|
| 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 |
| 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) |
| GSE35836 |
Expression data from mouse neonatal ovarian 3MC culture experiments |
|
