|
| Status |
Public on Oct 29, 2019 |
| Title |
p03: Pca_Sample03_Prognosis_bad |
| Sample type |
genomic |
| |
|
| Source name |
prostate tumor
|
| Organism |
Homo sapiens |
| Characteristics |
gender: male
age: 71.2
diagnosis: prostate cancer
tissue: prostate tumor
prognosis: bad
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
AllPrep® DNA/RNA FFPE kit (Qiagen)
|
| Label |
Standard Illumina labelling (Cy5, Cy3)
|
| Label protocol |
Standard Illumina Protocol
|
| |
|
| Hybridization protocol |
bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol
|
| Scan protocol |
Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
|
| Data processing |
The methylation data was processed using the RnBeads R package (Assenov et al, 2014). Probes with SNPs (dbSNP 144) overlapping with the C nucleotide of the CG site and having MAF>0.01 (28722 probes) were excluded. Probes with high likelihood of false hybridization (28736 probes, as defined in RnBeads) were also removed. Quality filtering was performed using the Greedycut algorithm, which removed 21040 probes and 11 samples. Additional 969 non-CpG probes and 9229 probes located on the sex chromosomes were removed. No normalization or background correction was used. The top 10000 most variable CpG sites showing differences based on the souce of tissue (fresh frozen vs. formalin-fixed, paraffin embedded) were removed. These probes were identified using prinipal component analysis.
|
| |
|
| Submission date |
Mar 07, 2019 |
| Last update date |
Oct 29, 2019 |
| Contact name |
Reka Toth |
| E-mail(s) |
r.toth@dkfz-heidelberg.de
|
| Phone |
+496221424322
|
| Organization name |
DKFZ
|
| Street address |
Im Neuenheimer Feld 280
|
| City |
Heidelberg |
| ZIP/Postal code |
69120 |
| Country |
Germany |
| |
|
| Platform ID |
GPL18809 |
| Series (1) |
| GSE127985 |
Random forest-based modelling to detect novel biomarkers for prostate cancer progression |
|
