|
| Status |
Public on Mar 10, 2012 |
| Title |
CRD vs 688T |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
CRD
|
| Organism |
Homo sapiens |
| Characteristics |
sample type: pooled DNA of 12 adjacent normal samples
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
genomic DNA extracted using Qiaquick DNA mini kit following manufacturer's instructions
enrichment protocol: 0.5ug sonicated gDNA was incubated with MBD2bt protein, and then purification using Magnetic bead.
|
| Label |
Cy3
|
| Label protocol |
4 µg of amplified enriched DNA were labeled using Bioprime kit as following manufacturer's instructions
|
| |
|
| Channel 2 |
| Source name |
688T
|
| Organism |
Homo sapiens |
| Characteristics |
sample type: enriched methylated DNA of colorectal tumor tissue
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
genomic DNA extracted using Qiaquick DNA mini kit following manufacturer's instructions
enrichment protocol: 0.5ug sonicated gDNA was incubated with MBD2bt protein, and then purification using Magnetic bead.
|
| Label |
Cy5
|
| Label protocol |
4 µg of amplified enriched DNA were 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, slides were washed sequential Oligo aCGH/ChIP-on-chip Wash buffer1, 2, ACN, and Stabilization and Drying Solution as following manufacturer's instructions.
|
| Scan protocol |
Scanned on an Agilent G2565AA scanner.
Images were quantified using Agilent Feature Extraction Software (version 9.3.2.1).
|
| Description |
methylation profiling in 688T sample
|
| Data processing |
Agilent Feature Extraction Software (v 9.3.2.1) was used for background subtraction and LOWESS normalization.
|
| |
|
| Submission date |
Mar 08, 2012 |
| Last update date |
Mar 10, 2012 |
| 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 |
GPL4126 |
| Series (1) |
| GSE36380 |
Methylation profiling in colorectal cancer |
|
