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Sample GSM1342175 Query DataSets for GSM1342175
Status Public on Mar 09, 2014
Title genomic DNA from patient mHGA24
Sample type genomic
Source name mHGA24
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
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
mHGA24 Detection Pval

Data table
ID_REF VALUE mHGA24 Detection Pval
cg00050873 0.908296011942845 0.0147014149018142
cg00212031 0.235590045491036 0.58894433504559
cg00213748 0.0293390982087708 0.0349395216835992
cg00214611 0.014938335938857 0.427526680897662
cg00455876 0.829665933186637 1.6503243216448e-11
cg01707559 0.00867250952140596 0
cg02004872 0.823713284828887 2.24453788888468e-12
cg02011394 0.975676125951019 0.804323242738019
cg02050847 0.0113447703375761 0.632034034588155
cg02233190 0.152331189710611 0.0302697490836722
cg02494853 0.0690889565061751 0
cg02839557 0.114684056667416 0.162648154721534
cg02842889 0.894149900097579 0.716288491683454
cg03052502 0.285215070843129 0.857227046291551
cg03155755 0.828504043126685 0.0152325129045743
cg03244189 0.980515273832661 0
cg03443143 0.953045445973977 0.2455555608655
cg03683899 0.52636186770428 0.418676764049173
cg03695421 0.737887596899225 4.16888745746746e-13
cg03706273 0.0481715893108298 0

Total number of rows: 485512

Table truncated, full table size 14828 Kbytes.

Supplementary data files not provided
Processed data included within Sample table

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