|
| Status |
Public on Jan 19, 2013 |
| Title |
128454 PVTT |
| Sample type |
RNA |
| |
|
| Source name |
portal vein tumor thrombus tissue
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: portal vein tumor thrombus
patient id: 128454
disease state: hapatocellular carcinoma
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs are harvested using TRIzol (Invitrogen) and the RNeasy kit (Qiagen) according to manufacturer’s instructions, including a DNase digestion step.
|
| Label |
Cy3
|
| Label protocol |
Total RNA of each sample was used for labeling as the following steps: 1) Reverse transcription with by Invitrogen Superscript ds-cDNA synthesis kit; 2) ds-cDNA labeling with NimbleGen one-color DNA labeling kit
|
| |
|
| Hybridization protocol |
Array hybridization using the NimbleGen Hybridization System and followed by washing with the NimbleGen wash buffer kit.
|
| Scan protocol |
Array scanning using the Agilent Scanner G2505C. Scanned images (TIFF format) were then imported into NimbleScan software (version 2.5) for grid alignment and expression data analysis.
|
| Description |
PVTT is known to be an extension of liver parenchyma tumor (PT) into the main portal trunk and its branches.
|
| Data processing |
The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).
|
| |
|
| Submission date |
Jan 18, 2013 |
| Last update date |
Mar 18, 2013 |
| Contact name |
WEIXING GUO |
| E-mail(s) |
WEIXINGG88@126.COM
|
| Organization name |
ehbh
|
| Street address |
CHANGHAI ROAD
|
| City |
shanghai |
| ZIP/Postal code |
200438 |
| Country |
China |
| |
|
| Platform ID |
GPL14715 |
| Series (1) |
| GSE43630 |
The gene expression profiling array of mRNAs and LncRNA between portal vein tumor thrombus tissues and paired tumor tissues in hapatocellular carcinoma |
|
