|
| Status |
Public on Oct 05, 2012 |
| Title |
3208 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Spleen tumor DNA from AML mouse
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Spleen Tumor
pathology: Acute Myeloid Leukemia
strain: CBA
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Spleen tissues were flash-frozen in liquid nitrogen. Isolation of genomic DNA was peroformed using Dneasy Blood & tissue Kit from Qiagen according to the manufracturer's protocol. DNA quality and concentration was determined on the NanoDrop spectrophotometer.
|
| Label |
Cy3
|
| Label protocol |
Labeling reactions were prepared using the Roche NimbleGen Labeling Protocol for aCGH (Version 7.0). 1 μg of test DNA and reference DNA is labeled with Cyanine 5-Random Nonamers and Cyanine 3-Random Nonamers by Exo-Klenow fragment. Labeled DNA is then purified by isopropanol precipitation and the labeling efficiency determined by the NanoDrop spectrophotometer.
|
| |
|
| Channel 2 |
| Source name |
Input of CBA mouse DNA from Jackson's Lab
|
| Organism |
Mus musculus |
| Characteristics |
strain: CBA
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Spleen tissues were flash-frozen in liquid nitrogen. Isolation of genomic DNA was peroformed using Dneasy Blood & tissue Kit from Qiagen according to the manufracturer's protocol. DNA quality and concentration was determined on the NanoDrop spectrophotometer.
|
| Label |
Cy5
|
| Label protocol |
Labeling reactions were prepared using the Roche NimbleGen Labeling Protocol for aCGH (Version 7.0). 1 μg of test DNA and reference DNA is labeled with Cyanine 5-Random Nonamers and Cyanine 3-Random Nonamers by Exo-Klenow fragment. Labeled DNA is then purified by isopropanol precipitation and the labeling efficiency determined by the NanoDrop spectrophotometer.
|
| |
|
| |
| Hybridization protocol |
31 μg of the labeled DNA is prepared for hybridization and placed on the human or mouse 720K whole genome array and hybridized at 42ºC for ~72 hours using a Maui hybridization system.
|
| Scan protocol |
The arrays are washed and scanned at 2 μM resolution on a NimbleGen MS 200 High Resolution Scanner.
|
| Description |
Radiation-induced AML mouse vs normal CBA mouse
|
| Data processing |
Data was processed through NimbleScan 2.6 with default settings. Data was analyzed as Cy5 vs Cy3
|
| |
|
| Submission date |
Apr 13, 2012 |
| Last update date |
Oct 05, 2012 |
| Contact name |
Lianghao Ding |
| E-mail(s) |
lianghao.ding@utsouthwestern.edu
|
| Phone |
214-648-5892
|
| Organization name |
UT Southwestern Medical Center
|
| Street address |
5323 Harry Hines Blvd
|
| City |
Dallas |
| State/province |
TX |
| ZIP/Postal code |
75390 |
| Country |
USA |
| |
|
| Platform ID |
GPL10989 |
| Series (1) |
| GSE37233 |
DNA copy number analysis from mice with radiation-induced acute myeloid leukemia |
|
