|
| Status |
Public on Jul 21, 2014 |
| Title |
LTL311 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Prostate Tumor
|
| Organism |
Homo sapiens |
| Characteristics |
sample origin: Patient Derived Xenograft
tissue type: Tumor
patient age at diagnosis (yrs): NA
gleason score: NA
psa at diagnosis: NA
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA extracted with Promega Wizard Genomic DNA Extraction Kit
|
| Label |
Cyanine-5
|
| 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: reference DNA
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA extracted with Promega Wizard Genomic DNA Extraction Kit
|
| Label |
Cyanine-3
|
| 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
|
| Description |
4 x 180
Sample 28
|
| 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.7 (Biodiscovery Inc.) for analysis.
CGH data was processed using BioDiscovery’s FASST2 Segmentation Algorithm to estimate copy number state. These state values are then used to make calls based on a log-ratio threshold. The significance threshold for segmentation was set at 5.0E-6 also requiring a minimum of 3 probes per segment and a maximum probe spacing of 1000 between adjacent probes before breaking a segment. The log ratio thresholds for single copy gain and single copy loss were set at 0.2 and -0.23, respectively. The log ratio thresholds for two or more copy gain and homozygous loss were set at 1.14 and -1.1 respectively. Upon loading of raw data files, signal intensities are normalized via division by mean. All samples are corrected for GC wave content using a systematic correction algorithm.
|
| |
|
| Submission date |
Feb 13, 2014 |
| Last update date |
Jul 21, 2014 |
| 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 (1) |
| GSE55016 |
Heterogeneity in the inter-tumor transcriptome of high risk prostate cancer |
|
