|
| Status |
Public on May 21, 2010 |
| Title |
- time |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
MCF7_6hr_UT_1
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MCF-7
time: 6 hours
protocol: untreated
|
| Treatment protocol |
logarithmically growing cells were cultured in the presence or absence of 1 micromolar all-trans retinoic acid for 6 or 48 hours. At the end of the experiment total RNA, containing the microRNA fraction, was extracted and used for miR and GX profiling
|
| Growth protocol |
Cells were grown in F12 medium containing 5% charcoal stripped fetal bovine serum (lonza) containing 10 nM beta-estradiol
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted with miRNeasy minikit (Qiagen).
|
| Label |
Cy5
|
| Label protocol |
miRNA was labeled by RNA-ligase mediated ligation of Cy dye-coupled dinucleotides.
|
| |
|
| Channel 2 |
| Source name |
MCF7_48hr_UT_7
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MCF-7
time: 48 hours
protocol: untreated
|
| Treatment protocol |
logarithmically growing cells were cultured in the presence or absence of 1 micromolar all-trans retinoic acid for 6 or 48 hours. At the end of the experiment total RNA, containing the microRNA fraction, was extracted and used for miR and GX profiling
|
| Growth protocol |
Cells were grown in F12 medium containing 5% charcoal stripped fetal bovine serum (lonza) containing 10 nM beta-estradiol
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted with miRNeasy minikit (Qiagen).
|
| Label |
Cy3
|
| Label protocol |
miRNA was labeled by RNA-ligase mediated ligation of Cy dye-coupled dinucleotides.
|
| |
|
| |
| Hybridization protocol |
hybridysed at Adelaide Microarray Facility http://www.microarray.adelaide.edu.au/
|
| Scan protocol |
Slides were scanned with a GenePix 4000B Scanner (Axon Instruments)
|
| Description |
no additional information
|
| Data processing |
Image analysis and spot identification and intensity extraction was performed using the Spot software package (http://experimental.act.cmis.csiro.au/Spot/index.php, CSIRO, Australia). Spot uses a seeded region growing algorithm to identify spots and is able to identify non-uniform shaped spots. Morphological opening background correction was applied to mean spot signal intensities. Analysis was performed in R with LIMMA package of BioConductor. Intensity-dependent global loess normalization was applied and the linear model fitted.
VALUE = normalized log2 ratio (Cy5/Cy3)
|
| |
|
| Submission date |
Oct 19, 2009 |
| Last update date |
Mar 11, 2010 |
| Contact name |
Anna Tsykin |
| E-mail(s) |
anna.tsykin@adelaide.edu.au
|
| Phone |
61 8 8222 3479
|
| Organization name |
SA Pathology
|
| Department |
Hanson Institute
|
| Lab |
Centre for Cancer Research
|
| Street address |
Frome Road
|
| City |
Adelaide |
| State/province |
SA |
| ZIP/Postal code |
5000 |
| Country |
Australia |
| |
|
| Platform ID |
GPL9472 |
| Series (2) |
| GSE18628 |
MicroRNA profiling shows different response to retinoids in estrogen-receptor positive and negative cells |
| GSE18693 |
Effects of retinoids on estrogen-receptor-positive and -negative breast carcinoma cells: mRNA and miRNA profiling |
|
