|
| Status |
Public on Nov 16, 2013 |
| Title |
SS-07 |
| Sample type |
RNA |
| |
|
| Source name |
tumor sample
|
| Organism |
Homo sapiens |
| Characteristics |
gender: male
age (yrs): 19
sarcoma subtype: synovial sarcoma (SS)
|
| 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 |
total RNA |
| Extraction protocol |
RNA was isolated from snap-frozen tissue using Allprep DNA/RNA Mini Kit (Qiagen) according to manufacturer’s instructions. Quality control and quantification of total RNA was done with a RNA 6000 nano LabChip using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA). Only RNA with a RNA integrity number > 7 was used.
|
| Label |
biotin
|
| Label protocol |
Expression profiling was performed using the HumanHT-12 v3 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 |
Expression profiling was performed using the HumanHT-12 v3 BeadArrays (Illumina) according to the manufacturers’ instructions.
|
| Scan protocol |
Expression profiling was performed using the HumanHT-12 v3 BeadArrays (Illumina) according to the manufacturers’ instructions.
|
| Data processing |
Annotation and quantile normalization were performed using a lumi R-package (Du P et al. BMC Bioinformatics 2010, 11:587.; Du P et al. Cancer 2007, 2:1-31.)
|
| |
|
| 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 |
GPL6947 |
| Series (2) |
| GSE52390 |
Integrative DNA methylation and gene expression analysis in high-grade soft tissue sarcomas [gene expression] |
| GSE52392 |
Integrative DNA methylation and gene expression analysis in high-grade soft tissue sarcomas |
|
