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Sample GSM876023 Query DataSets for GSM876023
Status Public on Feb 16, 2012
Title 3-methylcholanthrene (5 µM) rep 3
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 3
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 6.436831944
ILMN_3122480 6.352423221
ILMN_2599935 8.019912124
ILMN_2675543 6.369713867
ILMN_2686883 6.511328692
ILMN_2751818 6.414407085
ILMN_2728634 6.595075745
ILMN_3040515 6.525287112
ILMN_2711608 6.409070031
ILMN_1232875 6.396582566
ILMN_1258507 6.313979708
ILMN_2746142 6.334869762
ILMN_1252690 6.564866245
ILMN_2655499 6.304418114
ILMN_1252870 6.420473924
ILMN_1248179 6.404754232
ILMN_2649955 7.340467251
ILMN_2628708 7.206726273
ILMN_3024781 8.214880163
ILMN_2705628 7.804180591

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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