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Sample GSM1342262 Query DataSets for GSM1342262
Status Public on Mar 09, 2014
Title genomic DNA from patient mHGA14
Sample type genomic
Source name mHGA14
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
mHGA14 Detection Pval

Data table
ID_REF VALUE mHGA14 Detection Pval
cg00050873 0.824705250360485 0.00133971157744972
cg00212031 0.635193757824555 0.46068586638501
cg00213748 0.0548346849656893 0.096864157124724
cg00214611 0.0270708161749814 0.402545083502073
cg00455876 0.838231514009082 0.00526184338242686
cg01707559 0.0133303873913684 0
cg02004872 0.817446110240919 0
cg02011394 0.956224899598394 0.0298069229946218
cg02050847 0.0107828205909229 0.876004905551116
cg02233190 0.0827330277232045 0.00827410549725915
cg02494853 0.0642020870450496 0
cg02839557 0.129345713668754 0.619566854804148
cg02842889 0.860407388479229 0.884599373333053
cg03052502 0.159460219285915 0.421752597420771
cg03155755 0.774048760583495 0.864816243075915
cg03244189 0.958369905956113 9.1882057517978e-13
cg03443143 0.939868586978164 0.0671913644936699
cg03683899 0.130905051449953 0.835432821738842
cg03695421 0.126827012025902 0.00123075609331968
cg03706273 0.0383348581884721 0

Total number of rows: 485512

Table truncated, full table size 14808 Kbytes.

Supplementary data files not provided
Processed data included within Sample table

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