|
| Status |
Public on Jan 31, 2024 |
| Title |
Genomic DNA from ependymoma 636 |
| Sample type |
genomic |
| |
|
| Source name |
ependymoma 636
|
| Organism |
Homo sapiens |
| Characteristics |
Sex: F
age: 18.6
localization: supratentorial
resection: GTR
patho diagnosis: Ependymoma III
OS status: 1
os [months]: 34.2
pfs status: 1
pfs [months]: 17.64
classification result v12: EPN_ST_ZFTA_RELA_A
classification score: '1
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was isolated using the ReliaPrep™ FFPE gDNA Miniprep System (Promega) according to manufacturer’s instructions. About 100-500 ng DNA was used for bisulfite conversion by the EZ DNA Methylation Kit (Zymo Research). The DNA Clean & Concentrator-5 (Zymo Research) and the Infinium HD FFPE DNA Restore Kit (Illumina) were employed to clean and restore the converted DNA.
|
| Label |
Cy5 and Cy3
|
| Label protocol |
Standard Illumina protocol
|
| |
|
| Hybridization protocol |
Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip or the Illumina Infinium MethylationEPIC BeadChip using standard Illumina protocol.
|
| Scan protocol |
Arrays were imaged using the iScan System and the standard recommended Illumina scanner setting.
|
| Data processing |
Statistical analysis was performed using the minfi package version 1.46.0 with the statistical programming language R version 4.3.0.
Average beta-values after combining arrays and normalization using the Noob method.
|
| |
|
| Submission date |
Sep 14, 2023 |
| Last update date |
Jan 31, 2024 |
| Contact name |
Michael Bockmayr |
| E-mail(s) |
m.bockmayr@uke.de
|
| Organization name |
University Medical Center Hamburg-Eppendorf
|
| Department |
Pediatric Hematology and Oncology
|
| Street address |
Martinistr. 52
|
| City |
Hamburg |
| ZIP/Postal code |
20251 |
| Country |
Germany |
| |
|
| Platform ID |
GPL13534 |
| Series (1) |
| GSE243240 |
Molecular characteristics and improved survival prediction in a cohort of 2023 ependymomas |
|
