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Status |
Public on May 03, 2013 |
Title |
Bladder cancer BT148 |
Sample type |
genomic |
|
|
Source name |
non-muscle invasive bladder cancer
|
Organism |
Homo sapiens |
Characteristics |
tissue: non-muscle invasive bladder cancer tnm stage: T1N0M0 grade: LOW overall survival (1: survival, 2:death): 1 survival time (month): 75.33
|
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 |
Bladder cancer BT148
|
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.
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|
|
Submission date |
May 07, 2012 |
Last update date |
May 03, 2013 |
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 (2) |
GSE37816 |
DNA methylation and expression profiling study for bladder cancer [methylation] |
GSE37817 |
DNA methylation and expression profiling study for bladder cancer |
|