|
| Status |
Public on Apr 22, 2024 |
| Title |
genomic DNA from FFPE material of MB patient biopsie 3 |
| Sample type |
genomic |
| |
|
| Source name |
FFPE material of MB patient biopsie 3
|
| Organism |
Homo sapiens |
| Characteristics |
gender: Female
proteome subtype: pSHHt
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Illumina FFPE Restore Kit for was used to extract DNA from FFPE samples,100 - 250 ng DNA was hybridized. Concentrations of DNA was measured with Qubit High Sensitivity DNA Kit
|
| Label |
Cy5 and Cy3
|
| Label protocol |
Standard Illumina Protocol
|
| |
|
| Hybridization protocol |
Bisulphite converted DNA was amplified, fragmented and hybridised to the Illumina Infinium MethylationEPIC BeadChip using standard Illumina protocol
|
| Scan protocol |
Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
|
| Description |
SHH sample
|
| Data processing |
raw .idat files were processed in Rstudio (Version 4.0.5). (minfi package, Version 1.36.0). Briefly, samples were read from EPIC and 450k arrays separately and combined using combinedarrays(). The samples were normalized using single sample noob normalization since we combined intensities from two different arrays and casted as a 450k array.
|
| |
|
| Submission date |
Jan 09, 2023 |
| Last update date |
Apr 22, 2024 |
| Contact name |
Julia Elisabeth Neumann |
| Organization name |
University Hospital Hamburg Eppendorf
|
| Department |
ZMNH
|
| Street address |
Martinistrasse 52
|
| City |
Hamburg |
| ZIP/Postal code |
20251 |
| Country |
Germany |
| |
|
| Platform ID |
GPL23976 |
| Series (2) |
| GSE222478 |
Multiomic profiling of medulloblastoma reveals subtype-specific targetable alterations at the proteome and N-glycan level [methylation 1] |
| GSE243796 |
Multiomic profiling of medulloblastoma reveals subtype-specific targetable alterations at the proteome and N-glycan level |
|
