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Sample GSM1538158 Query DataSets for GSM1538158
Status Public on Apr 23, 2015
Title 14R
Sample type genomic
Source name Relapsed medulloblastoma tumor tissue
Organism Homo sapiens
Characteristics tissue: medulloblastoma tumor
gender: F
age class at diagnosis (infant < 4 yrs): Non-infant
pathology: LCA
subgroup: WNT
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
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

Data table header descriptions
VALUE Average Beta

Data table
cg00050873 null 0.760095367
cg00212031 null 0.802655067
cg00213748 null 0.999753811
cg00214611 null 0.932348818
cg00455876 null 0.739684212
cg01707559 0.3873488 6.70E-07
cg02004872 0.523626167 0.001201848
cg02011394 null 0.862590627
cg02050847 null 0.646064559
cg02233190 0.182389227 0.01793422
cg02494853 0.015751486 0
cg02839557 null 0.932348818
cg02842889 null 0.795137479
cg03052502 null 0.744869536
cg03155755 null 0.570109261
cg03244189 0.329476909 0
cg03443143 null 0.894829021
cg03683899 null 0.755916326
cg03695421 null 0.59621656
cg03706273 0.011653826 0

Total number of rows: 485577

Table truncated, full table size 13116 Kbytes.

Supplementary data files not provided
Processed data included within Sample table
Processed data are available on Series record

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