|
| Status |
Public on Oct 19, 2011 |
| Title |
Breast cancer cell line SKBR3 5 AZA (methylation data) |
| Sample type |
genomic |
| |
|
| Source name |
Breast cancer cell line
|
| Organism |
Homo sapiens |
| Characteristics |
conditions: 5-AZA
treatment protocol: Cells were treated with 5-aza-2’-deoxycytidine (1µM) during 4 days before being harvested. They were detached from the culture flask using a cell scraper.
growth protocol: SKBR3 5-AZA cells were maintained in DMEM medium (Gibco) supplemented with 10% fetal calf serum (Gibco). Cells were treated with 5-aza-2’-deoxycytidine (1µM) during 4 days. The medium was refreshed every day.
cell line: SKBR3
agent: 5-AZA
methylation barcode: 5324215024_J
|
| Treatment protocol |
Cells were harvested after 5 or 6 passages. They were detached from the culture flask using a cell scraper.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted using the QIAamp DNA Mini Kit according to the supplier’s instructions (Qiagen, Hilden, Germany). This included the recommended proteinase K and RNase A digestions. DNA was quantitated with the NanoDrop® ND-1000 UV-Vis Spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA).
Genomic DNA from cells was extracted using the QIAamp DNA Mini Kit according to the supplier’s instructions (Qiagen, Hilden, Germany). This included the recommended proteinase K and RNase A digestions. DNA was quantitated with the NanoDrop® ND-1000 UV-Vis Spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA).
|
| Label |
C-Bio and A-DNP
|
| Label protocol |
Labelled nucleotides were added to extend the primers hybridized to the DNA and primers were stained according to the Infinium® Methylation Manual Protocol (Illumina, San Diego, USA).
|
| |
|
| Hybridization protocol |
DNA samples were hybridized onto the HumanMethylation27 BeadChips during 16 hours at 48°C. Unhybridized and non-specifically hybridized DNA were washed from the BeadChips, according to the Infinium® Methylation Manual Protocol (Illumina, San Diego, USA).
|
| Scan protocol |
The BeadChips were scanned with the Illumina BeadArrayTM Reader.
|
| Data processing |
Initial data analysis was performed with the Methylation module of the Genome Studio software provided by Illumina.
|
| |
|
| Submission date |
Jun 10, 2010 |
| Last update date |
Oct 19, 2011 |
| Contact name |
Benjamin Haibe-Kains |
| E-mail(s) |
benjamin.haibe.kains@utoronto.ca
|
| Phone |
+14165818626
|
| Organization name |
Princess Margaret Cancer Centre
|
| Department |
Princess Margaret Research
|
| Lab |
Bioinformatics and Computational Genomics
|
| Street address |
610 University Avenue
|
| City |
Toronto |
| State/province |
Ontario |
| ZIP/Postal code |
M5G 2M9 |
| Country |
Canada |
| |
|
| Platform ID |
GPL8490 |
| Series (2) |
| GSE20713 |
Epigenetic portraits of human breast cancers |
| GSE22281 |
Epigenetic portraits of human breast cancers (various cell lines methylation data) |
|
