|
| Status |
Public on Nov 16, 2013 |
| Title |
LMS-09 [methylation] |
| Sample type |
genomic |
| |
|
| Source name |
tumor sample
|
| Organism |
Homo sapiens |
| Characteristics |
gender: male
age (yrs): 65
sarcoma subtype: leiomyosarcoma (LMS)
|
| Treatment protocol |
All sarcoma samples of this set were obtained prior to any cytotoxic treatment and were snap-frozen immediately after surgery. Prior to RNA extraction tumor cell content was checked by a pathologist and only samples with >80% tumor content were processed further.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was isolated using Allprep DNA/RNA Mini Kit (Qiagen, Hilden, Germany) followed by ethanol precipitation with 5 M ammonium acetate. Bisulfite conversion was carried out by using the EZ DNA Methylation Kit (Zymo Research, Irvine, USA) according to the manufacturer’s instruction and 500 ng of the bisulfite converted genomic DNA was used with the Infinium bead array platform.
|
| Label |
biotin
|
| Label protocol |
DNA methylation profiling was performed using the HumanMethylation 27k BeadArrays (Illumina) according to the manufacturers’ instructions. Quality control as well as labeling and hybridization were performed in the Core Facility of the DKFZ Heidelberg.
|
| |
|
| Hybridization protocol |
DNA methylation profiling was performed using the HumanMethylation 27k BeadArrays (Illumina) according to the manufacturers’ instructions. Quality control as well as labeling and hybridization were performed in the Core Facility of the DKFZ Heidelberg.
|
| Scan protocol |
DNA methylation profiling was performed using the HumanMethylation 27k BeadArrays (Illumina) according to the manufacturers’ instructions. Quality control as well as labeling and hybridization were performed in the Core Facility of the DKFZ Heidelberg.
|
| Data processing |
The methylation status obtained from this assay can be expressed as the ratio of fluorescence intensity of the methylated probe over the overall intensity (beta value) or the log2 ratio of the intensities of methylated probe versus unmethylated probe (M-value).
The 'qnorm.txt' file contains the quantile normalized beta values as provided by the DKFZ (German Cancer Research Center) Core Facility.
M-values were generated as described in: PMID:21118553
|
| |
|
| Submission date |
Nov 14, 2013 |
| Last update date |
Nov 16, 2013 |
| Contact name |
Marcus Renner |
| E-mail(s) |
marcus.renner@med.uni-heidelberg.de
|
| Organization name |
Institute of Pathology
|
| Department |
General Pathology
|
| Street address |
Im Neuenheimer Feld 224
|
| City |
Heidelberg |
| ZIP/Postal code |
69120 |
| Country |
Germany |
| |
|
| Platform ID |
GPL8490 |
| Series (2) |
| GSE52391 |
Integrative DNA methylation and gene expression analysis in high-grade soft tissue sarcomas [methylation] |
| GSE52392 |
Integrative DNA methylation and gene expression analysis in high-grade soft tissue sarcomas |
|
