|
| Status |
Public on Oct 01, 2013 |
| Title |
malignant T4-2 with reverted phenotype - sample 11 |
| Sample type |
RNA |
| |
|
| Source name |
malignant T4-2 cells of the breast cancer progression series HMT-3522, treated with reverting agents
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: mammary epithelial cells, malignant T4-2 with reverted phenotype
treatment: Dominant negative Rap1 overexpression
|
| Treatment protocol |
S1 and T4-2 cells were treated with different reverting agents with every feeding and isolated from 3D cultures with PBS/EDTA as previously described (Lee et al.,Nat Methods. 2007; 4(4):359-365)
|
| Growth protocol |
HMT-3522 S1 and T4-2 cells were maintained on tissue culture plastic as described in Petersen et al., Proc Natl Acad Sci U S A. 1992; 89(19):9064-9068. Three dimensional laminin-rich extracellular matrix (3D lrECM) on-top cultures (Lee et al., Nat Methods. 2007; 4(4):359-365) were prepared by trypsinization of cells from tissue culture plastic, seeding of single cells on top of a thin gel of Engelbreth-Holm-Swarm (EHS) tumor extract (Matrigel: BD Biosciences; Cultrex BME: Trevigen), and addition of medium containing 5% EHS. S1 cells were seeded at a density of 3.1×104 cells per cm2; T4-2 cells were seeded at 2.1 ×104 cells per cm2. S1 and T4-2 were maintained in their propagation medium with media change every 2 days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Purified total cellular RNA was extracted using RNeasy Mini Kit with on-column DNase digestion (Qiagen).
|
| Label |
biotin
|
| Label protocol |
The array was labeled according to the manufacturer's instructions (Affymetrix).
|
| |
|
| Hybridization protocol |
Hybridization was performed according to the manufacturer's instructions (Affymetrix).
|
| Scan protocol |
The array was scanned according to the manufacturer's instructions (Affymetrix).
|
| Description |
Dominant negative Rap1 overexpression (Itoh et al., Cancer Res 2007)
|
| Data processing |
The data sets (96 well and cartridge) were analyzed separately with R Bioconductor using MAS 5.0 and Affymetrix default analysis settings. Arrays of the two platforms were row-centered separately (mean and variance), the standard deviation of the whole dataset was normalized to 1.
|
| |
|
| Submission date |
Aug 29, 2013 |
| Last update date |
Oct 01, 2013 |
| Contact name |
Sabine Becker-Weimann |
| E-mail(s) |
SBecker-Weimann@lbl.gov
|
| Organization name |
Lawrence Berkeley National Laboratory
|
| Department |
Life Sciences
|
| Lab |
Bissell
|
| Street address |
1 Cyclotron Rd
|
| City |
Berkeley |
| State/province |
CA |
| ZIP/Postal code |
94720 |
| Country |
USA |
| |
|
| Platform ID |
GPL4685 |
| Series (1) |
| GSE50444 |
Gene expression in organized and disorganized human breast epithelial cells |
|
