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Sample GSM137576 Query DataSets for GSM137576
Status Public on Aug 23, 2007
Title Eker Kidney C d7 biological rep3 21
Sample type RNA
 
Source name Kidney cortex and outer medulla_Eker_time mached vehicle control (AA)_d7_biological replicate 3
Organism Rattus norvegicus
Characteristics Genotype: Eker
Gender: male
Age: 10-14 weeks
Biomaterial provider MD Anderson Cancer Center, Smithville, Texas, USA
Treatment protocol Daily gavaged with 0,1M sodium bicarbonate. After 7 days: 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 kidney 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 12.949832 0.095214844
1371512_at 267.91367 0.000244141
1368536_at 51.405926 0.000244141
1373608_at 12.600137 0.33447266
1388833_at 191.04565 0.000244141
1371146_at 38.20361 0.001220703
1375696_at 18.156408 0.000244141
1375404_at 26.25414 0.008056641
1370217_at 274.5052 0.000732422
1388467_at 255.83855 0.000244141
1390514_at 207.15057 0.000732422
1374767_at 80.442085 0.010742188
1389992_at 10.55218 0.46606445
1377492_at 10.225537 0.17138672
1387538_at 22.129824 0.018554688
1377200_at 9.814049 0.19458008
1376563_at 0.068417534 0.90478516
1374109_at 109.208694 0.000732422
1389334_at 450.39377 0.000244141
1370660_at 1.701499 0.7258301

Total number of rows: 15923

Table truncated, full table size 503 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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