|
| Status |
Public on Jan 22, 2014 |
| Title |
LIVER_CONTROL_repl5 |
| Sample type |
RNA |
| |
|
| Source name |
human liver
|
| Organism |
Homo sapiens |
| Characteristics |
treatment: control
batch: 7
donor: 53
tissue: Human liver slices (diameter 4 mm, thickness 250 µm)
|
| Treatment protocol |
Diclofenac sodium, carbamazepine, nefazodone and ketoconazole were obtained from Sigma (Zwijndrecht, the Netherlands). Methotrexate was from Acros Organics (Geel, Belgium). Human recombinant TNFα was acquired from R&D Systems (Abingdon, United Kingdom).
|
| Growth protocol |
Human hepatoma HepG2 cells were obtained from American Type Culture Collection (ATCC, Wesel, Germany), cultured in DMEM supplemented with 10% (v/v) FBS, 25 U/mL penicillin and 25 µg/mL streptomycin and used for experiments between passage 5 and 20.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using the RNeasy® Plus Mini Kit (Qiagen, Venlo, the Netherlands) and RNA integrity and quality was assessed using the Agilent bioanalyser (Agilent Technologies, Palo Alto, CA, USA).
|
| Label |
biotin
|
| Label protocol |
The Affymetrix 3' IVT-Express Labeling Kit (#901229) was used to synthesize Biotin-labeled cRNA. From each RNA sample 100 ng was used as input for the labeling reactions.
|
| |
|
| Hybridization protocol |
cRNA was denaturized to prepare for the hybridization on the array. The fragmented cRNA with a concentration of 0.0375 μg/μl was finally utilized for the hybridization on the Affymetrix HT HG U133 plus PM. The Affymetrix HWS Kit (#901530) was used for the hybridization, washing and staining of the chips.
|
| Scan protocol |
Scanning of the Array Plates was performed using the Affymetrix GeneTitan scanner
|
| Description |
Human liver slices (diameter 4 mm, thickness 250 µm)
|
| Data processing |
BRB Array Tools software was used to normalize the CEL data using the Robust Multichip Average (RMA) method. Significantly differentially expressed genes (p-value < 0.001) between the various experimental conditions were identified with an ANOVA test followed by calculation according to Benjamini and Hochberg (Benjamini and Hochberg, 1995).
|
| |
|
| Submission date |
Jan 21, 2014 |
| Last update date |
Jan 22, 2014 |
| Contact name |
Steven Wink |
| E-mail(s) |
[email protected]
|
| Organization name |
LACDR
|
| Department |
Division of Toxicology
|
| Street address |
Einsteinweg 55
|
| City |
Leiden |
| State/province |
Zuid Holland |
| ZIP/Postal code |
2333CC |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL13158 |
| Series (2) |
| GSE54255 |
Gene expression data from precision cut human liver slices treated to diclofenac |
| GSE54257 |
Drug-induced liver injury |
|
