|
| Status |
Public on Nov 29, 2011 |
| Title |
Ls174T-pTER-β-catenin dox1 |
| Sample type |
RNA |
| |
|
| Source name |
Ls174T, β-catenin siRNA, induced
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: Ls174T
cell type: intestinal colorectal carcinoma cells
induction: shRNA against β-catenin
time: 72hr
|
| Treatment protocol |
Cells were grown in the presence or absence of doxycycline for 24 hours for Ls174T-L8 or 72 hours for Ls174T-pTER-β-catenin cells.
|
| Growth protocol |
Appr. 10 million cells were cultured in RPMI (Invitrogen) containing 5% fetal calf serum at 37 degrees Celsius.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using Trizol (Invitrogen) and purified with RNeasy (Qiagen) according to manufacturer’s protocol.
|
| Label |
biotin
|
| Label protocol |
RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies). 4 µg of total RNA was used for cRNA synthesis and fragmented. Labeling was performed with One-Cycle cDNA synthesis Kit (Affymetrix) according to manufacturer’s protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation.
|
| |
|
| Hybridization protocol |
10 µg of labeled cRNA was hybridized to the Affymetrix Human Genome U133 Plus 2.0 arrays according to manufacturer’s protocol (Affymetrix).
|
| Scan protocol |
Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer’s protocol.
|
| Description |
Ls174T-pTER-β-catenin cells carry a doxycyclin-inducible shRNA against β-catenin. Cells were left untreated (con) or shRNA was induced for 72 hours with doxycycline (dox). Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0 to generate expression profiles.
|
| Data processing |
Expression data (cel files) were normalized with the MAS5.0 algorithm (target signal = 100) using GCOS software (Affymetrix).
|
| |
|
| Submission date |
Oct 14, 2009 |
| Last update date |
Nov 29, 2011 |
| Contact name |
Richard Volckmann |
| E-mail(s) |
[email protected]
|
| Organization name |
Academic Medical Centre, University of Amsterdam
|
| Department |
Department of Oncogenomics
|
| Street address |
P.O. Box 22700
|
| City |
Amsterdam |
| ZIP/Postal code |
1100DE |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL570 |
| Series (1) |
| GSE18560 |
Deciphering the Wnt-dependent gene signature in colorectal cancer cells |
|
