|
| Status |
Public on Jul 12, 2013 |
| Title |
EFM19_day3_expression |
| Sample type |
RNA |
| |
|
| Source name |
EFM19 breast cancer cell line, day 3
|
| Organism |
Homo sapiens |
| Characteristics |
gender: Female
disease: Breast cancer
er: +
|
| Growth protocol |
Cells were grown for three days changing media every day
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using TriZol (Invitrogen) followed by RNeasy Mini Kit (Qiagen) according to manufacturers’ manuals. RNA quality was assessed by Nanodrop-1000 spectrometer for OD260/280 and OD260/230 ratio and Bioanalyzer (Agilent Technologies).
|
| Label |
Cy3
|
| Label protocol |
400 ng total RNA was amplified and labeled using the Low RNA Input Fluorescent Linear Amplification Kit (Cat# 5190-0447, Agilent Technologies) with oligo dT primers (Cat# RA300A-2, System Bioscience) and cyanine-labeled CTPs (Perkin Elmer) according to manufacturer’s manual. Labeled cRNA was purified using RNeasy Mini Kit (Qiagen). RNA spike-in controls (Agilent Technologies) were added to RNA samples before amplification and labeling according to manufacturer’s protocol.
|
| |
|
| Hybridization protocol |
825 ng of labeled RNA was fragmented, denatured and hybridized to the array at 60ºC for 17 hours in a hybridization oven with rotation. After hybridization, arrays were washed and dried according to the Agilent microarray processing protocol.
|
| Scan protocol |
Arrays were scanned by Agilent G2505C Scanner controlled by Agilent Scan Control 7.0 Software. Data were extracted with Agilent Feature Extraction Software.
|
| Description |
EFM19_day3
jhu_251485070372_S01_GE2_107_Sep09_1_2_EFM19 Mock Day3 RNA-Cy3_EFM19 AZA Day3 RNA_Cy5
|
| Data processing |
Raw median foreground signals were taken for both channels. LOESS normalization for within-array normalization, and A-quantile normalization for between-arrays normalization were performed using R and Bioconductor. 2-channel arrays were analyzed as single-channel. The second color is not analyzed in this analysis.
|
| |
|
| Submission date |
Mar 04, 2013 |
| Last update date |
Jul 12, 2013 |
| Contact name |
Francescopaolo Di Cello |
| E-mail(s) |
fdicello@hotmail.com
|
| Organization name |
The Johns Hopkin University School of Medicine
|
| Street address |
1650 Orleans Street
|
| City |
Baltimore |
| State/province |
MD |
| ZIP/Postal code |
21287 |
| Country |
USA |
| |
|
| Platform ID |
GPL6480 |
| Series (2) |
| GSE44836 |
Gene expression profile of breast cancer cells. |
| GSE44838 |
Gene expression and methylation profile of breast cancer cells. |
|
