|
| Status |
Public on Feb 23, 2011 |
| Title |
Methylation profile in breast nontumor |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Common reference
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: reference control
|
| Growth protocol |
Common reference source : Normal placental gDNA without any history of malignancy was purchased from Biochain, Inc (CA, USA, Cat. No. D1234200).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Qiagen DNA mini kit
Isolation of methylated DNA using MBD protein (for complete protocol see supplementary file on the Series record).
|
| Label |
Cy3
|
| Label protocol |
Labeling with klenow enzyme
|
| |
|
| Channel 2 |
| Source name |
breast nontumor
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: nontumor breast
|
| Growth protocol |
tumor and nontumor source : Fresh-frozen tissue specimens were obtained from the School of Medicine, ChungNam National University, Daejeon, South Korea. All specimens and pertinent patient information were treated in accordance with the Institutional Review Board of the School of Medicine, ChungNam National University, Daejeon, South Korea. Each tumor specimen was histologically verified by a board-certified pathologist and archived for further DNA study.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Qiagen DNA mini kit
Isolation of methylated DNA using MBD protein (for complete protocol see supplementary file on the Series record).
|
| Label |
Cy5
|
| Label protocol |
Label with klenow enzyme
|
| |
|
| |
| Hybridization protocol |
agilent CpG microarray protocol
|
| Scan protocol |
agilent scanner
|
| Data processing |
Raw data was generated using Feature extraction 9.3.2.1 (Agilent). And then, import the data into the GenespringGX 7.3.1 (Agilent). LOWESS normalization was applied. I didn't transform Cy5/Cy3 ratio to the Log value.
|
| |
|
| Submission date |
Feb 16, 2011 |
| Last update date |
Feb 23, 2011 |
| Contact name |
Myung Soon Kim |
| E-mail(s) |
mskim@genomictree.com
|
| Phone |
82-10-9407-0448
|
| Organization name |
Genomictree
|
| Department |
R&D
|
| Street address |
Yeusung-gu
|
| City |
Daejeon |
| ZIP/Postal code |
305-510 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL9767 |
| Series (1) |
| GSE27374 |
Methylation profile in breast cancer |
|
