|
| Status |
Public on Oct 01, 2015 |
| Title |
MCF-10Acells_untreated_1_cy3 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Mammary epithelium
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MCF-10A
|
| Treatment protocol |
Cells were untreated.
|
| Growth protocol |
MCF-10A cells were cultured in a 1:1 mix of DMEM:F-12 media supplemented with 5% horse serum, 1% pen/strep, 10 ug/ml insulin, 0.5 ug/ml hydrocortisone, 20 ng/ml EGF, and 100 ng/ml cholera toxin. Cells were incubated at 37oC, and 5% CO2.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was purified using a Qiagen Gentra Puregene Cell kit.
|
| Label |
cy3
|
| Label protocol |
Dye swap labelling of 2ug of test and reference DNA was preformed according to directions supplied by Perkin Elmer for the Constitutional Chip 4.0.
|
| |
|
| Channel 2 |
| Source name |
Reference
|
| Organism |
Homo sapiens |
| Characteristics |
reference: Pooled reference DNA
|
| Treatment protocol |
Cells were untreated.
|
| Growth protocol |
MCF-10A cells were cultured in a 1:1 mix of DMEM:F-12 media supplemented with 5% horse serum, 1% pen/strep, 10 ug/ml insulin, 0.5 ug/ml hydrocortisone, 20 ng/ml EGF, and 100 ng/ml cholera toxin. Cells were incubated at 37oC, and 5% CO2.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was purified using a Qiagen Gentra Puregene Cell kit.
|
| Label |
cy5
|
| Label protocol |
Dye swap labelling of 2ug of test and reference DNA was preformed according to directions supplied by Perkin Elmer for the Constitutional Chip 4.0.
|
| |
|
| |
| Hybridization protocol |
Hybridization was according to the Perkin Elmer protocol. Slides were incubated for 16 hours in Corning
|
| Scan protocol |
The slides were scanned on a GenePix 4200A microarray scanner at a resolution of 5 um.
|
| Data processing |
Data were analyzed using oneClickCGH software. The following analysis parameters were selected: Background correction: local; Normalization: LOWESS, pin-wise, X&Y adjusted, var stab, Detection algorithm: CBS v2, P-value: 0.01, Gain:0.25, Loss: -0.25, Minimum clones: 1.
|
| |
|
| Submission date |
Jun 23, 2015 |
| Last update date |
Oct 01, 2015 |
| Contact name |
Caitlin Mills |
| Organization name |
McMaster University
|
| Street address |
1280 Main St West
|
| City |
Hamilton |
| ZIP/Postal code |
L8S 4L8 |
| Country |
Canada |
| |
|
| Platform ID |
GPL20610 |
| Series (1) |
| GSE70206 |
Genetic characterization of the MCF-10A cell line |
|
