|
| Status |
Public on Sep 01, 2012 |
| Title |
MCF10A_Empty vector_2 |
| Sample type |
RNA |
| |
|
| Source name |
MCF10A cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MCF10A
transduction: Empty vector
|
| Treatment protocol |
Cells were grown in three-dimensional cultures in DMEM/F12 medium supplemented with heregulin, horse serum, epidermal growth factor, hydrocortisone, cholera toxin, insulin, penicillin and streptomycin.
|
| Growth protocol |
MCF10A cells expressing empty vector, HER2, HER3 or HER2/HER3 were grown in three-dimensional cultures for 15 days in the presence of heregulin.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from the three-dimensional structures with a standard TRIZOL extraction method.
|
| Label |
biotin
|
| Label protocol |
200 ng total RNA were amplified using the GeneChipWT cDNA Synthesis Kit (Affymetrix) and 5.5ug of the resulting single-stranded cDNA (ssDNA) were fragmented and labeled with the GeneChip WT Terminal Labeling Kit (Affymetrix).
|
| |
|
| Hybridization protocol |
2 ug of fragmented and labeled ssDNA was hybridized to Affymetrix Human Gene 1.0 ST arrays for 16h according to the manufacturers instructions. Washing prior to scanning was done with the Affymetrix Fluidic Station protocol FS450_0007.
|
| Scan protocol |
Arrays were scanning using an Affymetrix GeneChip Scanner 3000 and Affymetrix AGCC software.
|
| Data processing |
Raw data was normalized and probeset-level values calculated using the rma() function of the R/bioconductor (R version version 2.8) package affy using the Bioconductor annotation packages.
|
| |
|
| Submission date |
Apr 03, 2012 |
| Last update date |
Sep 02, 2012 |
| 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 (1) |
| GSE37009 |
MCF10A cells expressing HER2 and HER3 and grown in three-dimensional cultures |
|
