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Sample GSM267989 Query DataSets for GSM267989
Status Public on Oct 01, 2008
Title Kidney_Aqp11-/-_P7_3-4
Sample type RNA
 
Source name Aquaporin-11-/-_mouse P7 kidney #3-4
Organism Mus musculus
Characteristics Strain: C57BL/6J
Gender: male
Age: 7 days
Tissue: kidney
Extracted molecule total RNA
Extraction protocol Mice were sacrificed by cervical dislocation. Kidneys were rapidly excised on ice, washed in ice-cold phosphate-buffered saline (PBS), immersed in RNAlater (Ambion) and stored at –20°C. Total RNA was isolated using TRIzol Reagent (Invitrogen) and cleaned up using an RNeasy minikit with DNase treatment (Qiagen). The RNA quality and quantity were examined by agarose-gel electrophoresis and a spectrophotometer (GE Healthcare).
Label Biotin
Label protocol Three micrograms of total RNA obtained from each kidney was individually reverse-transcribed, amplified, and labeled using GeneChip One-Cycle Target Labeling and Control Reagent package (Affymetrix) according to the manufacturer’s protocol.
 
Hybridization protocol Standard Affymetrix protocol
Scan protocol Standard Affymetrix protocol. The arrays were washed, stained using Fluidics Station (Affymetrix), and then scanned with the GeneChip Scanner (Affymetrix). Data collection was performed using GeneChip Operating Software (Affymetrix).
Description Standard Affymetrix protocol
Data processing GeneChip Scanner 3000, GCOS v1.3, raw data
 
Submission date Feb 26, 2008
Last update date Aug 28, 2018
Contact name Shinji Okada
E-mail(s) asoka@mail.ecc.u-tokyo.ac.jp
Organization name The University of Tokyo
Street address 1-1-1 Yayoi
City Bunkyo-ku, Tokyo
ZIP/Postal code 113-8657
Country Japan
 
Platform ID GPL1261
Series (1)
GSE10634 Aquaporin-11 knockout effect on kidney
Relations
Reanalyzed by GSE119085

Data table header descriptions
ID_REF
VALUE Signal by Affymetrix MAS5
ABS_CALL Flagged as present, absent, or marginal by Affymetrix MAS5
DETECTION P-VALUE Detection p-value by Affymetrix MAS5

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-BioB-5_at 94.9554 P 0.000445901
AFFX-BioB-M_at 211.396 P 4.42873e-05
AFFX-BioB-3_at 166.579 P 8.14279e-05
AFFX-BioC-5_at 332.941 P 4.42873e-05
AFFX-BioC-3_at 276.277 P 4.42873e-05
AFFX-BioDn-5_at 855.855 P 4.42873e-05
AFFX-BioDn-3_at 1370.59 P 4.42873e-05
AFFX-CreX-5_at 3794.61 P 4.42873e-05
AFFX-CreX-3_at 4497.51 P 4.42873e-05
AFFX-DapX-5_at 107.153 P 9.4506e-05
AFFX-DapX-M_at 165.184 P 0.000224668
AFFX-DapX-3_at 255.177 P 5.16732e-05
AFFX-LysX-5_at 9.83645 A 0.156732
AFFX-LysX-M_at 16.3176 P 0.0429619
AFFX-LysX-3_at 39.7544 P 0.0012475
AFFX-PheX-5_at 15.1913 P 0.00933744
AFFX-PheX-M_at 26.0991 P 0.00227496
AFFX-PheX-3_at 42.8586 P 0.00844047
AFFX-ThrX-5_at 30.5023 P 8.14279e-05
AFFX-ThrX-M_at 33.7716 P 0.000224668

Total number of rows: 45101

Table truncated, full table size 1396 Kbytes.




Supplementary file Size Download File type/resource
GSM267989.CEL.gz 3.5 Mb (ftp)(http) CEL
GSM267989.CHP.gz 5.3 Mb (ftp)(http) CHP
Raw data provided as supplementary file
Processed data included within Sample table
Processed data provided as supplementary file

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