|
| Status |
Public on Jun 30, 2012 |
| Title |
SKBR3-R_Control_2 |
| Sample type |
RNA |
| |
|
| Source name |
human breast cancer cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: SKBR3 resistant
treatment: basal conditions
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from tissues with mirVana RNA Isolation labeling kit (Ambion Inc) according to the manufacturer 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 the Illumina HumanHT-12 V3.0 expression beadchip 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 48697 probes on the Human-6 beadChip ver. 2 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 |
May 31, 2012 |
| Last update date |
Jun 30, 2012 |
| Contact name |
Prahlad Ram |
| E-mail(s) |
pram@mdanderson.org
|
| Phone |
7135634227
|
| Organization name |
UT MDACC
|
| Street address |
7435 Fannin St, Unit 950
|
| City |
Houston |
| State/province |
TEXAS |
| ZIP/Postal code |
77054 |
| Country |
USA |
| |
|
| Platform ID |
GPL6947 |
| Series (1) |
| GSE38376 |
Acquired resistance to lapatinib |
|
