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Sample GSM1052767 Query DataSets for GSM1052767
Status Public on Dec 13, 2012
Title Control rep 1
Sample type RNA
Source name Adult ovary from room air exposed mouse
Organism Mus musculus
Characteristics tissue: Ovary
genetic background: C57BL/6
treatment: control
Treatment protocol Twenty-one C57BL/6 5 week old female mice were simultaneously exposed to cigarette smoke [twelve 3R4F reference cigarettes (University of Kentucky, USA) twice/day, 2.7 mg particulate matter, five times per week, for 12-18 weeks] using a custom-designed and purpose-built nose-only, directed flow inhalation and smoke-exposure system (CH Technologies, NJ, USA) housed in a fume and laminar flow hood. Each exposure lasted 60 minutes. Control mice received room air.
Growth protocol All experimental procedures involving the use of animals were performed with the approval of the University of Newcastle’s Animal Care and Ethics Committee (ACEC). Specific pathogen-free adult female (6-week-old) C57BL/6 mice were obtained from the animal services unit and maintained according to the recommendations prescribed by the ACEC. Mice were housed under a controlled lighting regime (16L:8D) at 21–22°C and supplied with food and water ad libitum.
Extracted molecule total RNA
Extraction protocol Total RNA (approximately 3 µg) was isolated from adult ovaries using a QIAGEN RNeasy Mini Kit (Hilden, Germany) in accordance with the manufacturer’s recommendations.
Label biotin
Label protocol Biotinylated cRNA were prepared with Ambion's Illumina RNA Amplification kit for Illumina arrays
Hybridization protocol Standard Illumina hybridization protocol
Scan protocol Standard Illumina scanning protocol
Data processing The data were normalised using quantile normalisation using BioConductor's lumi package in R statistical software
Submission date Dec 12, 2012
Last update date Dec 13, 2012
Contact name Alexander Peter Sobinoff
Organization name University of Newcastle Australia
Department Science and IT
Lab Reproductive Science Group
Street address University Drive
City Newcastle
State/province NSW
ZIP/Postal code 2308
Country Australia
Platform ID GPL6885
Series (1)
GSE42889 Expression data from adult mouse ovaries exposed to cigarette smoke in vivo

Data table header descriptions
VALUE Quantile normalized signal intensity

Data table
ILMN_1250052 7.772852894
ILMN_3122480 7.757121589
ILMN_2599935 9.304591242
ILMN_2675543 7.687584322
ILMN_2686883 7.751602003
ILMN_2751818 7.653420963
ILMN_2728634 7.78569972
ILMN_3040515 7.706138396
ILMN_2711608 7.733258459
ILMN_1232875 7.923586547
ILMN_1258507 7.698127797
ILMN_2746142 7.733606898
ILMN_1252690 7.76607412
ILMN_2655499 7.678304483
ILMN_1252870 7.763944862
ILMN_1248179 7.653420963
ILMN_2649955 7.950911733
ILMN_2628708 8.144746727
ILMN_3024781 9.102821764
ILMN_2705628 8.270974525

Total number of rows: 25697

Table truncated, full table size 624 Kbytes.

Supplementary data files not provided
Raw data are available on Series record
Processed data included within Sample table
Processed data are available on Series record

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