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Sample GSM525577 Query DataSets for GSM525577
Status Public on Jun 24, 2010
Title Prostate tumor PCA0003 (aCGH)
Sample type genomic
 
Channel 1
Source name tumor DNA
Organism Homo sapiens
Characteristics sample id: PCA0003
tissue: prostate
disease status: prostate cancer
tumor type: Primary tumor
biopsy_gleason_grade: 7
clint_stage: T2B
pathological_stage: T3A
Extracted molecule genomic DNA
Extraction protocol Genome DNA was extracted from all samples with standard proteinase K digestion and phenol/chloroform extraction.
Label Cy5
Label protocol Bioprime Array CHG labeling kit (Invitrogen) using Cy3/Cy5
 
Channel 2
Source name adjacent normal prostate DNA
Organism Homo sapiens
Characteristics tissue: prostate
disease status: normal
Extracted molecule genomic DNA
Extraction protocol Genome DNA was extracted from all samples with standard proteinase K digestion and phenol/chloroform extraction.
Label Cy3
Label protocol Bioprime Array CHG labeling kit (Invitrogen) using Cy3/Cy5
 
 
Hybridization protocol Per manufacturer's instructions
Scan protocol Per manufacturer's instructions
Description DNA copy number
Data processing Images quantified with Agilent Feature Extraction ver9.1. Probe sequences were re-mapped to the hg18 build of the human genome and merged. Probe-level data was subsequently normalized for local GC content with a two-stage LOESS fit. Probe-level data is the log2 ratio of tumor-to-normal.
 
Submission date Mar 24, 2010
Last update date Jun 15, 2010
Contact name Barry Stephen Taylor
Organization name Memorial Sloan-Kettering Cancer Center
Street address 1275 York Avenue, Box #460
City New York
State/province NY
ZIP/Postal code 10065
Country USA
 
Platform ID GPL4091
Series (2)
GSE21032 Integrative genomic profiling of human prostate cancer
GSE21035 Agilent 244K aCGH data for human primary and metastatic prostate cancer samples

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

Data table
ID_REF VALUE
1 1.480385521e-002
2 -3.951325750e-001
3 0.000000000e+000
4 2.685635019e-002
5 -9.519690151e-002
6 -9.402564539e-002
7 2.141993982e-002
8 1.032146836e-002
9 7.810299063e-002
10 2.281045480e-002
11 1.545095369e-002
12 2.868826041e-003
13 -8.773698798e-002
14 5.199703749e-002
15 8.630019396e-003
16 -1.379776733e-001
17 -3.027883708e-002
18 -9.153573744e-002
19 -1.399119818e-001
20 7.083710695e-002

Total number of rows: 243430

Table truncated, full table size 5711 Kbytes.




Supplementary file Size Download File type/resource
GSM525577.txt.gz 60.9 Mb (ftp)(http) TXT
Processed data included within Sample table
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