|
| Status |
Public on Aug 01, 2014 |
| Title |
low-grade GIST |
| Sample type |
genomic |
| |
|
| Source name |
Gastro-intestinal stromal tumour, gastric resection
|
| Organism |
Homo sapiens |
| Characteristics |
gender: male
age: 53
tissue: stomach
morphology: spindle
kit: positive
sdhb: positive
cd34: positive
dog-1: positive
mitotic rate: 3 per 50 high-power fields
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Tissue was homogenized and subsequently mixed with lysis buffer (700µl/g tissue) containing 2.1% (v/v) Proteinase K (10mg/ml) and 0.7% SDS in TE (pH 8.0). Samples were incubated o/n at 37°C. Phenol extraction followed by butanol treatment and ethanol precipitation was performed as described by Sambrook and Russell. 500ng of DNA was used for the assay.
|
| Label |
biotin/DNP
|
| Label protocol |
Illumina Protocol
|
| |
|
| Hybridization protocol |
Sample was processed at genomics and proteomics core facility at German Cancer Research Center (DKFZ), Heidelberg according to manufactureres recommendations.
|
| Scan protocol |
llumina iScan System according to the manufacturer's protocol.
|
| Description |
methylation data from a low-grade invasive gastro-intestinal stromal tumour
|
| Data processing |
The raw intensity values (two channels for each probe) were extracted from the Illumina .idat files using the LUMI software package for R. The standard signals available from Illumina and reported in Bibikova et. al., "High density DNA methylation array with single CpG site resolution", Genomics 98(4), 2011 were used for normalisation as follows. For every probe, the two color channels of the two reference samples (unmethylated and methylated DNA) define a 2x2 matrix, whose inverse was multiplied onto the measured signals. Thus, the reference unmethylated signal gets transformed into (1,0) and the methylated signal into (0,1). Probes where the two reference samples showed insufficient differences (e.g. the control probes) were not processed. To project onto a single value, the angle with the first axis was taken, with 90 degrees normalised to 1.
|
| |
|
| Submission date |
Feb 28, 2014 |
| Last update date |
Aug 01, 2014 |
| Contact name |
Henri-Jacques Delecluse |
| E-mail(s) |
H.Delecluse@dkfz-heidelberg.de
|
| Organization name |
German Cancer Research Center (DKFZ)
|
| Department |
Pathogenesis of virus-associated tumours
|
| Street address |
Im Neuenheimer Feld 242
|
| City |
Heidelberg |
| ZIP/Postal code |
69120 |
| Country |
Germany |
| |
|
| Platform ID |
GPL13534 |
| Series (1) |
| GSE55521 |
Methylome of a low-grade invasive GIST |
|
