|
| Status |
Public on May 21, 2010 |
| Title |
MDA-MB-231 cells, retinoic acid effect, time 6h, repl1 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
MDA-MB-231 cells, untreated, time 6h, repl1
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MDA-MB-231
treatment: Vehicle
time: 6 hours
|
| 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 |
total RNA extracted using Qiagen miRNeasy kit, followed by Rneasy MinElute Cleanup, following manufacturer's instructions
|
| Label |
Cy5
|
| Label protocol |
Amino Allyl cDNA Labeling Kit (cat 1705, Ambion), following manufacturer's instructions. Samples were then diluted 1:10 and 15 picomoles of each dye were used for hyhbridization
|
| |
|
| Channel 2 |
| Source name |
MDA-MB-231 cells, retinoic acid treated, time 6h, repl1
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MDA-MB-231
treatment: 1 microM Retinoic Acid
time: 6 hours
|
| 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 |
total RNA extracted using Qiagen miRNeasy kit, followed by Rneasy MinElute Cleanup, following manufacturer's instructions
|
| Label |
Cy3
|
| Label protocol |
Amino Allyl cDNA Labeling Kit (cat 1705, Ambion), following manufacturer's instructions. Samples were then diluted 1:10 and 15 picomoles of each dye were used for hyhbridization
|
| |
|
| |
| Hybridization protocol |
hybridization and washing were done according to Agilent protocol (GE version 5.5 )
|
| Scan protocol |
Agilent Technologies Scanner G2505B US45102933, 5 micron resolution and XDR protocol, using the Agilent scan control software.
|
| Description |
Biological replicates 1 of 2
|
| Data processing |
Image data analysis was performed using the Feature extraction software (v9.1). The raw data FE files report log10 (Cy5/Cy3) ratios. Detailed description of the protocols used is reported in each raw data file. LogRatios are derived by Lowess normalizatin of Median Signals (maNorm function of marray package in Bioconductor).
|
| |
|
| Submission date |
Oct 02, 2009 |
| Last update date |
Mar 11, 2010 |
| Contact name |
Maddalena Fratelli |
| E-mail(s) |
maddalena@marionegri.it
|
| Phone |
+390239014217
|
| Organization name |
"Mario Negri" Institute
|
| Lab |
Molecular Biology
|
| Street address |
Via La Masa, 19
|
| City |
Milano |
| ZIP/Postal code |
I20156 |
| Country |
Italy |
| |
|
| Platform ID |
GPL4133 |
| Series (2) |
| GSE18390 |
Effects of retinoids on estrogen-receptor-positive and -negative breast carcinoma cells: mRNA profiling |
| GSE18693 |
Effects of retinoids on estrogen-receptor-positive and -negative breast carcinoma cells: mRNA and miRNA profiling |
|
