|
| Status |
Public on Apr 12, 2011 |
| Title |
Sum190-CG4 (Agilent-021827 miRNA v12.0) |
| Sample type |
RNA |
| |
|
| Source name |
SUM190PT 5µM CG-1521
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: SUM190PT
er: ER(-)
p53: mut (Q317X)
|
| Treatment protocol |
SUM190PT cells were plated at 1.5 x 10^6 cells per 150 x 25mm dish with 25mL of growth media containing 2%FBS and allowed to adhere for 24h. The media in each plate was then replaced with 25mL fresh media without FBS. After another 24h, each treatment was prepared at 6x concentration, so that 5mL of treatment solution was added to the 25mL growth media.
|
| Growth protocol |
SUM190PT cells were grown in Ham's F-12 media supplemented with 5 µg/mL insulin, 1 µg/mL hydrocortisone, 10 mM HEPES, 5mM Ethanolamine, 5µg/mL Transferrin, 10nM Triiodo Thyronine, 50nM Sodium Selenite, 1g/L Bovine Serum Albumin and Antibiotic/Antimycotic at 37° 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 5µM CG-1521 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 |
|
