|
| Status |
Public on May 02, 2013 |
| Title |
minor non-tumor1 |
| Sample type |
RNA |
| |
|
| Source name |
resected non-tumor liver tissue
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: resected non-tumor liver tissue
genotype: minor [rs8099917 TG/GG]
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using the RNeasy Mini kit (QIAGEN, Valencia, CA)
|
| Label |
Biotin
|
| Label protocol |
Aliquots of total RNA (50 ng) isolated from the liver biopsy specimens were subjected to amplification with the WT-OvationTM Pico RNA Amplification System (NuGen, San Carlos, CA, USA) as recommended by the manufacturer (http://www.nugeninc.com/).5 microgram of resultant cDNA was used for fragmentation and biotin labeling using the FL-OvationTM cDNA Biotin Module V2 (NuGen) as recommended by the manufacturer.
|
| |
|
| Hybridization protocol |
The biotin-labeled cDNA was suspended in hybridization cocktail (NuGen), and used for the hybridization. Affymetrix Human 133 Plus 2.0 microarray chip (Affymetrix, Santa Clara, CA, USA) containing 54,675 gene transcripts was used for the analysis. Hybridization (45°C for 16hrs at 60 rpm), washing and staining (using Fluidics Station) were performed according to the standard protocol (Affymetrix).
|
| Scan protocol |
The probe array was scanned by GeneChip® Scanner 3000(Affymetrix).
|
| Description |
LC-MI1
Gene expression data from resected non-tumor liver tissue
|
| Data processing |
Hybridized data files (CEL) were obtained with the GeneChip® Operating Software 1.4 (GCOS) (Affymetrix).The intensity of each gene chip was normalized by one patient using GeneChip® Operating Software 1.4 (GCOS) and further processed by using R 2.13.0(http://www.r-project.org) and Bioconductor (http://www.bioconductor.org) software.Raw CEL file data were normalized using the MAS 5.0 algorithm as implemented in the affy package. Normalized data were log2 transformed.
|
| |
|
| Submission date |
Oct 24, 2012 |
| Last update date |
May 02, 2013 |
| Contact name |
Yuji Hodo |
| Organization name |
Kanazawa University Graduate School of Medical Sciences
|
| Street address |
13-1 Takara-Machi
|
| City |
Kanazawa |
| ZIP/Postal code |
920-8641 |
| Country |
Japan |
| |
|
| Platform ID |
GPL570 |
| Series (1) |
| GSE41804 |
Hepatic gene expression of HCV related Hepatocellular carcinoma and non-cancerous tissue with Il28B rs8099917 TT genotype and TG/GG genotype |
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