|
| Status |
Public on Jul 15, 2023 |
| Title |
Case 6 Primary |
| Sample type |
genomic |
| |
|
| Source name |
tumor tissue
|
| Organism |
Homo sapiens |
| Characteristics |
case-id: N2074/12
molecular_subtype: MYC
classifier_ atrt_score_ v11b4: 0.019
classifier_ subgroup_ score_v11b4: 0.594 for control tissue, reactive tumor microenvironment
conservation_ type: FFPE
disease_ status: Primary
location_of_diagnosis: Berlin
source_lab: Hamburg
Sex: Male
age_ onset_ years: 2.0
time_to_ relapse_ months: 1.5
localization: CNS, supratentorial
therapy_ protocol: EU-RHAB
life_ status: dead
follow_up_ months: 6.1
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted and purified from FFPE tissue using “Maxwell® FFPE DNA Kit” (Promega) and from KRYO tissue using “High Pure PCR Template Preparation Kit” (Roche) according to standard instructions.
|
| Label |
Cy5, Cy3
|
| Label protocol |
Bisulfite conversion was performed with the “EZ DNA Methylation Kit” (Zymo Research) using 100-500 ng DNA. FFPE DNA was cleaned and converted using the “DNA Clean & Concentrator-5 Kit” (Zymo Research) and the “Infinium HD FFPE DNA Restore Kit” (Illumina).
|
| |
|
| Hybridization protocol |
Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium "HumanMethylation450" or "MethylationEPIC" Beadchip array using standard Illumina protocol.
|
| Scan protocol |
Arrays were imaged using “iScan device” (Illumina) using standard recommended Illumina scanner setting.
|
| Data processing |
Mset: Noob-normalization; beta values; all probes of sex chromosomes and probes with SNPs within 2 nucleotides distant from CpG were removed; sorted by decreasing standard deviations; batch correction for array and conservation type
|
| |
|
| Submission date |
Mar 23, 2023 |
| Last update date |
Jul 15, 2023 |
| Contact name |
Lea Altendorf |
| E-mail(s) |
altendorf@kinderkrebs-forschung.de
|
| Organization name |
Universitätsklinikum Hamburg-Eppendorf
|
| Department |
Forschungsinstitut Kinderkrebszentrum Hamburg
|
| Lab |
AG Schüller
|
| Street address |
Martinistraße 52
|
| City |
Hamburg |
| ZIP/Postal code |
20251 |
| Country |
Germany |
| |
|
| Platform ID |
GPL13534 |
| Series (2) |
| GSE228091 |
Relapsed atypical teratoid/rhabdoid tumors (AT/RT) reveal distinct features of progression on histology, epigenetics, copy number profiling, and transcriptomics [DNA methylation] |
| GSE228103 |
Relapsed atypical teratoid/rhabdoid tumors (AT/RT) reveal distinct features of progression on histology, epigenetics, copy number profiling, and transcriptomics |
|
