|
| Status |
Public on Dec 13, 2013 |
| Title |
Knockout mouse at 24 months, biological replicate 2 |
| Sample type |
RNA |
| |
|
| Source name |
Mouse IQ-GAP2 knockout liver at 24 months
|
| Organism |
Mus musculus |
| Characteristics |
strain/background: 129J
genotype: IQGAP2 knockout
gender: male
age: 24 months
tissue: hepatocellular carcinoma (HCC) tumor
|
| Treatment protocol |
At the age specified, mice were humanely euthanized in accordance with the institutional guidelines, their livers immediately excised and submerged in liquid nitrogen until total RNA isolation.
|
| Growth protocol |
Both IQGAP2 -/- and wild-type mouse lines were maintained on 129J background, fed regular diet, housed in pathogen-free rooms in an environment with controlled temperature, humidity, and a 12 h light/dark cycle. The study was approved by the Stony Brook University Institutional Animal Care and Use Committee.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
|
| Label |
Biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
|
| |
|
| Hybridization protocol |
Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45oC on Affymetrix Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
GeneChips were scanned using Affymetrix 7G scanner.
|
| Description |
Mouse-HCC_KO5
Gene expression data in HCC tumor in liver of 24-month-old IQGAP2 knockout mouse.
|
| Data processing |
The data were analyzed using R bioconductor Simpleaffy package based on Robust Multichip Average (RMA) method. Data were further converted to gene symbols by averaging over duplicated probes later.
|
| |
|
| Submission date |
May 05, 2013 |
| Last update date |
Dec 13, 2013 |
| Contact name |
Dmitri V GNATENKO |
| E-mail(s) |
dimitri.gnatenko@stonybrook.edu
|
| Phone |
631-444-1264
|
| Organization name |
Stony Brook University
|
| Department |
Medicine
|
| Street address |
T15/053 HSC SUNY
|
| City |
Stony Brook |
| State/province |
NY |
| ZIP/Postal code |
11794 |
| Country |
USA |
| |
|
| Platform ID |
GPL1261 |
| Series (1) |
| GSE46646 |
IQGAP2 knockout model of hepatocellular carcinoma |
|
