
|
| Source name |
Liver sample
|
| Organism |
Homo sapiens |
| Characteristics |
group: diet intervention, age: 55 years, weight loss: -5.0 kg
|
| Biomaterial provider |
Oulu University Hospital
|
| Treatment protocol |
Hypocaloric, low-fat AHA step I diet
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from liver tissue using the RNeasy mini kit (Qiagen). RNA concentration and purity were assessed spectrophotometrically at wavelengths 260 and 280 nm. RNA integrity was checked by agarose gel electrophoresis.
|
| Label |
biotin
|
| Label protocol |
Using 8 µg of total RNA as template double-stranded DNA was synthesized by means of the One-cycle cDNA synthesis kit (Affymetrix) and T7-(dT)24 primer. The DNA was purified using GeneChip Sample Cleanup Module (Qiagen). In vitro transcription was performed to produce biotin labeled cRNA using a IVT labeling kit (Affymetrix) according to the manufacturer’s instructions.
|
| |
|
| Hybridization protocol |
Biotinylated cRNA was cleaned with an GeneChip Sample Cleanup Module (Qiagen), fragmented to 35 to 200 nt, and hybridized to Affymetrix Human Genome U133 Plus 2 arrays.
|
| Scan protocol |
After being washed, the array was stained with streptavidin-phycoerythrin (Molecular Probes). Staining signal was amplified by biotinylated anti-streptavidin (Vector Laboratories) and second staining with streptavidin-phycoerythrin, and then scanned on GeneChip Scanner 3000.
|
| Description |
Gene expression data from a liver biopsy obtained from an obese woman
|
| Data processing |
Affymetrix CEL files were imported into GeneSpring 7.2 software (Silicon Genetics) and RMA normalization was performed.
|
| |
|
| Submission date |
Feb 16, 2007 |
| Last update date |
Aug 28, 2018 |
| Contact name |
Mirella Hietaniemi |
| E-mail(s) |
mirella.hietaniemi@oulu.fi
|
| Organization name |
University of Oulu
|
| Department |
Department of Internal Medicine, Biocenter Oulu
|
| Street address |
Aapistie 5A
|
| City |
Oulu |
| ZIP/Postal code |
900014 Oulun yliopisto |
| Country |
Finland |
| |
|
| Platform ID |
GPL570 |
| Series (1) |
| GSE7117 |
Hepatic gene expression after a hypocaloric, low-fat diet in obese women and controls |
|
| Relations |
| Reanalyzed by |
GSE119087 |
