|
Status |
Public on Apr 23, 2015 |
Title |
1R |
Sample type |
genomic |
|
|
Source name |
Relapsed medulloblastoma tumor tissue
|
Organism |
Homo sapiens |
Characteristics |
tissue: medulloblastoma tumor gender: M age class at diagnosis (infant < 4 yrs): Infant pathology: CLA 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 |
|