|
| Status |
Public on Apr 02, 2014 |
| Title |
SB-431542 - 3 |
| Sample type |
RNA |
| |
|
| Source name |
MDA-MB-231-LM2-4 cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MDA-MB-231-LM2-4 breast cancer cells
treatment: SB-431542 (an inhibitor of the TBRI recpeptor) plus TGF-beta
|
| Treatment protocol |
RNA interference was performed by transfecting the indicated siRNA using Dharmafect 1 (Thermo Scientific) according to manufacturer’s protocol.
|
| Growth protocol |
MDA-MB-231-LM2-4 cells were cultured using RPMI media supplemented with 10% FBS.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated and purified by Quick-RNA MiniPrep (Zymogen Research) according to manufacturer’s protocol.
|
| Label |
biotin
|
| Label protocol |
Biotin labeling was performed using the Ambion WT Expression Kit (Life Technologies, Grand Island, NY) according to the manufacturer's protocol, followed by the GeneChip WT Terminal Labeling and Controls Kit (Affymetrix, Santa Clara, CA).
|
| |
|
| Hybridization protocol |
The labeled, fragmented DNA was hybridized to the Human Gene 1.0 ST Array (Affymetrix, Santa Clara, CA) for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix fluidics station 450.
|
| Scan protocol |
After staining, microarrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G Plus (Affymetrix, Santa Clara, CA).
|
| Description |
Gene expression data from LM2-4 treated with SB-431542 plus TGF-beta.
|
| Data processing |
Raw Affymetrix CEL files were normalized to produce Entrez Gene-identifier-specific expression values using the implementation of the Robust Multiarray Average (RMA) in the affy package in the Bioconductor software suite (version 2.7) and the Brainarray hugene10stv1hsentrezg R package (version 14.0.0) (http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/14.0.0/entrezg.download/HuGene10stv1_Hs_ENTREZG_14.0.0.zip).
|
| |
|
| Submission date |
Apr 02, 2014 |
| Last update date |
Jun 25, 2019 |
| Contact name |
Boston University Microarray and Sequencing Resource |
| E-mail(s) |
[email protected]
|
| Organization name |
Boston University
|
| Department |
Microarray and Sequencing Resource
|
| Street address |
72 East Concord Street, E631
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02118 |
| Country |
USA |
| |
|
| Platform ID |
GPL15034 |
| Series (1) |
| GSE56445 |
The transcriptional regulators TAZ and YAP direct Transforming Growth Factor-beta-induced tumorigenic phenotypes in breast cancer cells |
|
