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Sample GSM1538138 Query DataSets for GSM1538138
Status Public on Apr 23, 2015
Title 2D
Sample type genomic
Source name Diagnostic medulloblastoma tumor tissue
Organism Homo sapiens
Characteristics tissue: medulloblastoma tumor
gender: M
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
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 0.49296698 0
cg00212031 0.085310006 3.21E-08
cg00213748 0.921936295 0.037200716
cg00214611 null 0.376195727
cg00455876 0.795919084 0
cg01707559 0.06587374 0
cg02004872 0.062603156 0
cg02011394 0.9496732 0
cg02050847 0.961154253 0
cg02233190 0.143017055 0
cg02494853 0.053045244 0
cg02839557 0.060473621 1.24E-06
cg02842889 0.150823397 0
cg03052502 0.929571129 0
cg03155755 0.848500782 0
cg03244189 0.457232904 6.66E-16
cg03443143 0.499533325 0
cg03683899 0.080452549 0
cg03695421 0.524259192 0
cg03706273 0.051398584 0

Total number of rows: 485577

Table truncated, full table size 13079 Kbytes.

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

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