|
| Status |
Public on Jan 22, 2013 |
| Title |
56T vs 56N |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
56T
|
| Organism |
Homo sapiens |
| Characteristics |
tissue type: Colon
cell type: Tumor (Carcinoma)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
genomic DNA was isolated by phenol/chloroform extraction and ethanol precipitation from 10-20 sections of 30 mm and yielded 10-50 mg
|
| Label |
Cy3
|
| Label protocol |
genomic DNA (500 ng) was digested with MseI, ligated to linkers, and sequentially digested with two methylation-sensitive restriction enzymes (HpaII and BstUI). Digested linker-ligated DNA was used as template for polymerase chain reaction (PCR) amplification (20 cycles) and coupled to fluorescent dyes. Cy5- or Cy3-labeled amplicons.
|
| |
|
| Channel 2 |
| Source name |
56N
|
| Organism |
Homo sapiens |
| Characteristics |
tissue type: Colon
cell type: Normal
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
genomic DNA was isolated by phenol/chloroform extraction and ethanol precipitation from 10-20 sections of 30 mm and yielded 10-50 mg
|
| Label |
Cy5
|
| Label protocol |
genomic DNA (500 ng) was digested with MseI, ligated to linkers, and sequentially digested with two methylation-sensitive restriction enzymes (HpaII and BstUI). Digested linker-ligated DNA was used as template for polymerase chain reaction (PCR) amplification (20 cycles) and coupled to fluorescent dyes. Cy5- or Cy3-labeled amplicons.
|
| |
|
| |
| Hybridization protocol |
Hybridization was performed according to the standard Agilent protocol for 244 CpG island microarray hybridization
|
| Scan protocol |
Detection was done on a G2565BA scanner (Agilent Technologies) and feature extraction using Feature Extraction Software version 9.5.3.1 (Agilent Technologies)
|
| Data processing |
The raw text files were normalized by within-array loess normalization followed by between-array aquantile normalization using limma v3.2.1
|
| |
|
| Submission date |
Jul 13, 2012 |
| Last update date |
Jan 22, 2013 |
| Contact name |
Eddy H.J. van Roon |
| E-mail(s) |
ehjvr@hotmail.com
|
| Organization name |
LUMC
|
| Department |
Pathology
|
| Lab |
Morreau
|
| Street address |
Albinusdreef 2
|
| City |
Leiden |
| ZIP/Postal code |
2300 RC |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL9767 |
| Series (1) |
| GSE39334 |
DNA methylation profiling in colon cancer |
|
