|
| Status |
Public on May 08, 2014 |
| Title |
breast SKBR3 Mock/AZA Day7 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Control breast SKBR3 Day7
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: SKBR3
cell type: breast cancer cell line
time point: Day 7
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted using Trizol following manufacturer's instructions
|
| Label |
Cy3
|
| Label protocol |
400 ng total RNA was amplified and labeled using 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.
|
| |
|
| Channel 2 |
| Source name |
AZA-treated breast SKBR3 Day7
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: SKBR3
cell type: breast cancer cell line
time point: Day 7
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted using Trizol following manufacturer's instructions
|
| Label |
Cy5
|
| Label protocol |
400 ng total RNA was amplified and labeled using 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 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 G2505B Scanner controlled by Agilent Scan Control 7.0 Software.
|
| Description |
breast SKBR3 Mock Day7/SKBR3 AZA Day7
|
| Data processing |
Data were extracted with Agilent Feature Extraction Software.
|
| |
|
| Submission date |
May 06, 2014 |
| Last update date |
May 08, 2014 |
| Contact name |
Stephen Baylin |
| E-mail(s) |
sbaylin@jhmi.edu
|
| Phone |
4109558506
|
| Organization name |
Johns Hopkins UniversityJohns Hopkins Medical Institutions
|
| Department |
Oncology
|
| Street address |
1650 Orleans St CRB I RM 541
|
| City |
Baltimore |
| State/province |
Maryland |
| ZIP/Postal code |
21287 |
| Country |
USA |
| |
|
| Platform ID |
GPL4133 |
| Series (2) |
| GSE57341 |
Effect of AZA on gene expression of multiple breast, colon, and ovarian cell lines [expression] |
| GSE57343 |
Immune regulation by low doses of the DNA methyltransferase inhibitor 5-azacitidine in common human epithelial cancers |
|
