|
| Status |
Public on Jan 01, 2015 |
| Title |
L_ANEU_4.6N |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
liposarcoma
|
| Organism |
Homo sapiens |
| Characteristics |
disease state: Well differentiated liposarcoma
|
| Growth protocol |
Tumor sample from a liposarcoma was flash frozen and stored at -80 C until processed for flow sorting
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Tumor was chipped from flash frozen samples. Nuclei were extracted then resuspended in the presence of 10mg/ml DAPI in NST buffer prior to sorting with an Influx flow cytometer equipped with a UV laser. The DNA from each flow sorted sample was extracted with QIAGEN QIAamp DNA Micro Kit according to the manufacturer's protocol.
|
| Label |
Cy-5
|
| Label protocol |
DNA was digested with DNaseI then labeled with Cy-5 dUTP and Cy-3 dUTP respectively, using a BioPrime labeling kit (Invitrogen, Carlsbad, CA) according to manufacturer's protocol.
|
| |
|
| Channel 2 |
| Source name |
Reference pooled 46XX
|
| Organism |
Homo sapiens |
| Characteristics |
disease state: Normal female genome
|
| Growth protocol |
Tumor sample from a liposarcoma was flash frozen and stored at -80 C until processed for flow sorting
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Tumor was chipped from flash frozen samples. Nuclei were extracted then resuspended in the presence of 10mg/ml DAPI in NST buffer prior to sorting with an Influx flow cytometer equipped with a UV laser. The DNA from each flow sorted sample was extracted with QIAGEN QIAamp DNA Micro Kit according to the manufacturer's protocol.
|
| Label |
Cy-3
|
| Label protocol |
DNA was digested with DNaseI then labeled with Cy-5 dUTP and Cy-3 dUTP respectively, using a BioPrime labeling kit (Invitrogen, Carlsbad, CA) according to manufacturer's protocol.
|
| |
|
| |
| Hybridization protocol |
Labeled DNA was hybridized without ozone scavenger and chips washed according to manufacture's protocol
|
| Scan protocol |
The arrays were scanned using an Agilent Technologies G2656C Scanner and default setting according to manufacturer's recommendation.
|
| Data processing |
Data was extracted from the TIFF files using default settings in Agilent FE 7.5. The data quality was assessed using the QC reports in FE 7.5.
|
| |
|
| Submission date |
Jun 06, 2013 |
| Last update date |
Jan 01, 2015 |
| Contact name |
Mitesh Borad |
| Organization name |
Mayo Clinic in Arizona
|
| Street address |
13400 E Shea Blvd
|
| City |
Scottsdale |
| State/province |
AZ |
| ZIP/Postal code |
85259 |
| Country |
USA |
| |
|
| Platform ID |
GPL9777 |
| Series (1) |
| GSE47701 |
Whole Genome Analysis of a Well-Differentiated Liposarcoma Reveals Novel SYT1 and DDR2 Rearrangements |
|
