|
| Status |
Public on Mar 11, 2010 |
| Title |
FFPE195 - mAdbID:86633 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
EBV Control Sample
|
| Organisms |
Homo sapiens; human gammaherpesvirus 4 |
| Characteristics |
strain: 1558
cell line: Epstein-Barr virus (EBV)-transformed lymphoblastoid cell line
cell type: lymphoblastoid
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Sample Extraction Protocol
Other: Total RNA was isolated from 20um sections from FFPE tissue blocks using RecoverAll™ Total Nucleic Acid Isolation Kit for FFPE Tissues (Ambion, Austin, TX USA). Small RNA was enriched and purified by flashPAGE Fractionator (Ambion, Austin, TX USA) according to the manufacturer’s instruction.
|
| Label |
cy3
|
| Label protocol |
Cy3 Labeling Protocol
Other: Small RNA, equivalent to 10 ug of the total RNA from FFPE and EBV reference samples, was labeled with Cy3 using mirVana™ miRNA Labeling Kit (Ambion, Austin, TX USA).
|
| |
|
| Channel 2 |
| Source name |
FFPE195
|
| Organism |
Homo sapiens |
| Characteristics |
gender: male
age: 80
tissue: Lung
disease state: None Small Cell Carcinoma
clinical info: Final pathology diagnosis: Squamous Cell Carcinoma
clinical info: Histology of male smoker: male squamous smoker
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Sample Extraction Protocol
Other: Total RNA was isolated from 20um sections from FFPE tissue blocks using RecoverAll™ Total Nucleic Acid Isolation Kit for FFPE Tissues (Ambion, Austin, TX USA). Small RNA was enriched and purified by flashPAGE Fractionator (Ambion, Austin, TX USA) according to the manufacturer’s instruction.
|
| Label |
cy5
|
| Label protocol |
Cy5 Labeling Protocol
Other: Small RNA, equivalent to 10 ug of the total RNA from FFPE and EBV reference samples, was labeled with Cy5 using mirVana™ miRNA Labeling Kit (Ambion, Austin, TX USA).
|
| |
|
| |
| Hybridization protocol |
microRNA Hybridization Protocol
Other: Resuspend Cy3 and Cy5 labeled miR in 10ul and combine them together (20ul total) and add the following reagents: 1ul 50x Denhardt’s blocking solution ,1ul poly dA (8ug/), 1ul yeast tRNA (4mg/ml), 10ul Human Cot I DNA (10mg/ml), 3ul 20X SSC and 1ul 10% SDS. Heat sample at 70C for 3min and immediately hybridize after spin at 10,000g for 30 sec. Start hybridization at RT over night in the dark.
|
| Scan protocol |
Creator: GenePix Pro 4.0.0.54
Scanner: GenePix 4000B [84945]
PMTVolts: 940;; 790
ScanPower: 10;; 10
LaserPower: 3.24;; 4.13
Temperature: 30.11
|
| Description |
mAdb experiment ID: 86633
|
| Data processing |
BRB-ArrayTools Data Processing Protocol
Calculation Method: Included duplicate spots per each miR, whose intensity was averaged. A spot with signal intensity <100 in both channels was filtered out. If the signal intensity was <100 in one channel only, it was set to 100 in computing the log-ratio value. A spot size smaller than 25 pixels was also filtered out. The normalization method used is ratio median over entire array method.
|
| |
|
| Submission date |
Mar 11, 2009 |
| Last update date |
Apr 01, 2009 |
| Contact name |
Francesco Maria Marincola |
| E-mail(s) |
fmarincola@sidra.org
|
| Phone |
301-793-8210
|
| Organization name |
Sidra Medical and Research Center
|
| Street address |
Al Nasr Tower, AL Corniche Street, PO Box 26999
|
| City |
Doha |
| ZIP/Postal code |
PO Box 26999 |
| Country |
Qatar |
| |
|
| Platform ID |
GPL8377 |
| Series (1) |
| GSE15201 |
MicroRNA expression differentiates histology and predicts survival of lung cancer |
|
