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Sample GSM1538137 Query DataSets for GSM1538137
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

Data table header descriptions
ID_REF
VALUE Average Beta
1R_DET.PVAL

Data table
ID_REF VALUE 1R_DET.PVAL
cg00050873 0.909235672 0
cg00212031 null 0.128518411
cg00213748 null 0.998917093
cg00214611 0.097235938 6.69E-09
cg00455876 0.80478058 0
cg01707559 0.104638087 0
cg02004872 0.043721833 0
cg02011394 0.999072366 0
cg02050847 0.970957465 0
cg02233190 0.876025347 0
cg02494853 0.014302815 0
cg02839557 0.0296866 0
cg02842889 0.034472638 0
cg03052502 0.998108074 0
cg03155755 0.994080789 0
cg03244189 0.264419212 0
cg03443143 0.864539222 0
cg03683899 0.029216173 0
cg03695421 0.824457218 0
cg03706273 0.042111662 0

Total number of rows: 485577

Table truncated, full table size 12686 Kbytes.




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

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