|
| Status |
Public on Aug 17, 2014 |
| Title |
benign_PCPG_4 |
| Sample type |
RNA |
| |
|
| Source name |
pheochomocytoma/paraganglioma
|
| Organism |
Homo sapiens |
| Characteristics |
subject gender: M
subject age (yrs): 51
diagnosis: paraganglioma (PGL)
tissue: pheochromocytoma/paraganglioma (PCPG)
primary site: retoperitoneum
tissue type: benign
|
| Extracted molecule |
total RNA |
| Extraction protocol |
performed using the Agilent Oligo Microarray Kit 8_60K according to the Agilent One-Color Microarray-based Gene Expression Analysis Protocol (Agilent Technologies). Briefly, 0.1 mg of total RNA and diluted Spike-in mix was amplified and labelled using the Agilent Quick Amp Labeling Kit (Agilent Technologies).
|
| Label |
Cy3
|
| Label protocol |
Cyanine 3-labelled linearly amplified cRNA was mixed with 10 μl blocking agent, nuclease-free water, and 25 μl fragmentation buffer provided in the Agilent Gene Expression Hybridization Kit (Agilent Technologies) and incubated for 30 minutes at 60°C to fragment the RNA.
|
| |
|
| Hybridization protocol |
After addition of 2 μl GEx hybridisation buffer Hi-RPM, the amplified fragmented RNA was hybridised in a DNA microarray hybridisation oven (Agilent Technologies) at 10 rpm and 65°C for 17 hours.
|
| Scan protocol |
Agilent Technologies Scanner G2505C
|
| Data processing |
raw data was normalized by quantile normalization using qunatile normalizaion provided by limma package (http://bioconductor.org).
|
| |
|
| Submission date |
Aug 16, 2014 |
| Last update date |
Aug 17, 2014 |
| Contact name |
Yoon-La Choi |
| E-mail(s) |
yla.choi@samsung.com
|
| Organization name |
Samsung medical center
|
| Department |
Department of pathology
|
| Lab |
Laboratory of cancer genomics and molecular pathology
|
| Street address |
81 Irwon-Ro, Gangnam-gu
|
| City |
Seoul |
| ZIP/Postal code |
135-710 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL13607 |
| Series (2) |
| GSE60458 |
Expression profiles of pheochromocytoma and paraganglioma |
| GSE60459 |
Expression and copy number profiles of pheochromocytoma and paraganglioma |
|
