|
| Status |
Public on Sep 10, 2014 |
| Title |
Eµ-myc lymphoma 52 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Cluster 2 lymphoma
|
| Organism |
Mus musculus |
| Characteristics |
genotype/variation: Eµ-myc
tissue type: lymphoma tumor
|
| Treatment protocol |
N/A
|
| Growth protocol |
N/A
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA (gDNA) was extracted from flash frozen lymphoma pieces and normal tail tissue from background strain mice. Lymphoma tissue was homogenized with a mortar and pestle and then sonicated, and DNA was extracted with the DNeasy Blood and Tissue Kit (Qiagen). Tail tissue was digested, and DNA was extracted with isopropanol and subsequently cleaned up with the DNeasy Blood and Tissue Kit.
|
| Label |
Cy3
|
| Label protocol |
1.5 ug of gDNA was fragmented and labeled with ULS-Cy3 for lymphoma gDNA or ULS-Cy5 for reference gDNA (Agilent Genomic DNA ULS Labeling Kit) per the manufacturer’s instructions.
|
| |
|
| Channel 2 |
| Source name |
normal tail tissue from background strain mice
|
| Organism |
Mus musculus |
| Characteristics |
genotype/variation: normal background
tissue type: tail
|
| Treatment protocol |
N/A
|
| Growth protocol |
N/A
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA (gDNA) was extracted from flash frozen lymphoma pieces and normal tail tissue from background strain mice. Lymphoma tissue was homogenized with a mortar and pestle and then sonicated, and DNA was extracted with the DNeasy Blood and Tissue Kit (Qiagen). Tail tissue was digested, and DNA was extracted with isopropanol and subsequently cleaned up with the DNeasy Blood and Tissue Kit.
|
| Label |
Cy5
|
| Label protocol |
1.5 ug of gDNA was fragmented and labeled with ULS-Cy3 for lymphoma gDNA or ULS-Cy5 for reference gDNA (Agilent Genomic DNA ULS Labeling Kit) per the manufacturer’s instructions.
|
| |
|
| |
| Hybridization protocol |
After removing excess labeling dye, the gDNA was hybridized to Agilent Mouse Genome CGH Microarray 1x244K slides.
|
| Scan protocol |
The microarray slides were scanned using an Agilent G2565CA Microarray Scanner.
|
| Description |
harvested lymphoma tumor DNA
|
| Data processing |
Copy number changes (log2 ratio of Cy3 to Cy5) are called using Agilent Genomic Workbench 5.0.
Log2 ratio cut-offs were 0.2 for amplification, 0.85 for high amplification (≥ 2 copies), -0.2 for deletion, and -2 for homozygous deletion.
|
| |
|
| Submission date |
Sep 10, 2012 |
| Last update date |
Sep 10, 2014 |
| Contact name |
Daphne R Friedman |
| E-mail(s) |
daphne.friedman@duke.edu
|
| Organization name |
Duke University Medical Center
|
| Street address |
101 Science Drive, Room 2121, CIEMAS Bldg
|
| City |
Durham |
| State/province |
NC |
| ZIP/Postal code |
27708 |
| Country |
USA |
| |
|
| Platform ID |
GPL15076 |
| Series (2) |
| GSE40759 |
Transgenic Eµ-myc mouse lymphoma array CGH data |
| GSE40760 |
The Eµ-myc Mouse Model Represents Heterogeneity Across Human Aggressive B-cell Lymphomas |
|
