|
| Status |
Public on Jan 12, 2013 |
| Title |
Patient Derived Xenograft LTL-370 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
LTL-370
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: prostate cancer tumor
patient source: Patient 972
tumor foci: Patient Derived Xenograft
host genetic background: NOD/SCID
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA extracted with Promega Wizard Genomic DNA Extraction Kit
|
| Label |
Cy5
|
| Label protocol |
500ng gDNA labeled by following NimbleGen Arrays User’s Guide: CGH Analysis v5.0, which included a 98C heat fragmentation step and labeling with Cy-labeled random nanomers (TriLink Biotechnologies) and Klenow 3'-5'exo-(New England Biolabs).
|
| |
|
| Channel 2 |
| Source name |
male reference DNA (Promega Corp)
|
| Organism |
Homo sapiens |
| Characteristics |
sample type: male reference DNA (Promega Corp)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA extracted with Promega Wizard Genomic DNA Extraction Kit
|
| Label |
Cy3
|
| Label protocol |
500ng gDNA labeled by following NimbleGen Arrays User’s Guide: CGH Analysis v5.0, which included a 98C heat fragmentation step and labeling with Cy-labeled random nanomers (TriLink Biotechnologies) and Klenow 3'-5'exo-(New England Biolabs).
|
| |
|
| |
| Hybridization protocol |
5ug of Cy5-labeled sample was combined with 5ug of Cy3-labeled male reference, and samples were hybridized and washed by following Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis Protocol v6.2 on on Agilent SurePrint G3 Human Catalog CGH 8x60K (Design ID 021924) or SurePrint G3 Human Catalog CGH 4x180K (Design ID 022060)
|
| Scan protocol |
scanned at a 3um scan resolution and 20 bit tiff file setting on the Agilent DNA Microarray Scanner G2505C
|
| Data processing |
quantified signal intensities and pre-processed data with Agilent Feature Extraction 10.5.1.1
FE files loaded into Nexus Copy Number Software v.6 (Biodiscovery Inc.) for analysis.
|
| |
|
| Submission date |
Sep 27, 2012 |
| Last update date |
Jan 12, 2013 |
| Contact name |
Shawn Anderson |
| E-mail(s) |
Sanderson@prostatecentre.com
|
| Organization name |
Vancouver Prostate Centre
|
| Lab |
Laboratory for Advanced Genome Analysis
|
| Street address |
2660 Oak Street
|
| City |
Vancouver |
| State/province |
BC |
| ZIP/Postal code |
V6H3Z6 |
| Country |
Canada |
| |
|
| Platform ID |
GPL10123 |
| Series (2) |
| GSE41188 |
High fidelity patient-derived xenografts for accelerating prostate cancer discovery and drug development (aCGH) |
| GSE41193 |
High fidelity patient-derived xenografts for accelerating prostate cancer discovery and drug development |
|
