|
| Status |
Public on Jul 07, 2010 |
| Title |
4T1 treated with DMSO, biological replicate 2 |
| Sample type |
RNA |
| |
|
| Source name |
4T1 cells treated 16h with DMSO
|
| Organism |
Mus musculus |
| Characteristics |
cell type: 4T1 cells
agent: DMSO
|
| Treatment protocol |
24 hours after seeding, the medium was removed from the cells and was changed for DMEM supplemented with 10% FCS and 500nM TKI258 or the vehicle DMSO. The cells were kept 16 hours with these conditions
|
| Growth protocol |
750000 cells were seeded in 10cm dish and cultured in DMEM supplemented with 10% FCS for 24 hours.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the Qiashredder and RNeasy Mini Kit coupled with RNase-free DNase set following the manufacturer’s instructions.
|
| Label |
biotin
|
| Label protocol |
RNA from TKI258- or vehicle- treated 4T1 cells was amplified and labeled using the Ambion MesageAMP III RNA Amplification Kit (Applied Biosystems)
|
| |
|
| Hybridization protocol |
Biotinylated, fragmented cRNA was hybridized to Affymetrix Mouse Gene 1.0 ST Array (Affymetrix, Santa Clara, CA, USA)
|
| Scan protocol |
Standard Affymetrix procedures
|
| Description |
gene expression data from 4T1 cells after 16 hours of DMSO treatment
|
| Data processing |
The data analysis and gene filtering was performed using R/Bioconductor. Signal condensation was performed using only the RMA from the Bioconductor Affy package. Differentially expressed genes were identified using the empirical Bayes method (F-test) implemented in the LIMMA package and adjusted with the False Discovery Rate (FDR) method. Hierarchical clustering and visualization was performed in R. Probe sets with a Log2 average contrast signal of at least 5, an adjusted p-value < 0.05 and an absolute Log2 fold change of > 0.585 (1.5-fold in linear space) were selected.
|
| |
|
| Submission date |
Nov 30, 2009 |
| Last update date |
Jul 07, 2010 |
| Contact name |
Julien Herve Dey |
| Organization name |
FMI
|
| Department |
growth control
|
| Lab |
Hynes
|
| Street address |
Maulbeerstrasse
|
| City |
Basel |
| ZIP/Postal code |
4058 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL6246 |
| Series (2) |
| GSE19220 |
Expression data from TKI258 treated 4T1 cells |
| GSE19222 |
Expression data from TKI258 treated 4T1 cells and 4T1 tumors |
|
