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Sample GSM1342258 Query DataSets for GSM1342258
Status Public on Mar 09, 2014
Title genomic DNA from patient mHGA25
Sample type genomic
Source name mHGA25
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
mHGA25 Detection Pval

Data table
ID_REF VALUE mHGA25 Detection Pval
cg00050873 0.813109149359596 0.5
cg00212031 0.0985369676913699 0.482756470010786
cg00213748 0.053973386394727 0.667262240673524
cg00214611 0.0287038083399254 0.876719018699897
cg00455876 0.752356548000366 6.68422495131438e-09
cg01707559 0.0152089812637488 0
cg02004872 0.608938719090769 1.22124532708767e-15
cg02011394 0.950494163946156 0.348590255783797
cg02050847 0.0243334196220554 0.587261681428054
cg02233190 0.0893420222829514 0.00850111261573916
cg02494853 0.0809541019154319 0
cg02839557 0.139084836756352 0.301936493466845
cg02842889 0.909559326919612 0.461251097569387
cg03052502 0.548705160176482 0.113019686529561
cg03155755 0.861444855206408 0.0120056043349919
cg03244189 0.970119219378844 7.79265540984397e-13
cg03443143 0.881735654201716 0.0743551412956243
cg03683899 0.108428058189528 0.474144772444887
cg03695421 0.208089070665758 1.39946297772475e-07
cg03706273 0.0340626939788951 0

Total number of rows: 485512

Table truncated, full table size 14796 Kbytes.

Supplementary data files not provided
Processed data included within Sample table

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