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Sample GSM1342257 Query DataSets for GSM1342257
Status Public on Mar 09, 2014
Title genomic DNA from patient mHGA19
Sample type genomic
Source name mHGA19
Organism Homo sapiens
Characteristics mutation: H3F3A.K27M
tissue: glioblastomas
brain region: Infratentorial Midline (DIPG)
Extracted molecule genomic DNA
Extraction protocol genomic DNA was extracted and purified from LBC samples using Qiagen DNeasy Kit according to standard instructions
Label Cy5 and Cy3
Label protocol Standard Illumina Protocol
Hybridization protocol bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450k Beadchip using standard Illumina protocol
Scan protocol Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
Description BIOPSY
Data processing We removed probes with missing values, binding multiple genomic regions, binding targets with known sequence variants (1000 Genomes Project, SNPs with a minor allele frequency ≥ 2/120), or being located on the X or Y chromosomes. The final set contains 309,015 probes
Submission date Mar 08, 2014
Last update date Jan 05, 2015
Contact name Simon Papillon-Cavanagh
Organization name McGill University
Department Human Genetics
Lab Majewski
Street address 740 Dr Penfield
City Montrea
State/province Quebec
ZIP/Postal code H3A0G1
Country Canada
Platform ID GPL13534
Series (1)
GSE55712 Genome wide methylation profliling of pediatric glioblastomas.

Data table header descriptions
VALUE Average Beta
mHGA19 Detection Pval

Data table
ID_REF VALUE mHGA19 Detection Pval
cg00050873 0.858199151747176 0.0199352030135758
cg00212031 0.0223062562826097 0.541966499783129
cg00213748 0.0482295059247453 0.0130839230063835
cg00214611 0.0216604163972585 0.756650480532336
cg00455876 0.697751536719508 8.60000722857635e-08
cg01707559 0.0118587264758958 0
cg02004872 0.541483471747272 0
cg02011394 0.932399901744043 3.39578697072795e-06
cg02050847 0.0259017187121762 0.648206159915984
cg02233190 0.133775440201235 0.00138590919223081
cg02494853 0.0778374507697816 0
cg02839557 0.0871454711802379 0.0714727891527938
cg02842889 0.816770829021978 0.34221557387435
cg03052502 0.288216467849869 0.831231092712252
cg03155755 0.75 8.12531662397475e-07
cg03244189 0.791708356897377 1.11022302462516e-16
cg03443143 0.939652668873788 0.0134428671356708
cg03683899 0.378457956724185 0.760862592361111
cg03695421 0.632563857396531 2.29272156815341e-12
cg03706273 0.0491730981256891 0

Total number of rows: 485512

Table truncated, full table size 14812 Kbytes.

Supplementary data files not provided
Processed data included within Sample table

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