|
| Status |
Public on Dec 21, 2023 |
| Title |
HCC_rep16 |
| Sample type |
RNA |
| |
|
| Source name |
HCC,liver,replicate 16
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: hepatocallular carcinoma
tissue: liver
gender: female
age(yrs): 61
|
| Treatment protocol |
Twenty-four samples were surgically resected from hepatocallular carcinoma and twenty-four samples of chronic hepatitis type C were obtained by fine needle biopsy
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was prepared using the mirVana miRNA isolation kit (Ambion) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-2000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
|
| Label |
Cy3
|
| Label protocol |
Cyanine-3 (Cy3) labeled cRNA was prepared from 0.075 ug RNA using the Low Input Quick Amp Labeling Kit, One-color (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.
|
| |
|
| Hybridization protocol |
0.6 ug of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Hmn GE 8x60K Microarray (G4851A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.
|
| Scan protocol |
Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3 um, Dye channel is set to Green and Green PMT is set to 100%).
|
| Description |
Gene expression in liver of HCC patient
|
| Data processing |
The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 028004_D_F_20120411) to obtain background subtracted and spatially to detrend Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
|
| |
|
| Submission date |
Mar 12, 2013 |
| Last update date |
Dec 21, 2023 |
| Contact name |
Y-H. Taguchi |
| E-mail(s) |
tag@granular.com
|
| Phone |
+81-3-3817-1791
|
| Organization name |
Chuo University
|
| Department |
Physics
|
| Street address |
1-13-27 Kasuga,Bukyo-ku
|
| City |
Tokyo |
| State/province |
Non-US/Canada |
| ZIP/Postal code |
112-8551 |
| Country |
Japan |
| |
|
| Platform ID |
GPL13607 |
| Series (1) |
| GSE45032 |
Gene expression in liver of HCC and CHC patients |
|
