|
Status |
Public on Mar 11, 2010 |
Title |
FFPE119 - mAdbID:86619 |
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).
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|
|
Channel 2 |
Source name |
FFPE119
|
Organism |
Homo sapiens |
Characteristics |
gender: male age: 60 tissue: Lung disease state: None Small Cell Carcinoma clinical info: Final pathology diagnosis: Adenocarcinoma clinical info: Histology of male smoker: male adenocarcinoma 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] ScanPower: 10;; 10 LaserPower: 3.3;; 4.07 Temperature: 30.75
|
Description |
mAdb experiment ID: 86619
|
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.
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|
|
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 |
|