|
| Status |
Public on Jul 07, 2010 |
| Title |
4T1 tumor treated with water, biological replicate 2 |
| Sample type |
RNA |
| |
|
| Source name |
tumors from 4T1 cells after 14 days of treatment with water
|
| Organism |
Mus musculus |
| Characteristics |
cell type: 4T1 tumor
agent: water
|
| Treatment protocol |
7 days after tumor cell injection, the mice were randomized in the different groups and oral treatment with water or TKI258 (40mg/kg) was performed daily for 14 days.
|
| Growth protocol |
750000 cells in 75ml PBS were injected in the 4th mammary gland of Balb/C mice.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
At the end of the experiment, tumors were removed and snap frozzen. RNA extraction was performed following extraction with TRIzol reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturers’s protocol. RNAs were washed using the RNeasy Mini Kit (Qiagen) and treated with RNase-free DNase set (Qiagen)
|
| Label |
biotin
|
| Label protocol |
RNA from TKI258- or water- treated 4T1 tumors 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 tumors after 14 days of treatment with water
|
| 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) |
| GSE19221 |
Expression data from TKI258 treated 4T1 tumors |
| GSE19222 |
Expression data from TKI258 treated 4T1 cells and 4T1 tumors |
|
