|
| Status |
Public on Dec 06, 2012 |
| Title |
Uveal melanoma from enucleation 35 [UCSF] |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Uveal melanoma from enucleation 35
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Fresh frozen sample from enucleated eye
disease: Primary uveal melanoma tumor
gep class: 1
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was prepared using the Wizard Genomic DNA purification kit (Promega).
|
| Label |
Cy3
|
| Label protocol |
1μg of reference and test sample genomic DNA were individually fluorescently labeled using the BioPrime DNA Labeling System following manufacturer's protocol.
|
| |
|
| Channel 2 |
| Source name |
Normal Human Male Reference DNA
|
| Organism |
Homo sapiens |
| Characteristics |
reference: Normal Human Male Reference DNA
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was prepared using the Wizard Genomic DNA purification kit (Promega).
|
| Label |
Cy5
|
| Label protocol |
1μg of reference and test sample genomic DNA were individually fluorescently labeled using the BioPrime DNA Labeling System following manufacturer's protocol.
|
| |
|
| |
| Hybridization protocol |
DNA was hybridized to the arrays at 37 °C for over 16-72 h in 50% formamide, 2 x SSC, 10% dextran sulfate, 4% SDS and 500 μg yeast tRNA, pH 7.
|
| Scan protocol |
16 bit 1024x1024 pixel DAPI, Cy3 (test) and Cy5 (control) images using a custom built CCD camera system.
“UCSF SPOT” software was used to automatically analyze the spots based on the DAPI images, and to calculate log2ratios of the total integrated Cy3 and Cy5 intensities for each spot.
|
| Data processing |
SPROC software was used to reject data based on low reference/DAPI signal intensity and low correlation of the Cy3 and Cy5 intensities with a spot.
|
| |
|
| Submission date |
Dec 05, 2012 |
| Last update date |
Dec 06, 2012 |
| Contact name |
Michael D Onken |
| Organization name |
Washington University School of Medicine
|
| Department |
Biochemistry & Molecular Biophysics
|
| Lab |
Box 8231
|
| Street address |
660 S. Euclid Ave
|
| City |
Saint Louis |
| State/province |
MO |
| ZIP/Postal code |
63110 |
| Country |
USA |
| |
|
| Platform ID |
GPL4420 |
| Series (2) |
| GSE42739 |
Chromosomal changes in primary human uveal melanomas [UCSF] |
| GSE42740 |
Chromosomal changes in primary human uveal melanomas |
|
