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Sample GSM1342256 Query DataSets for GSM1342256
Status Public on Mar 09, 2014
Title genomic DNA from patient mHGA18
Sample type genomic
Source name mHGA18
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
mHGA18 Detection Pval

Data table
ID_REF VALUE mHGA18 Detection Pval
cg00050873 0.845099159389537 0.0110861426967099
cg00212031 0.541134408401922 0.523385103289839
cg00213748 0.0468107819589005 0.0722890443133726
cg00214611 0.0178902650631245 0.278765177588679
cg00455876 0.753544813031722 2.14676709742179e-09
cg01707559 0.0135457631676246 0
cg02004872 0.818330441745629 6.60493881809998e-12
cg02011394 0.949484978540773 0.159364466779209
cg02050847 0.0202804356983812 0.497864431773216
cg02233190 0.0991769547325103 0.00332358415420442
cg02494853 0.0663937879973515 0
cg02839557 0.117408266554197 0.197538899190178
cg02842889 0.922052614485222 0.444653706120313
cg03052502 0.26923602569359 0.229506351991639
cg03155755 0.795626576955425 0.152351778888838
cg03244189 0.93272515673687 3.85676046654737e-10
cg03443143 0.928886709171162 0.0110861426967099
cg03683899 0.707508799374267 0.698207078960788
cg03695421 0.685315196723709 1.50421672673318e-07
cg03706273 0.0619411477808486 0

Total number of rows: 485512

Table truncated, full table size 14786 Kbytes.

Supplementary data files not provided
Processed data included within Sample table

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