|
| Status |
Public on Jun 23, 2008 |
| Title |
Kidney_Control_Rep2 |
| Sample type |
RNA |
| |
|
| Source name |
kidney cortex, saline, 24 h
|
| Organism |
Rattus norvegicus |
| Characteristics |
Strain: Fisher 344
Gender: male
Age: 8 weeks
Tissue: kidney cortex
|
| Treatment protocol |
CER was dissolved in saline and intravenously administered as a single dose of 0 (vehicle only), 150, 300 or 600 mg/kg. The animals were sacrificed 24 h after the administration.
|
| Growth protocol |
Male Fisher 344 rats (7-week-old) were purchased from Charles River Laboratories Japan (Kanagawa, Japan) and housed in plastic cages in an environmentally controlled room (12 h light-dark cycle, 23 ± 3°C and 50 ± 20% relative humidity). The animals had ad libitum access to certified rodent chow (Oriental Yeast, Tokyo, Japan) and water, and were acclimatized under these conditions for a week before experimentation.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The kidney cortex was disrupted and homogenized in QIAzol Lysis Reagent with TissueLyser (Qiagen). Total RNA was isolated from the homogenates using a BioRobot® M48 Workstation (Qiagen) in combination with MagAttract® RNA Cell Mini M48 Kit following the manufacturer’s instructions, including a DNase digestion step.
|
| Label |
Cy3
|
| Label protocol |
Labeled cRNA targets were prepared using Low RNA Input Linear Amplification Kit according to the “One-Color Microarray-Based Gene Expression Analysis” protocol provided by the manufacturer (Agilent Technologies). Briefly, 500 ng of total RNA was reverse-transcribed using a primer containing oligo-dT and a T7 promoter. Using the resultant cDNAs as templates, cRNA targets were synthesized by in vitro transcription in the presence of cyanine 3-CTP. The resultant labeled cRNAs were purified using RNeasy Mini Kit and quantified by absorbance at 260 nm.
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| |
|
| Hybridization protocol |
Cyanine 3-labeled cRNA targets were hybridized to Whole Rat Genome Oligo Microarray at 65°C for 17 h following the procedures recommended by the manufacturer (Agilent Technologies). After hybridization, the microarray slide was washed and dried according to the protocol provided by the manufacturer.
|
| Scan protocol |
The microarray slide was scanned on an Agilent DNA microarray scanner (Agilent Technologies). The scan resolution was 5 micrometer and the eXtended Dynamic Range feature (XDR Hi 100%, XDR Low 10%) was used to scan the array twice at two different PMT levels. Hybridization images were quantified using Feature Extraction Software 9.1 (Agilent Technologies), and background-subtracted signal values were utilized for following analyses.
|
| Description |
Raw data file contains a variety of information. The raw signals used for analysis are located in the column Q, which is entitled gProcessedSignal in the spreadsheet.
|
| Data processing |
Raw microarray data were processed and analyzed with GeneSpring GX 7.3.1 (Agilent Technologies). For per array normalization, the 50th percentile of the signal values taken from each microarray was used as the normalizing reference. Per gene normalization was based on calculating fold expression levels relative to the median of the control animals (n = 3).
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| |
|
| Submission date |
Dec 27, 2007 |
| Last update date |
Jun 23, 2008 |
| Contact name |
Masatomo Rokushima |
| Organization name |
SHIONOGI & CO., LTD.
|
| Department |
Discovery Research Laboratories
|
| Street address |
12-4, Sagisu 5-chome, Fukushima-ku
|
| City |
Osaka |
| State/province |
Osaka |
| ZIP/Postal code |
553-0002 |
| Country |
Japan |
| |
|
| Platform ID |
GPL4135 |
| Series (1) |
| GSE10034 |
Transcriptomic Analysis of Nephrotoxicity Induced by Cephaloridine, a Representative Cephalosporin Antibiotic |
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