|
| Status |
Public on Aug 17, 2014 |
| Title |
benign_PCPG_4 [aCGH] |
| Sample type |
mixed |
| |
|
| Channel 1 |
| Source name |
benign_PCPG
|
| 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 |
genomic DNA |
| Extraction protocol |
Array CGH was performed using the Agilent Human whole genome CGH 60 K microarray.1.5 g of test DNA and reference DNAs was digested with Alu I and Rsa I (Promega, Madison, WI) and purified using the QIAprep Spin Miniprep kit (Qiagen, Germantown, MD).
|
| Label |
Cy3
|
| Label protocol |
Test DNA and reference DNA samples were labelled by random priming with either Cy3-dUTP or Cy5-dUTP using the Agilent Genomic DNA Labeling Kit PLUS.
|
| |
|
| Channel 2 |
| Source name |
reference DNA
|
| Organism |
Homo sapiens |
| Characteristics |
sample type: reference DNA (Promega human genomic DNA male G1471)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Array CGH was performed using the Agilent Human whole genome CGH 60 K microarray.1.5 g of test DNA and reference DNAs was digested with Alu I and Rsa I (Promega, Madison, WI) and purified using the QIAprep Spin Miniprep kit (Qiagen, Germantown, MD).
|
| Label |
Cy3
|
| Label protocol |
Test DNA and reference DNA samples were labelled by random priming with either Cy3-dUTP or Cy5-dUTP using the Agilent Genomic DNA Labeling Kit PLUS.
|
| |
|
| |
| Hybridization protocol |
After labelling, the individual samples and reference samples were combined and concentrated using Microcon YM-30 filters (Millipore, Billerica, MA). After probe denaturation and preannealing with Cot-1 DNA, hybridisation was performed at 65°C with rotation for 40 hours. Four washing steps were completed with Agilent Oligo CGH washes as follows: Wash Buffer 1 at room temperature for 5 min, Wash Buffer 2 at 37°C for 1 min, an acetonitrile rinse at room temperature for 1 min, and a 30-second wash at room temperature in Agilent’s Stabilization and Drying Solution.
|
| Scan protocol |
All slides were scanned on an Agilent DNA microarray scanner G2505C.
|
| Data processing |
Raw log2 ratio was normalized 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 |
GPL10152 |
| Series (2) |
| GSE60457 |
Copy number profiles of pheochromocytoma and paraganglioma |
| GSE60459 |
Expression and copy number profiles of pheochromocytoma and paraganglioma |
|
