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Sample GSM702536 Query DataSets for GSM702536
Status Public on Aug 29, 2011
Title prostate cancer_sample_7 [aCGH]
Sample type genomic
 
Channel 1
Source name prostate cancer_recurrence, castration-resistant
Organism Homo sapiens
Characteristics disease state: Castration-resistant prostate cancer
treatment: Casodex, Suprefact
tissue: prostate cancer tumor
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted from the samples after overnight proteinase K treatment using standard protocols.
Label Cy5
Label protocol 12 µg of genomic DNA was digested overnight with AluI and RsaI, followed by standard phenol-chloroform purification. 3 µg of digested tumor DNA and reference DNA was labeled with Cy5-dUTP and Cy3-dUTP (PerkinElmer, Waltham, MA), respectively, in a random priming reaction using Bioprime Array CGH Genomic Labeling Module (Invitrogen).
 
Channel 2
Source name Male genomic DNA, Promega, Cat# G1471
Organism Homo sapiens
Characteristics reference: Promega normal male genomic DNA
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted from the samples after overnight proteinase K treatment using standard protocols.
Label Cy3
Label protocol 12 µg of genomic DNA was digested overnight with AluI and RsaI, followed by standard phenol-chloroform purification. 3 µg of digested tumor DNA and reference DNA was labeled with Cy5-dUTP and Cy3-dUTP (PerkinElmer, Waltham, MA), respectively, in a random priming reaction using Bioprime Array CGH Genomic Labeling Module (Invitrogen).
 
 
Hybridization protocol Hybridization was performed according to the protocol (oligonucleotide array-based CGH for genomic DNA analysis, protocol version 2.0, August 2005, Agilent Technologies).
Scan protocol Arrays were scanned with a laser confocal scanner (Agilent Technologies).
Data processing Feature Extraction software (version 8.1.1.1, Agilent Technologies) was used for image analysis using manufacturer’s recommended settings (44K_CGH_0605).
 
Submission date Apr 06, 2011
Last update date Aug 29, 2011
Contact name Maija K Wolf
E-mail(s) maija.wolf@helsinki.fi
Organization name Institute for Molecular Medicine Finland (FIMM)
Street address Biomedicum Helsinki 2U, Tukholmankatu 8,
City Helsinki
ZIP/Postal code FIN-00290
Country Finland
 
Platform ID GPL2879
Series (1)
GSE28403 Integrative genomic, transcriptomic and RNAi analysis indicates a potential oncogenic role for FAM110B in castration-resistant prostate cancer.

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

Data table
ID_REF VALUE
1 7.455498799e-002
2 0.000000000e+000
3 2.181115847e-002
4 -3.673105825e-002
5 1.358441025e-002
6 1.025925951e-001
7 -1.634026172e-001
8 7.886456042e-002
9 3.790703775e-003
10 -1.317880349e-001
11 -5.271483942e-002
12 -7.942244293e-002
13 -2.020925786e-001
14 1.409414392e-001
15 1.742674928e-001
16 -1.215955028e-001
17 2.265867355e-002
18 5.100914597e-002
19 -4.257298351e-002
20 -1.023470660e-001

Total number of rows: 43890

Table truncated, full table size 996 Kbytes.




Supplementary file Size Download File type/resource
GSM702536_140905_251328213001_S01.txt.gz 11.2 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data provided as supplementary file

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