|
| Status |
Public on Apr 03, 2021 |
| Title |
CRD vs 3770NT |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
CRD(common reference DNA)
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: pooled DNA of 9 adjacent normal samples
|
| Growth protocol |
Fresh-frozen primary tumors and paired tumor-adjacent normal tissues of bladder cancer patients
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA extracted using Qiaquick DNA mini kit following manufacturer's instructions
0.5ug genomic DNA was fragmented with sonication. The fragmented DNA was incubated with MBD2bt protein, and then the enriched methylated DNA fragments was purified using Magnetic bead.
|
| Label |
Cy3
|
| Label protocol |
The enriched DNA fragments was amplified using WGA2 kit (Sigma). 4 µg of amplified enriched DNA was labeled using Bioprime kit as following manufacturer's instructions
|
| |
|
| Channel 2 |
| Source name |
3770NT
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: enriched methylated DNA of adjacent normal tissue
sample id: 3770NT
Sex: male
age: 81
Stage: I
|
| Growth protocol |
Fresh-frozen primary tumors and paired tumor-adjacent normal tissues of bladder cancer patients
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA extracted using Qiaquick DNA mini kit following manufacturer's instructions
0.5ug genomic DNA was fragmented with sonication. The fragmented DNA was incubated with MBD2bt protein, and then the enriched methylated DNA fragments was purified using Magnetic bead.
|
| Label |
Cy5
|
| Label protocol |
The enriched DNA fragments was amplified using WGA2 kit (Sigma). 4 µg of amplified enriched DNA was labeled using Bioprime kit as following manufacturer's instructions
|
| |
|
| |
| Hybridization protocol |
Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, microarrays were washed 1 minute at room temperature with CGH/ChIP-on-chip Wash Buffer 1 (Agilent) and 1 minute with 37°C CGH/ChIP-on-chip Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.
|
| Scan protocol |
Scanned on an Agilent G2565AA scanner.
|
| Description |
methylation profiling in 3770NT sample
|
| Data processing |
The scanned images were analyzed with Feature Extraction Software 9.3.2.1 (Agilent) to obtain background subtracted and spatially detrended Processed Signal intensities.
|
| |
|
| Submission date |
Apr 02, 2021 |
| Last update date |
Apr 03, 2021 |
| 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) |
| GSE171369 |
Genome-wide DNA methylation study in bladder cancer |
|
