|
| Status |
Public on Dec 01, 2010 |
| Title |
Liver Non-Tumor Tissue LCS-104B |
| Sample type |
RNA |
| |
|
| Source name |
LCS-104B
|
| Organism |
Homo sapiens |
| Characteristics |
Tissue: Liver Non-Tumor Tissue
Disease state: Hepatocellular carcinoma (HCC)
Individual: 02-335B
|
| Extracted molecule |
total RNA |
| Extraction protocol |
TRIzol Extraction Protocol
Other: Total RNA was isolated from microdissected fresh frozen tissues using TRIzol (Invitrogen, Carlsbad, CA) according to the manufacturer's protocol. RNA integrity for each sample was confirmed with the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA Labeling for HT Arrays
Other: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, For HT Array Plates Using the GeneChip® Array Station, P/N 702063 Rev. 2, Affymetrix).
|
| |
|
| Hybridization protocol |
Hybridization Protocol
Other: The fragmented cRNA is added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C. The chips are then transferred to a fluidics instrument that performs washes to remove cRNA that has not hybridized to its complementary oligonucleotide probe. The bound cRNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE.
|
| Scan protocol |
Scanning Protocol for HT Arrays
Other: GeneChips were scanned using GeneChip® HT Array Plate Scanner by Affymetrix.
|
| Description |
No additional information.
|
| Data processing |
Data Processing Protocol
Calculation Method: The CEL files from the two Affymetrix series were combined using the matchprobes package in the R programming environment. Thereafter, the RMA method in the R affy package was used to obtain probe set expression summaries.
|
| |
|
| Submission date |
Jan 22, 2009 |
| Last update date |
Dec 18, 2009 |
| 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 |
GPL3921 |
| Series (1) |
| GSE14520 |
Gene expression data of human hepatocellular carcinoma (HCC) |
|
