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Sample GSM1247435 Query DataSets for GSM1247435
Status Public on Oct 23, 2013
Title Smoke_testis rep 1
Sample type RNA
 
Source name Adult testis from cigarette smoke exposed mouse
Organism Mus musculus
Characteristics strain: C57BL/6
age: adult
exposed to: cigarette smoke in utero
tissue: testis
Treatment protocol C57BL/6 5 week-old female mice were exposed via the nose-only to cigarette smoke [twelve 3R4F reference cigarettes (University of Kentucky, USA) twice/day, five times per week, for 12-18 weeks]. Each exposure lasted 60 minutes. Control mice received room air. In total, 27 mice underwent cigarette smoke exposure. Eleven week-old female mice exposed to cigarette smoke for 6 weeks were separated into groups of three and housed with a single control stud male aged 7-8 weeks with proven fertility for a maximum of 12 weeks. Females were monitored every second day for post-coital plugs and pregnancy. Pregnant females were separated into single cages and litter sizes/pup weights recorded. Smoke exposure via dams continued throughout mating/pregnancy/lactation until weaning of pups at 21days post birth.
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
Description Smoke 1
Data processing The data were normalised using quantile normalisation using BioConductor (v.2.12.)'s lumi package in R statistical software
 
Submission date Oct 22, 2013
Last update date Oct 23, 2013
Contact name Alexander Peter Sobinoff
E-mail(s) c3045119@uon.edu.au
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)
GSE51530 Expression data from adult mouse testis exposed to cigarette smoke in utero

Data table header descriptions
ID_REF
VALUE Quantile normalized signal intensity

Data table
ID_REF VALUE
ILMN_1250052 11.13134745
ILMN_3122480 8.889949774
ILMN_2599935 8.75274153
ILMN_2675543 7.683720029
ILMN_2686883 7.727935142
ILMN_2751818 7.699343658
ILMN_2728634 7.75495385
ILMN_3040515 7.724330612
ILMN_2711608 7.693493317
ILMN_1232875 7.877110471
ILMN_1258507 7.727042468
ILMN_2746142 7.650176474
ILMN_1252690 8.133428439
ILMN_2655499 7.70142285
ILMN_1252870 7.741163843
ILMN_1248179 7.694109245
ILMN_2649955 9.952672129
ILMN_2628708 8.391359726
ILMN_3024781 7.714847181
ILMN_2705628 7.691156078

Total number of rows: 25697

Table truncated, full table size 624 Kbytes.




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

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