|
| Status |
Public on Jul 01, 2009 |
| Title |
Normal adrenal cortex replicate1 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
adrenal cortex, normal cortex tissue
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: adrenal cortex
gender: male
age at the time of surgery: 52.19 years
hormonal status: normal hormonal status
|
| Treatment protocol |
After surgical removal tissue samples were immediately snap frozen in liquid nitrogen and stored at -80○ until RNA isolation. Histological diagnoses were confirmed in each cases.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from homogenized tissue samples using Rneasy Lipid Tissue Mini Kit (Qiagen GmbH, Hilden, Germany) following the manufacturer's instructions.
|
| Label |
Cy5
|
| Label protocol |
1 µg of total RNA mixed with RNA Spike-In-Kit (Agilent Tech. Inc., Santa Clara, CA) was reverse transcribed and Cyanine 5 or Cyanine 3-CTP-labeled (Perkin-Elmer, Waltham, Massachusetts, MA, USA) complementary RNA (cRNA) was synthetized using the Low RNA Input Linear Amplification Kit (Agilent Tech. Inc., Santa Clara, CA) according to the manufacturer’s Dual Color Expression Microarray Protocol version 5.5. Successful labeling, cRNA yield and purity were controlled on a Nanodrop ND-1000 Spectrophotometer (Thermo Scientific, Wilmington, DE).
|
| |
|
| Channel 2 |
| Source name |
Uniform reference RNA pooled from total RNA of all 16 tissues examined.
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: adrenal cortex
|
| Treatment protocol |
After surgical removal tissue samples were immediately snap frozen in liquid nitrogen and stored at -80○ until RNA isolation. Histological diagnoses were confirmed in each cases.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from homogenized tissue samples using Rneasy Lipid Tissue Mini Kit (Qiagen GmbH, Hilden, Germany) following the manufacturer's instructions.
|
| Label |
Cy3
|
| Label protocol |
1 µg of total RNA mixed with RNA Spike-In-Kit (Agilent Tech. Inc., Santa Clara, CA) was reverse transcribed and Cyanine 5 or Cyanine 3-CTP-labeled (Perkin-Elmer, Waltham, Massachusetts, MA, USA) complementary RNA (cRNA) was synthetized using the Low RNA Input Linear Amplification Kit (Agilent Tech. Inc., Santa Clara, CA) according to the manufacturer’s Dual Color Expression Microarray Protocol version 5.5. Successful labeling, cRNA yield and purity were controlled on a Nanodrop ND-1000 Spectrophotometer (Thermo Scientific, Wilmington, DE).
|
| |
|
| |
| Hybridization protocol |
825 ng of cyanine 5-CTP-labeled cRNA per sample was mixed with an equal amount of cyanine 3-CTP-labeled uniform reference cRNA, and hybridized to 4x44 K Whole Human Genome Microarrays (Agilent Tech. Inc., Santa Clara, CA) according to the manufacturer’s protocol.
|
| Scan protocol |
Array scan was performed with Agilent DNA Microarray Scanner G2565BA.
|
| Description |
N/A
|
| Data processing |
Agilent Feature Extraction Software 8.5 was used for feature extraction and array normalization with default normalization scenario for Agilent 4x44 K two-colour array platforms.
|
| |
|
| Submission date |
Feb 20, 2009 |
| Last update date |
Jul 01, 2009 |
| 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 |
GPL6480 |
| Series (1) |
| GSE14922 |
Human Adrenocortical Tumors: normal cortex vs inactive adenoma vs cortisol secreting adenoma vs adrenocortical cancer |
|
