|
| Status |
Public on Apr 21, 2011 |
| Title |
Sporadic benign pheochromocytoma replicate 5_FFPE |
| Sample type |
RNA |
| |
|
| Source name |
Sporadic benign, human pheochromocytoma, FFPE sample
|
| Organism |
Homo sapiens |
| Characteristics |
tumor localization: adrenal
hereditary or sporadic: sporadic
germline mutations: -
gender: male
age at the time of surgery (years): 34.7
time until recurrence (years): -
type of starting material: formalin-fixed paraffin-embedded tissue block
age of starting material (years): 0.6
|
| Treatment protocol |
A total of 21 formalin-fixed paraffin-embedded (FFPE) pheochromocytoma tissue samples were collected from pathological archives. From three patients fresh frozen tissue samples were obtained, as well. After surgical removal these three tissue samples were immediately snap frozen in liquid nitrogen and stored at -80oC until RNA isolation. Histological diagnoses were confirmed in all FFPE and frozen tissue samples.
|
| Growth protocol |
-
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA isolation was carried out after 100% xylene deparaffinization from altogether 5 slices of FFPE tissue sections with 15 μm thickness by Ambion RecoverAll Total Nucleic Acid Isolation Kit (Applied Biosystems/Ambion, Austin, TX, USA) according to the manufacturer’s protocol. If required, extended deparaffinization and protease digestion at 50oC was performed. Total RNA extraction from fresh-frozen samples was performed after tissue homogenization with Qiagen miRNeasy Mini Kit (Qiagen GmbH, Hilden, Germany) completed with optional on-column DNase digestion carried out by RNase-Free DNase Set (Qiagen GmbH).
|
| Label |
Cy3
|
| Label protocol |
Total RNA of 100 nanograms was dephosphorylated, denaturated and Cyanine3-pCp ligated according to the manufacturer’s instructions using miRNA Complete Labeling and Hyb Kit (Agilent Tech. Inc.). Labeled RNA was purified on Micro Bio-Spin P-6 Columns (Bio-Rad Laboratories, Hercules, CA, USA).
|
| |
|
| Hybridization protocol |
Samples were hybridized to Agilent Human miRNA Microarray Rel12.0 (Agilent Tech. Inc.) at 55oC, for 20 hours according to the manufacturer’s instructions.
|
| Scan protocol |
After washing microarray slides array scanning was performed by Agilent DNA Microarray Scanner G2565BA (Agilent Tech. Inc.).
|
| Description |
Pheochromocytoma_5_FFPE
|
| Data processing |
Feature extraction and data processing was performed with default scenario for Agilent Human MiRNA Microarray Rel12.0 by Feature Extraction Software 9.5.3 (Agilent Tech. Inc.) to calculate gProcessed signal
|
| |
|
| Submission date |
May 10, 2010 |
| Last update date |
Apr 21, 2011 |
| Contact name |
Zsófia Tömböl |
| Organization name |
Semmelweis University
|
| Department |
2nd Department of Medicine
|
| Street address |
Szentkirályi u. 46.
|
| City |
Budapest |
| ZIP/Postal code |
H-1088 |
| Country |
Hungary |
| |
|
| Platform ID |
GPL10406 |
| Series (1) |
| GSE21767 |
MicroRNA expression profiling on formalin-fixed paraffin-embedded (FFPE) tissue blocks of human adrenal pheochromocytomas |
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