|
Status |
Public on Jan 12, 2013 |
Title |
Patient Derived Xenograft LTL-412 |
Sample type |
genomic |
|
|
Channel 1 |
Source name |
LTL-412
|
Organism |
Homo sapiens |
Characteristics |
tissue: prostate cancer tumor patient source: Patient 1005 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 |
GPL10152 |
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 |
|