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Sample GSM137606 Query DataSets for GSM137606
Status Public on Aug 23, 2007
Title Wild type Kidney AA d1 biological rep3 51
Sample type RNA
 
Source name Kidney cortex and outer medulla_wild type_AA treated_d1_biological replicate 3
Organism Rattus norvegicus
Characteristics Genotype: wild type
Gender: male
Age: 10-14 weeks
Biomaterial provider MD Anderson Cancer Center, Smithville, Texas, USA
Treatment protocol Gavaged with one single dose AA (10mg_ kg BW), dissolved in 0,1M sodium bicarbonate. 24h later: Anesthesia with pentobarbital, exsanguination subsequent to retrograde perfusion with PBS. Kidney collection and storage in RNAlater.
Extracted molecule total RNA
Extraction protocol Extraction of total RNA was performed according to the manufacturer's instructions: RNeasy Midi Kit (Qiagen, Cat No. 75144)
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 microg total RNA (Affymetrix, USA; GeneChip® Expression Analysis, GeneChip sample Cleanup Module, 701194 Rev.1)
 
Hybridization protocol According to the manufacturer’s instructions (Affymetrix, USA; GeneChip® Expression Analysis, Section 2, Chapter 3, 701027 rev1), fragmented cRNA samples were hybridized on Affymetrix Rat Genome RAE230A arrays , and hybridized cRNA was stained using Phycoerythrin-conjugated Streptavidin
Scan protocol The stained Genechips were scanned with the GCS3000 Scanner according to the manufacturer’s instructions, using GCOS software Vers 1 (Affymetrix, USA; GeneChip® Expression Analysis, Section 2, Chapter 4, 701028 rev1)
Description total RNA from kindey cortex and outer medulla
Data processing Dark and white spots, gradients and distortions were detected and corrected in the CEL file data using GeneData Expressionist Refiner software. Then the data were condensed using Mas 5 algorithms and scaled to a target intensity of 100.
 
Submission date Sep 27, 2006
Last update date Aug 23, 2007
Contact name Daniel R. Dietrich
E-mail(s) [email protected]
Phone 0049-7531-883518
Fax 0049-7531-883170
Organization name University of Konstanz
Department Environmental Toxicology
Street address Jakob-Burckhardt-Str. 25
City Konstanz
ZIP/Postal code 78467
Country Germany
 
Platform ID GPL341
Series (1)
GSE5923 Expression data from Aristolochic Acid and Ochratoxin A treated Tsc2 mutant (Eker) and corresponding wild type rats

Data table header descriptions
ID_REF Affymetrix RAE230A probe set ID
VALUE MAS5-calculated Signal intensity
DETECTION P-VALUE 'detection p-value', p-value that indicates the significance level of the detection call

Data table
ID_REF VALUE DETECTION P-VALUE
1369465_at 14.066814 0.037684117
1371512_at 295.74872 0.001672809
1368536_at 48.808743 0.001672809
1373608_at 2.9705064 0.671679
1388833_at 221.30101 0.001672809
1371146_at 30.66748 0.025230302
1375696_at 21.206633 0.002923538
1375404_at 28.355501 0.016427109
1370217_at 282.85522 0.002219546
1388467_at 322.22766 0.002219546
1390514_at 148.463 0.004962743
1374767_at 37.1756 0.054755468
1389992_at 8.470442 0.60516244
1377492_at 7.2167516 0.32832095
1387538_at 30.25527 0.02042992
1377200_at 15.005099 0.123873115
1376563_at 0.7518647 0.60516244
1374109_at 95.42214 0.002219546
1389334_at 428.46097 0.001672809
1370660_at 10.48803 0.6389462

Total number of rows: 15923

Table truncated, full table size 499 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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