|
| Status |
Public on Oct 10, 2013 |
| Title |
genomic DNA from WT 13 |
| 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
G30
|
| 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 |
| E-mail(s) |
vasupunj@gmail.com
|
| 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 |
|
