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Sample GSM876022 Query DataSets for GSM876022
Status Public on Feb 16, 2012
Title 3-methylcholanthrene (5 µM) rep 2
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 2
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 6.564489226
ILMN_3122480 6.320422479
ILMN_2599935 7.971711483
ILMN_2675543 6.314102217
ILMN_2686883 6.433784051
ILMN_2751818 6.416168117
ILMN_2728634 6.769706552
ILMN_3040515 6.375628216
ILMN_2711608 6.520444752
ILMN_1232875 6.399884996
ILMN_1258507 6.46018038
ILMN_2746142 6.292607163
ILMN_1252690 6.467471121
ILMN_2655499 6.350666388
ILMN_1252870 6.5613616
ILMN_1248179 6.46018038
ILMN_2649955 7.437807486
ILMN_2628708 7.31616076
ILMN_3024781 8.169617971
ILMN_2705628 7.788375323

Total number of rows: 25697

Table truncated, full table size 625 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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