|
| Status |
Public on Sep 20, 2011 |
| Title |
Tumor sample 2 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Promega Mouse gDNA
|
| Organism |
Mus musculus |
| Characteristics |
reference: common reference DNA
|
| Treatment protocol |
Fourteen-day-old mice were given a single interperitoneal (i.p.) injection of diethylnitrosamine (DEN) dissolved in 0.9% saline at a dose of 20 mg/kg body weight. Mouse liver tissues were analyzed 6-months post-treatment for CGH analysis.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
1ug of each sample at approximately 200ng/ul concentration was used for labeling, hybridization and scanning.
|
| Label |
Cy3
|
| Label protocol |
1ug of genomic DNA digested with Alu I and Rsa I restriction enzymes at 37C for 2 hours. Enzymes were inactivated to stop the reaction by heating the mixture to 65C for 20 minutes. 5ul of Random Primers were added to 24ul of digested gDNA randomly primed at 95C for 3 minutes. 19ul of Cy3/Cy5 labeling master mix was added to each reaction for a final volume of 50ul, Cy3 and Cy5 modified nucleotides were then incorporated by Exo-Klenow fragment at 37C for 2 hours.
|
| |
|
| Channel 2 |
| Source name |
frozen liver tissue
|
| Organism |
Mus musculus |
| Characteristics |
strain: FVB;129
treatment: Genomic DNA from dissected mouse liver tumor
p53 status: KO
rb status: KO
|
| Treatment protocol |
Fourteen-day-old mice were given a single interperitoneal (i.p.) injection of diethylnitrosamine (DEN) dissolved in 0.9% saline at a dose of 20 mg/kg body weight. Mouse liver tissues were analyzed 6-months post-treatment for CGH analysis.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
1ug of each sample at approximately 200ng/ul concentration was used for labeling, hybridization and scanning.
|
| Label |
Cy5
|
| Label protocol |
1ug of genomic DNA digested with Alu I and Rsa I restriction enzymes at 37C for 2 hours. Enzymes were inactivated to stop the reaction by heating the mixture to 65C for 20 minutes. 5ul of Random Primers were added to 24ul of digested gDNA randomly primed at 95C for 3 minutes. 19ul of Cy3/Cy5 labeling master mix was added to each reaction for a final volume of 50ul, Cy3 and Cy5 modified nucleotides were then incorporated by Exo-Klenow fragment at 37C for 2 hours.
|
| |
|
| |
| Hybridization protocol |
Labeled DNA was hybridized to Agilent Mouse Genome 244A CGH Microarrays and arrays were washed according to the manufacturer's instructions.
|
| Scan protocol |
Microarrays were scanned with the Agilent Technologies Scanner G2505C at 5 micron resolution.
|
| Description |
FGC_251469517444_S01_CGH_105_Dec08.txt
|
| Data processing |
Data was extracted from imaged sample TIFF files using Agilent Feature Extraction v10.5.1.1 using the CGH_105_Dec08 extraction protocol.
|
| |
|
| Submission date |
Jun 08, 2011 |
| Last update date |
Sep 20, 2011 |
| Contact name |
Adam Ertel |
| Organization name |
Thomas Jefferson University
|
| Department |
Cancer Biology
|
| Lab |
BLSB 1009
|
| Street address |
233 S 10TH ST
|
| City |
PHILADELPHIA |
| State/province |
PA |
| ZIP/Postal code |
19107 |
| Country |
USA |
| |
|
| Platform ID |
GPL4092 |
| Series (2) |
| GSE24347 |
Gene expression profiles of mouse liver tissue harboring deletion of RB and/or p53, untreated or post-hepatocarcinogen treatment |
| GSE29847 |
Genomic profiles of mouse liver tissue harboring deletion of RB and/or p53, untreated or post-hepatocarcinogen treatment [CGH data] |
|
