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Sample GSM267988 Query DataSets for GSM267988
Status Public on Oct 01, 2008
Title Kidney_Aqp11-/-_P7_3-3
Sample type RNA
 
Source name Aquaporin-11-/-_mouse P7 kidney #3-3
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 215.427 P 0.000146581
AFFX-BioB-M_at 287.52 P 4.42873e-05
AFFX-BioB-3_at 186.3 P 4.42873e-05
AFFX-BioC-5_at 541.841 P 4.42873e-05
AFFX-BioC-3_at 604.852 P 4.42873e-05
AFFX-BioDn-5_at 1289.94 P 4.42873e-05
AFFX-BioDn-3_at 2036.68 P 4.42873e-05
AFFX-CreX-5_at 6207 P 5.16732e-05
AFFX-CreX-3_at 7239.15 P 4.42873e-05
AFFX-DapX-5_at 187.036 P 6.02111e-05
AFFX-DapX-M_at 306.624 P 0.000146581
AFFX-DapX-3_at 426.483 P 6.02111e-05
AFFX-LysX-5_at 18.9781 P 0.00159257
AFFX-LysX-M_at 40.4598 P 0.00556451
AFFX-LysX-3_at 80.1209 P 5.16732e-05
AFFX-PheX-5_at 40.5443 P 7.00668e-05
AFFX-PheX-M_at 32.3038 P 0.000258358
AFFX-PheX-3_at 47.2073 P 0.000109401
AFFX-ThrX-5_at 61.2121 P 0.000146581
AFFX-ThrX-M_at 57.4513 P 4.42246e-05

Total number of rows: 45101

Table truncated, full table size 1404 Kbytes.




Supplementary file Size Download File type/resource
GSM267988.CEL.gz 3.6 Mb (ftp)(http) CEL
GSM267988.CHP.gz 5.2 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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