|
| Status |
Public on Jan 18, 2012 |
| Title |
PREC_3 |
| Sample type |
genomic |
| |
|
| Source name |
PrEC cells
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: prostate
cell line: PrEC
|
| Treatment protocol |
Native DNA was used
|
| Growth protocol |
37 deg C with 5% CO2
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted using the QIAamp Mini Kit (Qiagen) following manufacturers instructions.
|
| Label |
Cy5 and Cy3
|
| Label protocol |
According to manufacturer's protocol.
|
| |
|
| Hybridization protocol |
According to manufacturer's protocol.
|
| Scan protocol |
According to manufacturer's protocol.
|
| Description |
Sample name: 6264509024_R06C02
|
| Data processing |
R/Bioconductor 'minfi' package, with default parameters {RG.raw <- read.450k.exp(base = slide.folder, targets = files.table); methyl.norm <- preprocessIllumina(RG.raw, bg.correct = TRUE, normalize = controls); beta.table <- getBeta(methyl.norm)}, to generate beta values
|
| |
|
| Submission date |
Dec 12, 2011 |
| Last update date |
Jan 18, 2012 |
| Contact name |
Mark Robinson |
| E-mail(s) |
mark.robinson@imls.uzh.ch
|
| Organization name |
University of Zuerich
|
| Department |
Institute of Molecular Life Sciences
|
| Street address |
Winterthurerstrasse 190
|
| City |
Zuerich |
| ZIP/Postal code |
8057 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL13534 |
| Series (2) |
| GSE34340 |
Bisulphite sequencing of native LNCaP and PrEC DNA [methylation array] |
| GSE34403 |
Bisulphite-sequencing of chromatin immunoprecipitated DNA directly informs methylation status of histone-modified DNA |
|
