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Sample GSM93501 Query DataSets for GSM93501
Status Public on Mar 31, 2006
Title COPxACI F2 #5
Sample type RNA
 
Source name anterior pituitary
Organism Rattus norvegicus
Characteristics Copenhagen x ACI F2 rat, male, age 21 weeks, treated with the synthetic estrogen diethylstilbestrol (DES) for 12 weeks
Treatment protocol diethylstilbestrol (DES) treatment for 12 weeks starting at 9 weeks of age
Extracted molecule total RNA
Extraction protocol Anterior pituitary gland was harvested at the time of sacrifice, weighed and flash-frozen in liquid nitrogen. Tissue was homogenized in lysis buffer by passage through an 18- and then 22-guage needle. Total RNA was isolated using the Absolutely RNA Kit from Stratagene.
Label biotin
Label protocol Approximately 2 µg of total RNA was processed to produce biotinylated cRNA targets.
 
Hybridization protocol standard Affymetrix procedures
Scan protocol standard Affymetrix procedures
Description Copenhagen x ACI F2 rats were derived by crossing female COP rats with male ACI rats to generate the F1 generation, which was then intercrossed to generate F2 animals. At 9 weeks of age, a silastic tubing implant containing 5mg of the synthetic estrogen diethylstilbestrol (DES) was surgically implanted subcutaneously in the interscapular region of male rats. Each animal received an intraperitoneal injection of BrdU (50mg/kg) 4 hours prior to sacrifice. Animals were sacrificed at 21 weeks of age by decapitation and pituitary glands were immediately harvested, weighed and flash-frozen in liquid nitrogen. Tissues were homogenized through a 22-gauge needle and total RNA was extracted using the Absolutely RNA Kit (Stratagene). A total of 43 DES-treated F2 males were analyzed by microarray.
Data processing Affymetrix GeneChip Operating Software version 1.2
 
Submission date Jan 23, 2006
Last update date Nov 27, 2012
Contact name James Shull
E-mail(s) shull@oncology.wisc.edu
Phone 608-265-5003
Organization name University of Wisconsin-Madison
Department McArdle Laboratory for Cancer Research
Lab Shull Laboratory
Street address 1400 University Avenue
City Madison
State/province WI
ZIP/Postal code 53706
Country USA
 
Platform ID GPL1355
Series (2)
GSE4081 Expression QTL (eQTL) mapping in the anterior pituitary gland using DES-treated COPxACI F2 rats.
GSE4083 Diethylstilbestrol effects on rat anterior pituitary gland

Data table header descriptions
ID_REF
VALUE MAS5-calculated Signal intensity
ABS_CALL the call in an absolute analysis that indicates if the transcript was present (P), absent (A), marginal (M), or no call (NC)
DETECTION P-VALUE 'detection p-value', p-value that indicates the significance level of the detection call

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-BioB-5_at 538.5 P 0.000754
AFFX-BioB-M_at 1013 P 0.00006
AFFX-BioB-3_at 457.5 P 0.000044
AFFX-BioC-5_at 1611.9 P 0.000052
AFFX-BioC-3_at 1991.9 P 0.000052
AFFX-BioDn-5_at 2958.1 P 0.00006
AFFX-BioDn-3_at 5787.5 P 0.00006
AFFX-CreX-5_at 18276.3 P 0.000044
AFFX-CreX-3_at 24776.2 P 0.000044
AFFX-DapX-5_at 688.2 P 0.000052
AFFX-DapX-M_at 1478.7 P 0.000258
AFFX-DapX-3_at 1563.5 P 0.000044
AFFX-LysX-5_at 90.9 P 0.000127
AFFX-LysX-M_at 174 P 0.004017
AFFX-LysX-3_at 378.5 P 0.000225
AFFX-PheX-5_at 149.9 P 0.004014
AFFX-PheX-M_at 181.7 P 0.000972
AFFX-PheX-3_at 207 P 0.002023
AFFX-ThrX-5_at 167.7 P 0.004484
AFFX-ThrX-M_at 259.5 P 0.000509

Total number of rows: 31099

Table truncated, full table size 831 Kbytes.




Supplementary data files not provided

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