|
| Status |
Public on May 01, 2012 |
| Title |
4T1_Tw1KD/Twist1, rep1 |
| Sample type |
RNA |
| |
|
| Source name |
mouse breast cancer cell line 4T1 derivative
|
| Organism |
Mus musculus |
| Characteristics |
cell type: mouse breast cancer cell line 4T1 derivative
genotype/variation: compensatory expression of wildtype Twist1 in 4T1_Tw1KD
|
| Treatment protocol |
All cells were washed with PBS three times before extraction of RNA.
|
| Growth protocol |
All cells were grown to 70% confluency in standard DMEM growth medium containing 4ug/ml Puromycin and 800ug/ml G418.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with Qiagen RNeasy kit.
|
| Label |
biotin
|
| Label protocol |
100ng of RNA were processed with the Ambion® WT Expression Kit (#4411974 ) following the manufacturer's instructions.
|
| |
|
| Hybridization protocol |
Affymetrix GeneChip arrays were hybridized following the GeneChip Whole Transcript (WT) Sense Target Labeling Assay Manual (Affymetrix) with a hybridization time of 16h. The Affymetrix Fluidics protocol FS450_0007 was used for washing.
|
| Scan protocol |
Scanning was performed with Affymetrix GCC Scan Control v. 3.0.0.1214 on a GeneChip® Scanner 3000 with autoloader.
|
| Description |
Gene expression data from mouse breast cancer cells
|
| Data processing |
Probesets were summarized and probeset-level values normalized with justRMA() function from R (version 2.10.0) / Bioconductor (version 2.5) package affy using the CDF environment MoGene-1_0-st-v1.r3.cdf (as provided by Bioconductor) and annotation from Netaffx (www.netaffx.com) (as provided in the attached file).
|
| |
|
| Submission date |
Jun 06, 2011 |
| Last update date |
May 01, 2012 |
| Contact name |
Gongda Xue |
| E-mail(s) |
gongda.xue@fmi.ch
|
| Organization name |
Friedrich Miescher Institute for Biomedical Research
|
| Street address |
Maulbeerstrasse 66
|
| City |
Basel |
| ZIP/Postal code |
CH-4058 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL6246 |
| Series (1) |
| GSE29754 |
Differential regulation of Twist1-responsive genes in 4T1 cells |
|
