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Sample GSM453679 Query DataSets for GSM453679
Status Public on Dec 01, 2009
Title KIKO V vs._E2_24h
Sample type RNA
 
Channel 1
Source name KIKO uterus, vehicle, 24h
Organism Mus musculus
Characteristics strain: C57BL/6
gender: female
age: 10+ weeks
tissue: uterus
Extracted molecule total RNA
Extraction protocol Trizol with Qiagen RNA easy clean up
Label Cy3
Label protocol Total RNA was amplified using the Agilent Low RNA Input Fluorescent Linear Amplification Kit protocol.  Starting with 500ng of total RNA, Cy3 labeled cRNA was produced according to manufacturer’s protocol. 
 
Channel 2
Source name KIKO uterus, E2, 24h
Organism Mus musculus
Characteristics strain: C57BL/6
gender: female
age: 10+ weeks
tissue: uterus
Extracted molecule total RNA
Extraction protocol Trizol with Qiagen RNA easy clean up
Label Cy5
Label protocol Total RNA was amplified using the Agilent Low RNA Input Fluorescent Linear Amplification Kit protocol.  Starting with 500ng of total RNA, Cy5 labeled cRNA was produced according to manufacturer’s protocol. 
 
 
Hybridization protocol For each two color comparison, 750ng of each Cy3 and Cy5 labeled cRNAs were mixed and fragmented using the Agilent In Situ Hybridization Kit protocol.  Hybridizations were performed for 17 hours in a rotating hybridization oven using the Agilent 60-mer oligo microarray processing protocol. 
Scan protocol Slides were washed as indicated in the Agilent 60-mer oligo microarray processing protocol and then scanned with an Agilent Scanner. Data was obtained using the Agilent Feature Extraction software, using defaults for all parameters.
Description pooled RNA from three vehicle or three treated uteri
Data processing Data was obtained using the Agilent Feature Extraction software (v8.1), using defaults for all parameters and loaded into the Rosetta Resolver® system (v6.0) (Rosetta Biosoftware, Kirkland, WA).
 
Submission date Sep 17, 2009
Last update date Sep 22, 2009
Contact name NIEHS Microarray Core
E-mail(s) microarray@niehs.nih.gov, liuliw@niehs.nih.gov
Organization name NIEHS
Department DIR
Lab Microarray Core
Street address 111 T.W. Alexander Drive
City RTP
State/province NC
ZIP/Postal code 27709
Country USA
 
Platform ID GPL7202
Series (1)
GSE18168 Uterine gene profiles from WT, KIKO (DNA-binding deficient ERα) and aERKO mice treated with estradiol or xenoestrogens

Data table header descriptions
ID_REF Agilent probe IDs from the Mouse Genome 4x44 array
VALUE log2 of ratio of treatment/control
PRE_VALUE Ratio of Cy5/Cy3 exported from Rosetta Resolver

Data table
ID_REF VALUE PRE_VALUE
A_52_P305654 0.5653 1.47974
A_52_P891296 0.0000 1
A_51_P243283 -0.3576 0.78045
A_52_P62270 -0.0075 0.99483
A_51_P362627 0.8321 1.78027
A_52_P229709 0.1928 1.14298
A_52_P662142 0.3574 1.28113
A_52_P112017 -0.2923 0.81658
A_51_P163444 -0.0212 0.98538
A_51_P270605 -0.0717 0.95152
A_51_P239367 0.0000 1
A_51_P442759 0.4638 1.37919
A_51_P106443 0.6804 1.60253
A_51_P460247 0.6147 1.53129
A_51_P275658 0.3574 1.28111
A_52_P1044206 0.0000 1
A_52_P473542 -0.1316 0.91282
A_51_P145507 -0.1877 0.878
A_52_P441355 0.0000 1
A_52_P219216 0.0000 1

Total number of rows: 41171

Table truncated, full table size 1093 Kbytes.




Supplementary file Size Download File type/resource
GSM453679_US22502532_251486814792_S01_GE2-v5_91_0806_1_4.txt.gz 14.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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