|
| Status |
Public on May 15, 2012 |
| Title |
siLuc1_Dox_3 |
| Sample type |
RNA |
| |
|
| Source name |
MDA-MB-231 Breast Cacner Cell
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MDA-MB-231
transfection: siLuc
treatment: doxycline + doxorubicin
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from tissues with mirVana?? RNA Isolation labeling kit (Ambion Inc) according to the manufacturer¢®?s protocol. RNA quality and integrity were confirmed by ExperionTM Automated Electrophoresis System (BIO-RAD)
|
| Label |
Biotin
|
| Label protocol |
Biotin-labeled cRNA samples for hybridization were prepared according to Illumina's recommended sample labeling procedure: 500 ng of total RNA was used for cDNA synthesis, followed by an amplification/labeling step (in vitro transcription) to synthesize biotin-labeled cRNA using the Illumina?? TotalPrep RNA Amplification kit (Ambion Inc., Austin, TX). cRNA concentrations using spectrophotometer (Nanodrop, ND-1000)
|
| |
|
| Hybridization protocol |
Labeled, amplified material (750 ng per array) was hybridized to a ver. 3 of the Illumina Human-Ht-12 BeadChip (48K) according to the Manufacturer's instructions (Illumina, Inc., San Diego, CA).
|
| Scan protocol |
Arrays were scanned with an Illumina Bead array Reader confocal scanner (BeadStation 500GXDW; Illumina, Inc., San Diego, CA) according to the Manufacturer's instructions
|
| Description |
To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software. The whole 48803 probes on the Human-Ht12 beadChip ver. 3 were used.
|
| Data processing |
Array data processing were performed on Illumina BeadStudio software. We normalized gene expression data using Quantile normalization and log2 transformatoin. To export to a data matrix, Sample Gene Profile option of this software was used.
|
| |
|
| Submission date |
Dec 01, 2010 |
| Last update date |
May 15, 2012 |
| Contact name |
Yun-Yong Park |
| E-mail(s) |
[email protected]
|
| Phone |
7137458525
|
| Fax |
7135634235
|
| URL |
http://www.mdanderson.org
|
| Organization name |
UT, MD Anderson Cancer Center
|
| Department |
Systems Biology
|
| Street address |
7435 Fannin St.
|
| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77054 |
| Country |
USA |
| |
|
| Platform ID |
GPL6947 |
| Series (1) |
| GSE25741 |
Gene expression profile of FOXM1 with Doxorubicin in MDA-MB-231 breast cancer cells |
|
