|
| Status |
Public on Dec 20, 2011 |
| Title |
BT474 xenograft_CTRL miR_4 |
| Sample type |
RNA |
| |
|
| Source name |
BT474 tumors
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: BT474
transfection: CTRL miR
|
| Treatment protocol |
Doxycycline in drinking water (2 g per liter). The treatment started after tumor development and continued until the end of the experiment (day 30). The drinking water containing doxycycline was refreshed every two days.
|
| Growth protocol |
BT474 cells were injected orthotopically into the fat pad of mammary gland 2/3 of imuunodeficient mice. After tumor development, we depleted SHP2 for 30 days in vivo.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Tumors were dissected and total RNA was isolated with a standard TRIZOL extraction method.
|
| Label |
Biotin
|
| Label protocol |
100ng total RNA was processed according to the GeneChip Whole Transcript (WT) Double-Stranded Target Assay Manual from Affymetrix (GeneChip Whole Transcription Sense Target Labeling technical manual, Rev. 2).
|
| |
|
| Hybridization protocol |
Affymetrix Human Gene 1.0 st v1 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 |
HuGene-1_0-st-v1
|
| Data processing |
CEL files were read into R (v2.10) using the R/Bioconductor (v2.4) package oligo (v1.8) and normalized probeset level expression values were calculated with the command rma and the R/Bioconductor annotation package pd.hugene.1.0.st.v1
|
| |
|
| Submission date |
Dec 19, 2011 |
| Last update date |
Dec 20, 2011 |
| Contact name |
Tim Roloff |
| E-mail(s) |
tim.roloff@fmi.ch
|
| Organization name |
FMI
|
| Department |
Functional Genomics
|
| Street address |
Maulbeerstrasse 66
|
| City |
Basel |
| ZIP/Postal code |
4058 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL6244 |
| Series (2) |
| GSE34523 |
BT474 tumors in the presence or absence of SHP2 |
| GSE34525 |
BT474 tumors, primary TN tumors and MCF10A-HER2/3 cells in the presence or absence of SHP2 |
|
