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Sample GSM916785 Query DataSets for GSM916785
Status Public on Oct 10, 2013
Title genomic DNA from WT 5
Sample type genomic
Source name lymphoma biopsies
Organism Homo sapiens
Characteristics tissue: lymphoma biopsy
genotype: Wild type
Growth protocol Patient Samples
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted and purified from fresh frozen lymphoma biopsy samples obtained from cases of DLBCL and normal peripheral blood B lymphocytes. After proteinase K digestion DNA was isolated using Purescript DNA isolation Kit (Gentra system) as recommended by manufacturer.
Label Cy5 and Cy3
Label protocol Standard Illumina Protocol
Hybridization protocol Bisulphite conversion and subsequent cleanup was carried out using EZ DNA Methylation Kit ( Zymo Research); Each bisulfite-DNA samplewas whole genome amplified (WGA) followed by enzymatic fragmentation and hybrdization to Illumina Infinum Human Methylation 450 Beadchip (HumanMethylation450_15017482_v.1.1). During this hybridization, the WGA-DNA molecules anneal to methylation-specific DNA oligomers linked to individual bead types, with each bead type corresponding to a specific DNA CpG site and methylation state. There are two different bead types for each locus, one with an oligomer that anneals specifically to the methylated version of the locus, while the other oligomer anneals to the unmethylated version of the locus. The oligomer probe designs follow the Infinium I and II chemistries, in which locus-specific base extension follows hybridization to a methylation-specific oligomer as detailed by manufacturer. After labeled nucleotide incorporation, the intensities were obtained after scanning each hybridized array. BeadArrays are scanned and the raw data are extracted to calculate the beta value DNA methylation score for each probe and sample.
Scan protocol Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
Description TET2 wild type lymphoma biopsy
Data processing Genome Studio software 2011.1 and R statistical software
Genome Studio 2011.1 and R statistical software. Non_normalized data matrix contains unmethylated (U) and methylated (M) signal intensities for each CpG locus. The beta value is calculated as (M/(M+U)), in which M and U refer to the mean methylated and unmethylated probe signal intensities, respectively.The data points for the following conditions; 1) Probes containing single-nucleotide polymorphisms (SNPs), 2) those that overlap with a repetitive element that covers the targeted CpG dinucleotide, 3) those that overlap with regions of insertions and deletions in the human genome. Further,measurements in which the fluorescent intensity is not statistically significantly above background signal (detection p-value > 0.05) are removed from the data set. .
Submission date Apr 17, 2012
Last update date Oct 10, 2013
Contact name Vasu Punj
Organization name USC
Street address Biggy Street
City Los Angeles
State/province CA
ZIP/Postal code 90033
Country USA
Platform ID GPL13534
Series (2)
GSE37362 TET2 loss-of-function mutations associate with a DNA hypermethylation signature in diffuse large B-cell lymphoma (DNA methylation)
GSE37365 TET2 loss-of-function mutations associate with a DNA hypermethylation signature in diffuse large B-cell lymphoma

Data table header descriptions
VALUE beta
Detection Pval

Data table
ID_REF VALUE Detection Pval
cg00000029 0.610032362 1.53E-183
cg00000108 0.945555336 0
cg00000109 0.444644141 7.58E-259
cg00000165 0.80649652 0
cg00000236 0.90774989 0
cg00000289 0.43902439 1.92E-95
cg00000292 0.63681062 0
cg00000321 0.802962809 0
cg00000363 0.843809524 0
cg00000622 0.007978525 0
cg00000658 0.891340061 0
cg00000714 0.352241628 0
cg00000721 0.389701993 0
cg00000734 0.12171764 0
cg00000769 0.023863547 0
cg00000807 0.453858249 0
cg00000884 0.91902921 0
cg00000905 0.214025501 0
cg00000924 0.610442912 0
cg00000948 0.916685448 0

Total number of rows: 485577

Table truncated, full table size 12140 Kbytes.

Supplementary data files not provided
Processed data included within Sample table

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