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Sample GSM1342183 Query DataSets for GSM1342183
Status Public on Mar 09, 2014
Title genomic DNA from patient GLIOMA 3
Sample type genomic
 
Source name GLIOMA 3
Organism Homo sapiens
Characteristics mutation: H3F3A.K27M
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
ID_REF
VALUE Average Beta
GLIOMA 3 Detection Pval

Data table
ID_REF VALUE GLIOMA 3 Detection Pval
cg00050873 0.856361589190928 1.30673249998381e-13
cg00212031 0.370938519144824 0.341547124541492
cg00213748 0.0325140949148831 0.49645948224447
cg00214611 0.0198003600065456 0.795417429305069
cg00455876 0.579122825294301 0.00529468872901739
cg01707559 0.0041257877980638 0
cg02004872 0.512888773456269 3.25257267346224e-05
cg02011394 0.97415357903875 0
cg02050847 0.015787099684258 0.475231983048789
cg02233190 0.0580378824672171 0.00109993054657898
cg02494853 0.0556215696259831 0
cg02839557 0.283716594157862 0.761144915984527
cg02842889 0.879928374838346 0.102201342662601
cg03052502 0.429594980881316 0.00281175912008724
cg03155755 0.847068470684707 1.10824682764132e-10
cg03244189 0.96297454744497 1.32116539930394e-14
cg03443143 0.919123321500232 0
cg03683899 0.350074716623538 0.935442897393895
cg03695421 0.0543132655720615 3.63807141672279e-05
cg03706273 0.0326298701298701 0

Total number of rows: 485512

Table truncated, full table size 14837 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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