|
| Status |
Public on Dec 03, 2013 |
| Title |
SUM149_siControl_rep3 |
| Sample type |
RNA |
| |
|
| Source name |
SUM149 cells transfected with siGENOME Non-Targeting siRNA Pool (control siRNA)
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: SUM149
|
| Treatment protocol |
SUM149 cells were transfected with ON-TARGET Plus SMART Pools against TIG1 (NM_002888) and siGENOME Non-Targeting siRNA Pool (control siRNA) at a final concentration of 200 nmol/L by using oligofectamine (Invitrogen) according to the manufacturer’s guidelines.
|
| Growth protocol |
SUM149 human IBC cells were cultured in Ham’s F-12 medium supplemented with 5% FBS, 5 µg/ml insulin, and 1 µg/ml hydrocortisone.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted and purified using RNeasy mini kit (Qiagen, Inc.) according to the manufacturer’s instructions.
|
| Label |
Biotin
|
| Label protocol |
The double-stranded cDNA was transcribed into cRNA in the presence of biotin-labeled ribonucleotides using the ENZO BioArray HighYield RNA Transcript Labeling Kit (Affymetrix) as described by the manufacturer.
|
| |
|
| Hybridization protocol |
The fragmented cRNA was used for hybridization to the Affymetrix HGU133 chip overnight at 45°C with rotation.
|
| Scan protocol |
Using a GeneArray Scanner (Hewlett-Pacrkard, Palo Alto, CA, USA).
|
| Data processing |
The data pre-processing and statistical analysis were performed in R. As part of the standard quality control(QC) analysis, the data were first quantified using the MAS5 algorithm. The Robust Multiarray Analysis (RMA) algorithm that borrows strength across arrays was used to normalize and quantify the data.
|
| |
|
| Submission date |
Jul 11, 2011 |
| Last update date |
Dec 03, 2013 |
| Contact name |
Naoto T Ueno |
| E-mail(s) |
[email protected]
|
| Organization name |
UT MD Anderson Cancer Center
|
| Department |
Breast Medical Oncology
|
| Street address |
1515 Holcombe Blvd.
|
| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL570 |
| Series (1) |
| GSE30543 |
Differential gene expression profiles between SUM149 cells transfected with control siRNA and SUM149 cells transfected with siRNA targeting tarzarotene-induced gene 1 (TIG1) |
|
