|
| Status |
Public on Apr 12, 2011 |
| Title |
Sum149-control1 (Agilent-021827 miRNA v12.0) |
| Sample type |
RNA |
| |
|
| Source name |
SUM149PT Vehicle CTRL
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: SUM149PT
er: ER(-)
p53: mut (M237I)
|
| Treatment protocol |
SUM149PT cells were plated at 1.5 x 10^6 cells per 150 x 25mm dish with 25mL of growth media, and allowed to adhere for 48h prior to treatment. The media in each plate was replaced with 25mL fresh media containing the drug treatment.
|
| Growth protocol |
SUM149PT cells were grown in Ham's F-12 media with 5% fetal bovine serume supplemented with 5 µg/mL insulin, 1 µg/mL hydrocortisone, 10 mM HEPES and Antimycotic/Antibiotic at 37°C with 5%CO2 and 85% humidity.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the miRNeasy Mini kit (Qiagen Inc., Valencia, CA, USA). RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer at the Center for Functional Genomics at State University of New York at Albany (Rensselaer, NY, USA)
|
| Label |
cy3
|
| Label protocol |
Cyanine-3 (Cy3) labeled miRNA was prepared from 100ng total RNA using the miRNA Complete Labeling and hyb kit (Agilent) according to the manufacturer's instructions
|
| |
|
| Hybridization protocol |
labeled miRNA was hybridized onto Agilent Human miRNA microarrays v3 (G4771-A) rel 12.0 according to the manufacturer's instructions.
|
| Scan protocol |
The arrays were scanned on a Agilent G2565C scanner using the standard settings for 8x15k array slides.
|
| Description |
miRNA expression after treatment with vehicle (ethanol and DMSO) for 48h
|
| Data processing |
The scanned images were analyzed with Feature Extraction Software 10.1.1 (Agilent) using default parameters (protocol miRNA-v1_10_Apr08 and Grid: 021827_D_20081121) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
|
| |
|
| Submission date |
Apr 12, 2011 |
| Last update date |
Apr 12, 2011 |
| Contact name |
Sridar V Chittur |
| E-mail(s) |
[email protected]
|
| Phone |
518-591-7215
|
| Organization name |
SUNY-University at Albany
|
| Department |
Center for Functional Genomics
|
| Lab |
Microarray Core
|
| Street address |
One Discovery Drive, CRC 342G
|
| City |
Rensselaer |
| State/province |
NY |
| ZIP/Postal code |
12144 |
| Country |
USA |
| |
|
| Platform ID |
GPL10850 |
| Series (2) |
| GSE28543 |
Expression Profiling of Inflammatory Breast Cancer Cells Treated with the Novel Histone Deacetylase Inhibitor, CG-1521 (Agilent miRNA v12.0) |
| GSE28544 |
Expression Profiling of Inflammatory Breast Cancer Cells Treated with the Novel Histone Deacetylase Inhibitor, CG-1521 |
|
