|
| Status |
Public on Jan 14, 2008 |
| Title |
Hepatocellular carcinoma (HCC), metastasis free, 397A |
| Sample type |
RNA |
| |
|
| Source name |
03-397A
|
| Organism |
Homo sapiens |
| Characteristics |
Tissue: liver tissue (tumor)
Disease state: Hepatocellular carcinoma (HCC), metastasis free
Individual: 03-397A
Clinical info: Follow up status: alive
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Tri-Reagent Protocol
Other: Total RNA isolation was performed using the Tri-Reagent Protocol (Molecular Research Center, Cincinnati)
|
| Label |
alexa 647
|
| Label protocol |
Labeling Protocol
Other: Processed by using a method of direct detection of the biotin-containing transcripts by streptavidin-Alexa647 conjugate.
|
| |
|
| Hybridization protocol |
Sample Hybridization Protocol
Qty. of labeled target: 5 ug of total RNA
Other: Labeled targets from 5ug of total RNA were used for hybridization on each miRNA microarray chip containing human and mouse miRNA genes. All probes on these microarrays are 40-mer oligonucleotides spotted by contacting technologies and covalently attached to a polymeric matrix. The microarrays were hybridized in 6x SSPE (0.9 M NaCl / 60 mM NaH2PO4 H20 / 8 mM EDTA, pH 7.4) / 30% formamide at 25C for 18 hr, washed in 0.75x TNT (Tris HCL/NaCl/Tween 20) at 37C for 40 min.
|
| Scan protocol |
Scanning Protocol
Other: Processed slides were scanned by using a PerkinElmer ScanArray XL5K Scanner, with the laser set to 635 nm, at Power 80 and PMT 70 setting, and a scan resolution of 10 um.
|
| Description |
No additional information.
|
| Data processing |
Data Processing Protocol
Calculation Method: Raw data were normalized and analyzed in GENESPRING software version 6.1.1 (Silicon Genetics, Redwood City, CA). GENESPRING generated an average value of the spot replicates of each miRNA. After data transformation (to convert any negative value to 0.01), normalization was performed by using a per-chip on median normalization and a normalization to specific samples used as common reference for miRNA expression.
|
| |
|
| Submission date |
Jan 24, 2007 |
| Last update date |
Nov 04, 2008 |
| Contact name |
Xin Wei Wang |
| E-mail(s) |
xw3u@nih.gov
|
| Phone |
240-760-6858
|
| Organization name |
National Cancer Institute
|
| Department |
Laboratory of Human Carcinogenesis
|
| Lab |
Liver Carcinogenesis Unit
|
| Street address |
37 Convent Drive
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892-4255 |
| Country |
USA |
| |
|
| Platform ID |
GPL4700 |
| Series (1) |
| GSE6857 |
Unique MicroRNA Expression Signature Predicts Survival, Metastases and Recurrence of HCC |
|
