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Sample GSM876021 Query DataSets for GSM876021
Status Public on Feb 16, 2012
Title 3-methylcholanthrene (5 µM) rep 1
Sample type RNA
Source name neonatal mouse ovaries_3-methylcholanthrene (5 µM)_96hr
Organism Mus musculus
Characteristics strain: Swiss
age: Post natal day 3-4
tissue: ovary
Treatment protocol Ovaries were treated with vehicle control medium (0.01% DMSO) or 3MC (5 µM). 3MC culture concentration was determined by pilot studies performed in our laboratory with the intention of inducing overt toxicity.
Growth protocol Swiss neonates were sacrificed by CO2 inhalation followed by decapitation. Ovaries were excised, trimmed of excess tissue and placed on culture plate inserts in 6-well tissue culture plate wells floating atop 1.5ml DMEM/F12 medium containing 5% (v/v) fetal calf serum, 1mg/ml bovine serum albumin, 50µg/ml ascorbic acid, 27.5μg/ml insulin–transferrin–selenium, 2.5 mM glutamine and 5U/ml penicillin/streptomycin. Media were supplemented with 40 ng/ml basic fibroblast growth factor, 50 ng/ml leukemia inhibitory factor, and 25 ng/ml stem cell factor. Using fine forceps a drop of medium was placed over the top of each ovary to prevent drying. Ovaries were cultured for 4 days at 37°C and 5% CO2 in air, with media changes every two days.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from ovaries using two rounds of a modified acid guanidinium thiocyanate–phenol–chloroform protocol: washed cells resuspended in lysis buffer (4 M guanidinium thiocyanate, 25 mM sodium citrate, 0.5% sarkosyl, 0.72% β-mercaptoethanol). RNA was isolated by phenol/chloroform extraction and isopropanol precipitated.
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 3MC 1
Data processing The data were normalised using quantile normalisation using BioConductor's lumi package in R statistical software
Submission date Feb 15, 2012
Last update date Feb 16, 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)
GSE35836 Expression data from mouse neonatal ovarian 3MC culture experiments

Data table header descriptions
VALUE Quantile normalized signal intensity

Data table
ILMN_1250052 6.619967772
ILMN_3122480 6.416672126
ILMN_2599935 8.066252888
ILMN_2675543 6.361875711
ILMN_2686883 6.447221893
ILMN_2751818 6.434876393
ILMN_2728634 6.73116028
ILMN_3040515 6.573181087
ILMN_2711608 6.407668659
ILMN_1232875 6.475037298
ILMN_1258507 6.276180534
ILMN_2746142 6.499579144
ILMN_1252690 6.527737834
ILMN_2655499 6.378424706
ILMN_1252870 6.500774807
ILMN_1248179 6.381578071
ILMN_2649955 7.338790624
ILMN_2628708 7.251197111
ILMN_3024781 8.30637741
ILMN_2705628 7.684206863

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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