|
| Status |
Public on Nov 14, 2013 |
| Title |
HCC 2 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
hepatocellular carcinoma (HCC)
|
| Organism |
Homo sapiens |
| Characteristics |
specimen group: hepatitis B virus [HBV]-related
tissue: liver
|
| Treatment protocol |
HCC and non-cancerous liver specimens were obtained from 17 patients with HCV-related HCC and 17 with HBV-related HCC who underwent surgical resection of the liver. For the control normal liver, a surgically obtained tissue sample from a patient who showed no clinical signs of hepatitis was used as described previously
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from liver biopsy or operated samples using an RNA extraction kit (Micro RNA Extraction Kit, Stratagene, La Jolla, CA, USA). Aliquots of total RNA (5 ug) were subjected to amplification with antisense RNA (aRNA) using a Message AmpTM aRNA kit (Ambion, Austin, TX, USA) as recommended by the manufacturer
|
| Label |
Cy5
|
| Label protocol |
As a reference for each microarray analysis, aRNA samples prepared from the normal liver tissue from one of the patients were used. Test RNA samples fluorescently labeled with cyanine (Cy) 5 and reference RNA labeled with Cy3 were used for microarray hybridization.
|
| |
|
| Channel 2 |
| Source name |
normal liver sample from a patient
|
| Organism |
Homo sapiens |
| Characteristics |
sample type: reference
tissue: liver
|
| Treatment protocol |
HCC and non-cancerous liver specimens were obtained from 17 patients with HCV-related HCC and 17 with HBV-related HCC who underwent surgical resection of the liver. For the control normal liver, a surgically obtained tissue sample from a patient who showed no clinical signs of hepatitis was used as described previously
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from liver biopsy or operated samples using an RNA extraction kit (Micro RNA Extraction Kit, Stratagene, La Jolla, CA, USA). Aliquots of total RNA (5 ug) were subjected to amplification with antisense RNA (aRNA) using a Message AmpTM aRNA kit (Ambion, Austin, TX, USA) as recommended by the manufacturer
|
| Label |
Cy3
|
| Label protocol |
As a reference for each microarray analysis, aRNA samples prepared from the normal liver tissue from one of the patients were used. Test RNA samples fluorescently labeled with cyanine (Cy) 5 and reference RNA labeled with Cy3 were used for microarray hybridization.
|
| |
|
| |
| Hybridization protocol |
according to Honda et al. Hepatology. 2006 Nov;44(5):1122-38, Honda M, et al. Gastroenterology. 2001 Mar;120(4):955-66.
|
| Scan protocol |
Quantitative assessment of the signals on the slides was carried out by scanning on a ScanArray 5000 (General Scanning, Watertown, MA, USA) followed by image analysis using GenePix Pro 4.1 (Axon Instruments, Union City, CA, USA).
|
| Description |
HBV well
|
| Data processing |
Because the levels of expression of some housekeeping genes were also changed, especially in advanced stages of liver disease, for the normalization of data we averaged intensities of all spots obtained with Cy3 and Cy5 in each of the 16 rectangles and adjusted intensity of each corrected DNA spot as the average intensity ratio Cy5/Cy3 = 1.0. This global normalization of intensity provided smaller variance of CyS/Cy3 ratio and almost equivalent results to normalization using the housekeeping genes [Honda et al. Hepatology. 2006 Nov;44(5):1122-38, Honda M, et al. Gastroenterology. 2001 Mar;120(4):955-66]. From the 9643 expression data, duplicated genes were averaged and final 8516 non redundant expression results were obtained.
|
| |
|
| Submission date |
Feb 05, 2013 |
| Last update date |
Nov 14, 2013 |
| Contact name |
Masao Honda |
| E-mail(s) |
mhondag@gmail.com
|
| Phone |
0762652243
|
| Organization name |
Kanazawa University
|
| Department |
Gastroenterology
|
| Street address |
Takara-Machi 13-1
|
| City |
Kanazawa |
| ZIP/Postal code |
920-8641 |
| Country |
Japan |
| |
|
| Platform ID |
GPL13536 |
| Series (1) |
| GSE44074 |
Gene expression profiling of hepatitis B- and hepatitis C-related hepatocellular carcinoma using graphical Gaussian modeling |
|
