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Sample GSM1327950 Query DataSets for GSM1327950
Status Public on Jul 21, 2014
Title T19_518LP
Sample type genomic
 
Channel 1
Source name Prostate Tumor
Organism Homo sapiens
Characteristics sample origin: Clinical Patient
tissue type: Tumor
patient age at diagnosis (yrs): 53
gleason score: 8 (4+4)
psa at diagnosis: 7.7
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 8
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

Data table header descriptions
ID_REF
VALUE normalized log10 ratio Cy5/Cy3

Data table
ID_REF VALUE
1 -1.032145460e-002
2 0.000000000e+000
3 0.000000000e+000
4 0.000000000e+000
5 0.000000000e+000
6 0.000000000e+000
7 0.000000000e+000
8 0.000000000e+000
9 0.000000000e+000
10 0.000000000e+000
11 0.000000000e+000
12 0.000000000e+000
13 0.000000000e+000
14 0.000000000e+000
15 0.000000000e+000
16 0.000000000e+000
17 0.000000000e+000
18 0.000000000e+000
19 0.000000000e+000
20 0.000000000e+000

Total number of rows: 180880

Table truncated, full table size 4217 Kbytes.




Supplementary file Size Download File type/resource
GSM1327950_518LP_US09503746_252206026837_S01_CGH_1100_Jul11_1_1.txt.gz 18.7 Mb (ftp)(http) TXT
Processed data included within Sample table

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