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Sample GSM137584 Query DataSets for GSM137584
Status Public on Aug 23, 2007
Title Eker Kidney OTA d3 biological rep2 29
Sample type RNA
 
Source name Kidney cortex and outer medulla_Eker_OTA treated_d3_biological replicate 2
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 OTA (210µg_ kg BW), dissolved in 0,1M sodium bicarbonate. After 3 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
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
 
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 13.96214 0.080566406
1371512_at 353.03067 2.44E-04
1368536_at 44.96872 7.32E-04
1373608_at 15.099229 0.24609375
1388833_at 142.33324 2.44E-04
1371146_at 24.071455 0.023925781
1375696_at 19.314842 2.44E-04
1375404_at 25.876043 0.010742188
1370217_at 316.44275 2.44E-04
1388467_at 336.28983 2.44E-04
1390514_at 120.447876 0.001220703
1374767_at 111.41428 0.005859375
1389992_at 6.193717 0.66552734
1377492_at 1.6403401 0.33447266
1387538_at 23.36773 0.014160156
1377200_at 13.109339 0.095214844
1376563_at 0.10230253 0.93237305
1374109_at 93.7955 2.44E-04
1389334_at 562.5273 2.44E-04
1370660_at 2.9032032 0.8054199

Total number of rows: 15923

Table truncated, full table size 488 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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