|
| Status |
Public on Jul 31, 2014 |
| Title |
Patient 5 in group SynSa1 [transcriptome] |
| Sample type |
RNA |
| |
|
| Source name |
tumor sample
|
| Organism |
Homo sapiens |
| Characteristics |
histosubtype: synovial sarcoma
age at diagnosis [years]: 28
gender: Female
|
| Treatment protocol |
not applicable
|
| Growth protocol |
not applicable
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA of sufficient integrity and purity was obtained from 57 tumor specimens using the miRNeasy Mini Kit (Qiagen) with optional DNase treatment using RNase-free DNase Set (Qiagen). RNA quality was checked using Bio-Rad Experion system (Bio-Rad Laboratories).
|
| Label |
Cy3
|
| Label protocol |
Total RNA (25ng) was reverse transcribed into cDNA by incorporating a T7 oligo-dT promoter primer prior to the generation of fluorescent cRNA using an Agilent LowInput Quick Amp Labeling Kit (Agilent Technologies, SantaClara, CA, USA).
|
| |
|
| Hybridization protocol |
Gene expression analysis was performed using Human Gene Expression 4x44K v2 microarrays (G4845A) according to the one-color microarray-based expression analysis protocol (Agilent Technologies).
|
| Scan protocol |
The microarray slides were scanned using the Agilent G2565A DNA Microarray Scanner (Agilent Technologies, SantaClara, CA, USA).
|
| Description |
Gene expression in primary tumor sample
|
| Data processing |
Image analysis was done using the Feature Extraction V10.10.1.1 software (Agilent Technologies, SantaClara, CA, USA). Microarray data were analyzed using Gene Spring GX default workflow parameters for Agilent one-color expression experiments (Agilent Technologies, SantaClara, CA, USA).
|
| |
|
| Submission date |
Jan 17, 2014 |
| Last update date |
Jul 31, 2014 |
| Contact name |
Joanna Przybyl |
| E-mail(s) |
jprzybyl@stanford.edu
|
| Organization name |
Stanford University
|
| Department |
Department of Pathology
|
| Street address |
300 Pasteur Drive
|
| City |
Stanford |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL13497 |
| Series (2) |
| GSE54187 |
Metastatic potential is determined early in synovial sarcoma development and reflected by tumor molecular features [transcriptome] |
| GSE54188 |
Metastatic potential is determined early in synovial sarcoma development and reflected by tumor molecular features |
|
