|
| Status |
Public on Jul 25, 2011 |
| Title |
Prostate cancer cell line DU145 [MET] |
| Sample type |
genomic |
| |
|
| Source name |
prostate cancer cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: prostate cancer cell
cell line: DU-145
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA for the Infinium methylation assay was extracted by standard methods using the Wizard Genomic DNA Purification System (Promega, Madison, WI).
|
| Label |
biotin
|
| Label protocol |
Bisulfite conversion of genomic DNA was performed using the EZ DNA Methylation Kit (Zymo Research, Orange, CA) according to the Manufacturer's instructions.
|
| |
|
| Hybridization protocol |
Fluorescence signals corresponding to C or T nucleotides were measured and the data were used to assign a quantitative measure of methylation level (β value).
|
| Scan protocol |
Arrays were scanned with an Illumina Bead array Reader confocal scanner (BeadStation 500GXDW; Illumina, Inc., San Diego, CA) according to the Manufacturer's instructions.
|
| Description |
Prostate cancer cell line DU145
|
| Data processing |
Each methylation data point represents the fluorescent signal from the methylated (M) and unmethylated (U) allele. Background intensity was computed from a set of negative controls and subtracted from each analytical data point. The ratio of the fluorescent signals from the two alleles was then computed. The β value is a quantitative measure of DNA methylation levels of specific CpGs and ranges from 0 for completely unmethylated to 1 for completely methylated. Data processing were performed on Illumina BeadStudio software. We normalized β value data using Quantile normalization between samples.
|
| |
|
| Submission date |
Aug 03, 2010 |
| Last update date |
Jul 25, 2011 |
| Contact name |
Seon-Kyu Kim |
| E-mail(s) |
seonkyu@kribb.re.kr
|
| Phone |
+82-42-879-8107
|
| Organization name |
Korea Research Institutue of Bioscience & Biotechnology
|
| Department |
Personalized Genomic Medicine Research Center
|
| Street address |
125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Korea
|
| City |
Daejeon |
| ZIP/Postal code |
305-806 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL8490 |
| Series (1) |
| GSE23388 |
DNA methylation and expression profiling study for prostate cancer |
|
