|
| Status |
Public on Sep 08, 2006 |
| Title |
MAQC_ABI_L_CFY_3 |
| Sample type |
RNA |
| |
|
| Source name |
Sample type L_CFY (Liver Comfrey)
|
| Organism |
Rattus norvegicus |
| Characteristics |
MAQC rat toxicogenomics samples used in Guo L. et al., Nature Biotechnology, 24(9), 2006.
|
| Treatment protocol |
Groups of six 6-week-old Big Blue rats were gavaged with riddelliine (1 mg/kg body weight) or aristolochic acid (10 mg/kg body weight) five times a week for 12 weeks or Big Blue rats were fed a diet of 8% comfrey roots for 12 weeks. The animals were sacrificed after 12 weeks of treatment, and the tissues were isolated, frozen quickly in liquid nitrogen and stored at –80 °C.
|
| Extracted molecule |
total RNA |
| Label |
Chemiluminescence - Digoxigenin
|
| Label protocol |
Digoxigenin-UTP labeled cRNA was generated from 1 µg of total RNA for each sample using Applied Biosystems NanoAmp RT-IVT Labeling Kit (P/N 4365715) according to the manufacturer’s protocol. Rat Genome Survey Microarray was used.
|
| |
|
| Hybridization protocol |
Array hybridization, array processing, chemiluminescence detection, image acquisition, and analysis were performed using Applied Biosystems Chemiluminescence Detection Kit and Applied Biosystems 1700 Chemiluminescent Microarray Analyzer following manufacturer’s protocol.
|
| Scan protocol |
Chemiluminescent Detection Kit (P/N 4339627, http://docs.appliedbiosystems.com/pebiodocs/04339627.pdf) and Chemiluminescent Microarray Analyzer User Guide (P/N 4338852B).
|
| Description |
The samples were randomly labeled and each test site was provided an aliquot of each sample. To avoid potential confounding factors in experimental implementation, the identity of the RNA samples was kept unknown to the test sites before data were submitted to FDA/NCTR.
|
| Data processing |
The Expression Array System Software suite performs the auto-gridding, feature extraction, fluorescence normalization, and signal data generation. The quantification data contain many distinct measurements for each probe, including the three basic measurements: Signal, S/N, and Flag values. The Signal value is the fully corrected, background subtracted measurement of chemiluminescent signal for gene expression values. The S/N value represents the ratio of signal above noise, or the measurement uncertainty of the probe signal, and can be used as a confidence level for the probe measurement. An S/N of 3 represents approximately a 99.95% confidence that the probe is detected above the background noise. In situations where the probe showed S/N < 1, the signal measurement is replaced with a 1 SDEV upper limit based on its probe signal SDEV.
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| |
|
| Submission date |
Aug 26, 2006 |
| Last update date |
Sep 01, 2006 |
| Contact name |
Leming Shi |
| E-mail(s) |
lemingshi@fudan.edu.cn
|
| Phone |
+86-18616827008
|
| Organization name |
Fudan University
|
| Department |
School of Life Sciences
|
| Lab |
Center for Pharmacogenomics
|
| Street address |
2005 Songhu Road
|
| City |
Shanghai |
| ZIP/Postal code |
200438 |
| Country |
China |
| |
|
| Platform ID |
GPL2996 |
| Series (1) |
| GSE5350 |
MicroArray Quality Control (MAQC) Project |
|
