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Sample GSM1342189 Query DataSets for GSM1342189
Status Public on Mar 09, 2014
Title genomic DNA from patient cHGA-HGG16
Sample type genomic
Source name cHGA-HGG16
Organism Homo sapiens
Characteristics mutation: WT
tissue: glioblastomas
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
cHGA-HGG16 Detection Pval

Data table
ID_REF VALUE cHGA-HGG16 Detection Pval
cg00050873 0.837896645512239 0.39282174350847
cg00212031 0.00937326237191199 0.714201787574383
cg00213748 0.0424866142827342 0.699229720965063
cg00214611 0.00433601753466432 0.913062948118832
cg00455876 0.489025148849196 2.05383154713301e-05
cg01707559 0.0109465052411712 0
cg02004872 0.399591906138412 0
cg02011394 0.959129759129759 0.937475644163359
cg02050847 0.0357699636237658 0.761341426483671
cg02233190 0.0823220728107576 0.000678060021225835
cg02494853 0.0395931462898491 0
cg02839557 0.471183970856102 0.0958671110041602
cg02842889 0.583629893238434 0.768742894619295
cg03052502 0.172466680770044 0.900377966340398
cg03155755 0.790478905359179 0.143182314447141
cg03244189 0.873449842426227 0
cg03443143 0.960417283219888 0.405422746898133
cg03683899 0.032819145559576 0.636564143993476
cg03695421 0.0373109243697479 0
cg03706273 0.0285125386465132 0

Total number of rows: 485512

Table truncated, full table size 14843 Kbytes.

Supplementary data files not provided
Processed data included within Sample table

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