|
| Status |
Public on Dec 24, 2013 |
| Title |
whole_ctrl_1 |
| Sample type |
RNA |
| |
|
| Source name |
whole kidneys
|
| Organism |
Rattus norvegicus |
| Characteristics |
gender: male
strain: Wistar/ST
age: 8 weeks old
tissue: whole kidneys
agent: vehicle
dose: control
|
| Treatment protocol |
Cisplatin (0.5 mg/mL; Randa®; Nippon Kayaku Co. Ltd., Tokyo, Japan) was administered intraperitoneally; the same volume of saline solution was injected in the sham controls.
|
| Growth protocol |
Male Wistar/ST rats (8 weeks old) were purchased from SLC Animal Research Laboratories (Shizuoka, Japan). The rats were fed normal pellet food ad libitum, and given water freely.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with the RNeasy Mini Kit (Qiagen GmbH, Hilden, Germany)
|
| Label |
Digoxigenin-UTP
|
| Label protocol |
Digoxigenin (DIG)-labeled cRNA was generated from total RNA extracted from the proximal tubules or whole kidney using Applied Biosystems Chemiluminescent Reverse Transcription-In Vitro Transcription (RT-IVT) Labeling Kit v2.0 (Applied Biosystems part of Life Technologies, Foster City, CA, USA)
|
| |
|
| Hybridization protocol |
A total of 10 μg of labeled cRNA from each RT-IVT reaction was hybridized onto Rat Genome Survey Microarray at 55°C for 16 h.
|
| Scan protocol |
Microarrays were analyzed using the ABI 1700 Chemiluminescent Microarray Analyzer (Applied Biosystems)
|
| Description |
Rat Genome Survey Microarray® (Applied Biosystems)
|
| Data processing |
The array contained 34,656 oligonucleotide probes, including 26,857 individual gene probes and more than 1000 control probes. Microarray signal data were analyzed using Spotfire® software (TIBCO Software Inc. Palo Alto, CA). Expression values were normalized across the experiments with each 50% percentile values. Genes were defined as detectable on the basis of the recommendations from Applied Biosystems; a gene with a signal:noise ratio > 3.0 in 2 or 3 assays, and a FLAG value < 5000 was considered to be detectable. Normalized signal data were analyzed statistically with a one-way ANOVA. Probability values of less than 0.05 were considered statistically significant.
|
| |
|
| Submission date |
Apr 10, 2012 |
| Last update date |
Dec 24, 2013 |
| Contact name |
Satohiro Masuda |
| E-mail(s) |
masuda@kuhp.kyoto-u.ac.jp
|
| Phone |
+81-75-751-3586
|
| Fax |
+81-75-751-3586
|
| Organization name |
Kyoto University Hospital
|
| Department |
Pharmacy
|
| Lab |
Masuda
|
| Street address |
Shogoin
|
| City |
Kyoto |
| ZIP/Postal code |
606-8507 |
| Country |
Japan |
| |
|
| Platform ID |
GPL2996 |
| Series (1) |
| GSE37133 |
Gene expression profiles in isolated proximal tubules and whole kidneys of rats after cisplatin-administration |
|
