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Sample GSM937278 Query DataSets for GSM937278
Status Public on Feb 04, 2013
Title Patient-21-2a
Sample type RNA
 
Channel 1
Source name Prostate cancer metastasis
Organism Homo sapiens
Characteristics subject id: 21
sample id: 16068
tissue type: Prostate cancer metastasis
Growth protocol DNA was obtained from metastatic prostate cancer tissues from the PELICAN rapid autopsy program at Johns Hopkins University, and from normal prostate tissues from organ donors.
Extracted molecule total RNA
Extraction protocol TriZol extraction followed by RNeasy kit (Qiagen) clean-up with on-column DNase treatment
Label Cy5
Label protocol Agilent low RNA input linear amplification kit
 
Channel 2
Source name pooled reference
Organism Homo sapiens
Characteristics sample type: pooled reference
Growth protocol DNA was obtained from metastatic prostate cancer tissues from the PELICAN rapid autopsy program at Johns Hopkins University, and from normal prostate tissues from organ donors.
Extracted molecule total RNA
Extraction protocol TriZol extraction followed by RNeasy kit (Qiagen) clean-up with on-column DNase treatment
Label Cy3
Label protocol Agilent low RNA input linear amplification kit
 
 
Hybridization protocol Agilent Gene Expression Hybridization Kit using the manufacturer's protocol.
Scan protocol Microarrays are scanned with the Agilent G2565BA microarray scanner
Data processing The Bioconductor limma (v 3.10.3) was used to background correct (normexp model), loess and quantile normalize the data
 
Submission date May 25, 2012
Last update date Feb 04, 2013
Contact name Martin Aryee
E-mail(s) aryee.martin@mgh.harvard.edu
Organization name Massachusetts General Hospital
Department Pathology
Street address 149 13th Street
City Charlestown
State/province MA
ZIP/Postal code 02129
Country USA
 
Platform ID GPL4133
Series (2)
GSE38241 Gene expression profiling of normal prostates and prostate cancer metastases
GSE38242 DNA methylation alterations exhibit striking intra-individual stability and inter-individual heterogeneity across metastatic dissemination

Data table header descriptions
ID_REF
VALUE normalized log2 ratio (Cy5/Cy3) representing test/reference

Data table
ID_REF VALUE
1 -0.688567234
2 -0.021037132
3 0.081409794
4 0.020566625
5 0.041586889
6 -0.004500274
7 -0.03420289
8 0.08499028
9 0.003689937
10 0.080294024
11 0.031432406
12 0.054556581
13 -0.064261789
14 -0.163803494
15 -0.142140694
16 0.700239033
17 0.056330255
18 0.013393125
19 1.287132305
20 -0.086527361

Total number of rows: 45015

Table truncated, full table size 799 Kbytes.




Supplementary file Size Download File type/resource
GSM937278_jhu_251485045717_S01_1_2-16333_cy5-Mix-Ref_cy3.txt.gz 14.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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