|
| Status |
Public on May 23, 2023 |
| Title |
STM-rhabdomyosarcoma 5 |
| Sample type |
genomic |
| |
|
| Source name |
STM from germ cell tumor
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: STM-rhabdomyosarcoma
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was isolated from FFPE tissue using the ReliaPrep™ FFPE gDNA Miniprep System (Promega, Walldorf, Germany) according to manufacturer’s instructions.
|
| Label |
Cy3 and Cy5
|
| Label protocol |
The Infinium MethylationEPIC array BeadChip (Illumina, San Diego, CA, USA) was used to analyze DNA methylation profiles. 100 - 500 ng DNA were used for bisulfite conversion with the EZ DNA Methylation Kit (Zymo Research, Freiburg. i. B., Germany). Afterwards, the DNA Clean & Concentrator-5 (Zymo Research) and the Infinium HD FFPE DNA Restore Kit (Illumina) were used to clean and restore the converted DNA.
|
| |
|
| Hybridization protocol |
Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Bead array (850k) using standard Illumina protocol
|
| Scan protocol |
Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
|
| Data processing |
Data and bioinformatic analyses were carried out using ‘GenomeStudio’ software (version 2011.1, Methylation Module v1.9) (Illumina).
Data processing and QC according to the in-house analysis pipeline and calculation beta-values.
|
| |
|
| Submission date |
Nov 29, 2022 |
| Last update date |
May 24, 2023 |
| Contact name |
Daniel Nettersheim |
| Organization name |
Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University
|
| Department |
Dep. of Urology
|
| Lab |
Urological Research Laboratory, Translational UroOncology
|
| Street address |
Moorenstr. 5
|
| City |
Düsseldorf |
| State/province |
NRW |
| ZIP/Postal code |
40225 |
| Country |
Germany |
| |
|
| Platform ID |
GPL21145 |
| Series (1) |
| GSE219033 |
Illumina Infinium MethylationEPIC BeadChip (850k) data of germ cell tumor-related somatic-type maligancies |
|
