|
| Status |
Public on Apr 23, 2015 |
| Title |
5D |
| Sample type |
genomic |
| |
|
| Source name |
Diagnostic medulloblastoma tumor tissue
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: medulloblastoma tumor
gender: F
age class at diagnosis (infant < 4 yrs): Infant
pathology: DN
subgroup: SHH
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Extraction of DNA from fresh frozen tumor samples was performed using a Qiagen AllPrep Kit. Extraction of DNA from FFPE tumour samples was performed using a QIAamp DNA FFPE tissue kit
|
| Label |
Cy3 / Cy5
|
| Label protocol |
Standard Illumina Protocol
|
| |
|
| Hybridization protocol |
Illumina
|
| Scan protocol |
Bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol
|
| Description |
Methylation data from a medulloblastoma tumor sample
|
| Data processing |
Beta values were obtained using the R package minfi, performing background correction, normalisation to internal controls, and type I / type II correction using SWAN
The raw signal intensities can be found in the file matrixIntensitiesFinal.csv available on the series record. The Average Beta and Detection P-values are available in the Sample tables and on the series record in the file matrixProcessed.csv.
|
| |
|
| Submission date |
Nov 05, 2014 |
| Last update date |
Apr 23, 2015 |
| Contact name |
Ed Schwalbe |
| E-mail(s) |
ed.schwalbe@northumbria.ac.uk
|
| Organization name |
Northumbria University
|
| Department |
Applied Sciences
|
| Street address |
Ellison Place
|
| City |
Newcastle upon Tyne |
| ZIP/Postal code |
NE1 8ST |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL13534 |
| Series (2) |
| GSE62618 |
Methylation data from presentation and relapsed medulloblastoma tumour samples |
| GSE62626 |
Combined MYC and TP53 defects emerge at medulloblastoma relapse and define rapidly progressive, therapeutically targetable disease |
|
