|
| Status |
Public on Sep 01, 2016 |
| Title |
NSCLC 18 - BSchip - normoxic |
| Sample type |
genomic |
| |
|
| Source name |
non-small-cell lung tumor, normoxic, BS-chip
|
| Organism |
Homo sapiens |
| Characteristics |
dna pretreatment: none
batch: 4
tumor name: NSCLC 18
tabchip or bschip: BSchip
hypoxia status: normoxic
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted from fresh frozen tumor samples using the QIAGEN DNeasy Blood & Tissue Kit
|
| Label |
Cy5 and Cy3
|
| Label protocol |
Standard Illumina Protocol.
|
| |
|
| Hybridization protocol |
Infinium Human Methylation 450k BeadChip using standard Illumina protocol.
|
| Scan protocol |
Arrays were imaged using BeadArray Reader using standard recommended protocol.
|
| Description |
untreated and glycosylated, TET-oxidized DNA was bisulfite converted using theZYMO Research EZ DNA Methylation-Lightning™ Kit according to manufacturers instructions
SAMPLE 42
|
| Data processing |
Intensity data files were read directly into R. Each sample was normalized using Subset-quantile within array normalization (SWAN) for Illumina Infinium HumanMethylation450 BeadChips. Batch effects between chips and experiments were corrected using the runComBat function from the ChAMP bioconductor package.
|
| |
|
| Submission date |
Jul 27, 2015 |
| Last update date |
Sep 01, 2016 |
| Contact name |
Bernard thienpont |
| Organization name |
VIB
|
| Department |
Vesalius Research Center
|
| Lab |
Translational genetics
|
| Street address |
Herestraat 49
|
| City |
Heverlee |
| ZIP/Postal code |
3000 |
| Country |
Belgium |
| |
|
| Platform ID |
GPL16304 |
| Series (2) |
| GSE71398 |
Tumor hypoxia causes DNA hypermethylation by reducing TET activity (BeadChip) |
| GSE71403 |
Tumor hypoxia causes DNA hypermethylation by reducing TET activity |
|
