|
| Status |
Public on Aug 29, 2017 |
| Title |
HCC_HBV Tg mouse_18M_rep5 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
HCC, HBV Tg mouse, 18M
|
| Organism |
Mus musculus |
| Characteristics |
duration: 18 months
tissue: Hepatocellular carcinoma
strain: B10D2 (H-2d)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from snap-frozen hepatic parenchyma and HCC tissues. Total RNA was resuspended in DEPC water, cleaned up with a Qiagen RNeasy column, and quantified by UV-Vis spectroscopy.
|
| Label |
Cy5
|
| Label protocol |
One ug of total RNA from control and experimental animals was separately amplified and labeled with either Cy3- or Cy5-labeled CTP (Perkin Elmer, Wellesley, MA, USA) with an Agilent low input linear amplification kit (Agilent Technologies, Palo Alto, CA, USA) according to the manufacturer’s protocol.
|
| |
|
| Channel 2 |
| Source name |
Unmanipulated 7-month-old control Tg liver mixture
|
| Organism |
Mus musculus |
| Characteristics |
age: 7 months
tissue: Liver
strain: B10D2 (H-2d)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from snap-frozen hepatic parenchyma and HCC tissues. Total RNA was resuspended in DEPC water, cleaned up with a Qiagen RNeasy column, and quantified by UV-Vis spectroscopy.
|
| Label |
Cy3
|
| Label protocol |
One ug of total RNA from control and experimental animals was separately amplified and labeled with either Cy3- or Cy5-labeled CTP (Perkin Elmer, Wellesley, MA, USA) with an Agilent low input linear amplification kit (Agilent Technologies, Palo Alto, CA, USA) according to the manufacturer’s protocol.
|
| |
|
| |
| Hybridization protocol |
Samples (0.75 ug each) of Cy3- and Cy5-labeled targets were combined and hybridized to an Agilent catalog 44K feature mouse oligo array for 17 h at 60°C. In each assay, a hepatic RNA sample from an experimental animal was hybridized against a pooled RNA sample composed of equal amounts of RNA from the livers of five unmanipulated 7-month-old control Tg liver mixture.
|
| Scan protocol |
Data were extracted from the resulting images using Agilent's Feature Extraction Software (Agilent Technologies).
|
| Description |
Biological replicate 5 of 5.
|
| Data processing |
Expression analysis for all replicate microarray experiments was performed with GeneSpring GX, where its expression ratio (experiment group = Cy5 / control group = Cy3) was calculated and converted using the base two logarithm.
If flags (gIsPosAndSignif, rIsPosAndSignif, gIsWellAboveBG, or rIsWellAboveBG), indicating as reliable fluorescence probes, were 0, those probes were eliminated from the obtained data as well as probes with 1 or -1 in ControlType. For the logarithm ratio of each chronological sample in the unmanipulated control Tg mix, two color microarray analysis was performed by setting the samples with log2 ratios of 0. False Discovery Rate (FDR) with Welch P-values and RankProd FDR were respectively corrected for multiple testing with Benjamin-Hochberg (BH) procedure and RankProduct. While Welch P-values were calculated from TM4 MeV_4_6_1, R was used for RankProduct FDR.
|
| |
|
| Submission date |
Aug 28, 2017 |
| Last update date |
Jan 23, 2018 |
| Contact name |
Takuto Nosaka |
| E-mail(s) |
[email protected]
|
| Phone |
+81-776-61-8351
|
| Organization name |
University of Fukui
|
| Department |
Second Department of Internal Medicine
|
| Street address |
23-3 Matsuoka, Eiheiji-cho
|
| City |
Yoshida-gun |
| State/province |
Fukui |
| ZIP/Postal code |
910-1193 |
| Country |
Japan |
| |
|
| Platform ID |
GPL2872 |
| Series (1) |
| GSE103205 |
Gene expression profiling of hepatocarcinogenesis in a mouse model of chronic hepatitis B |
|
