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Sample GSM253592 Query DataSets for GSM253592
Status Public on Jun 23, 2008
Title Kidney_Middle-dose_Rep2
Sample type RNA
 
Source name kidney cortex, middle-dose of CER, 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.
 
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).
 
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

Data table header descriptions
ID_REF
VALUE GeneSpring-software computed normalized signal intensity
RATIO GeneSpring-software computed normalized ratio (Treated/Control); fold expression levels relative to the median of the control animals (n = 3)

Data table
ID_REF VALUE RATIO
12 0.19211116 1.2596062
13 0.37712553 0.9747129
14 8.324505 1.1936647
15 0.20909747 1.2479923
16 10.525993 1.1099542
17 143.93925 1.2866188
18 3.8729165 0.85521156
19 8.397854 0.97318506
20 16.04503 1.0734745
21 0.11179385 1.2478288
22 0.32441923 1.3303435
23 0.3066873 0.7068931
24 0.09241353 1.0429777
25 1.0046031 0.68217003
26 0.13227326 1.0009875
27 36.37817 1.0832647
28 24.592165 1.1357558
30 18.994762 0.95597756
32 0.4172995 1.6557746
33 13.03191 0.9077676

Total number of rows: 41012

Table truncated, full table size 1043 Kbytes.




Supplementary file Size Download File type/resource
GSM253592.txt.gz 6.6 Mb (ftp)(http) TXT
Processed data included within Sample table

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