|
| Status |
Public on Nov 01, 2015 |
| Title |
5111_Tumor |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Liver tumor from a male mouse treated with DEN+CCl11
|
| Organism |
Mus musculus |
| Characteristics |
tissue: liver tumor
strain: B6C3F1
Sex: male
|
| Treatment protocol |
At 2 weeks of age, mice were injected i.p. with DEN (1mg/kg) in sterile saline (15 µl/g). At 8 weeks of age (6 weeks after a single injection of DEN or vehicle as detailed above), and were injected i.p. twice weekly with CCl4 (0.2ml/kg) diluted in olive oil vehicle for 14 additional weeks. Mice were maintained on animal chow with free access to food/water for the duration of the study. Vehicle-control mice were injected with sterile saline and olive oil vehicles in place of DEN and CCl4, respectively. Liver tumors were separated at the time of sacrifice, and both tumor and non-tumor tissues were flash frozen in liquid nitrogen
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Total DNA was extracted using a Qiagen DNEasy kit according to the manufacturer's instructions
|
| Label |
Cy5
|
| Label protocol |
Genomic DNA (minimum 500ng) from samples (reference and samples) were digested by restrict enzymes (Alu I and Rsa I). The fragmented DNA was labeled with either Cy3-dUTP or Cy5-dUTP, amplified with Exo(-) Klenow, and purified.
|
| |
|
| Channel 2 |
| Source name |
pooled DNA from normal liver from vehicle-control mice
|
| Organism |
Mus musculus |
| Characteristics |
tissue: liver
strain: B6C3F1
Sex: male
|
| Treatment protocol |
At 2 weeks of age, mice were injected i.p. with DEN (1mg/kg) in sterile saline (15 µl/g). At 8 weeks of age (6 weeks after a single injection of DEN or vehicle as detailed above), and were injected i.p. twice weekly with CCl4 (0.2ml/kg) diluted in olive oil vehicle for 14 additional weeks. Mice were maintained on animal chow with free access to food/water for the duration of the study. Vehicle-control mice were injected with sterile saline and olive oil vehicles in place of DEN and CCl4, respectively. Liver tumors were separated at the time of sacrifice, and both tumor and non-tumor tissues were flash frozen in liquid nitrogen
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Total DNA was extracted using a Qiagen DNEasy kit according to the manufacturer's instructions
|
| Label |
Cy3
|
| Label protocol |
Genomic DNA (minimum 500ng) from samples (reference and samples) were digested by restrict enzymes (Alu I and Rsa I). The fragmented DNA was labeled with either Cy3-dUTP or Cy5-dUTP, amplified with Exo(-) Klenow, and purified.
|
| |
|
| |
| Hybridization protocol |
Equal amounts (minimum 3500 ng) of Cy3-labeled reference DNA and Cy5-labeled sample DNA were hybridized on the same array (Agilent 4x44K CGH microarray), hybridized and washed according to the manufacturer's (Agilent) protocol.
|
| Scan protocol |
The signals from both Cy3 and Cy5 on the hybridized array were detected by laser scanner (Agilent G2565 Series scanner Model C).
|
| Description |
biological replicate 11 of 26
|
| Data processing |
The images were converted to digital data by Agilent Feature Extraction Software (v 8.5.1.1). Samples underwent background subtraction and LOWESS normalization.
|
| |
|
| Submission date |
Aug 07, 2015 |
| Last update date |
Nov 01, 2015 |
| Contact name |
Grace Chappell |
| E-mail(s) |
gchappell@toxstrategies.com
|
| Organization name |
ToxStrategies, Inc.
|
| Department |
Health Sciences
|
| Street address |
9390 Research Blvd, Bldg 2, Ste. #100
|
| City |
Austin |
| State/province |
TX |
| ZIP/Postal code |
78723 |
| Country |
USA |
| |
|
| Platform ID |
GPL10449 |
| Series (1) |
| GSE71849 |
Mouse frozen liver: vehicle-control vs. CCl4+DEN treated |
|
