|
| Status |
Public on Aug 24, 2009 |
| Title |
Waldenstrom's Macroglobulinemia sample MC4780_aCGH |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
DNA tumor sample
|
| Organism |
Homo sapiens |
| Characteristics |
Tissue: bone marrow
Age: 52
Gender: Male
Bone marrow involvement: 90%
Hemoglobin: 12.3g/dL
B2M: 2.2mg/L
Newly diagnosed: No
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA obtained using standard phenol chloroform extraction method
|
| Label |
Cy5
|
| Label protocol |
1ug of tumor and reference DNA were independently labeled with Agilent Genomic DNA labeling Kit PLUS as recommended by the manafacture. Cy5 dye was used to label tumor DNA samples and Cy3 to label reference DNA samples. Next, labeled genomic reactions were cleaned-up with Microcon YM-30 columns
|
| |
|
| Channel 2 |
| Source name |
Female reference DNA sample
|
| Organism |
Homo sapiens |
| Characteristics |
reference
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA obtained using standard phenol chloroform extraction method
|
| Label |
Cy3
|
| Label protocol |
1ug of tumor and reference DNA were independently labeled with Agilent Genomic DNA labeling Kit PLUS as recommended by the manafacture. Cy5 dye was used to label tumor DNA samples and Cy3 to label reference DNA samples. Next, labeled genomic reactions were cleaned-up with Microcon YM-30 columns
|
| |
|
| |
| Hybridization protocol |
Aliquouts of agilent Oligo aCGH hybridization kit were added to the samples as recommended by the manafacture. Samples were heat at 95C for 3 minutes, then 37C for 30 minutes. Samples were dispense in the arrays and hybridized at 65C for 40 hours in a hybrization oven at 20rpm.
|
| Scan protocol |
Scanned on DNA Microarray Scanner (Agilent Technologies).
Images were quantified using Agilent Feature Extraction Software (version 9.5).
|
| Description |
no additional information
|
| Data processing |
LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Agilent software was used.
|
| |
|
| Submission date |
Sep 05, 2008 |
| Last update date |
Aug 24, 2009 |
| Contact name |
Esteban Braggio |
| E-mail(s) |
braggio.esteban@mayo.edu
|
| Organization name |
Mayo Clinic Arizona
|
| Street address |
13400 E. Shea Blvd, MCCRB-300
|
| City |
Scottsdale |
| State/province |
AZ |
| ZIP/Postal code |
85259 |
| Country |
USA |
| |
|
| Platform ID |
GPL4091 |
| Series (1) |
| GSE12668 |
Waldenstrom's Macroglobulinemia patients: expression and aCGH data |
|
