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Sample GSM296765 Query DataSets for GSM296765
Status Public on Jun 01, 2009
Title Cancer stroma, slide 9539, sample 2
Sample type RNA
 
Channel 1
Source name prostate cancer-associated stroma
Organism Homo sapiens
Characteristics grade 3 reactive stroma prostate cancer tissues
Extracted molecule total RNA
Extraction protocol Trizol extraction of total RNA was performed according to the manufacturer's instructions. Microarray analysis was performed using 2.5 micrograms of total RNA.
Label Alexa Fluor 647
Label protocol Complementary DNA (cDNA) reverse transcription and fluorescent labeling reactions were carried out using SuperScript Plus Direct cDNA Labeling system (Invitrogen, Carlsbad, CA).
 
Channel 2
Source name human, universal reference RNA
Organism Homo sapiens
Characteristics Stratagene, Universal Human Reference RNA Catalog #740000
Extracted molecule total RNA
Extraction protocol Trizol extraction of total RNA was performed according to the manufacturer's instructions. Microarray analysis was performed using 2.5 micrograms of total RNA.
Label Alexa Fluor 555
Label protocol Complementary DNA (cDNA) reverse transcription and fluorescent labeling reactions were carried out using SuperScript Plus Direct cDNA Labeling system (Invitrogen, Carlsbad, CA).
 
 
Hybridization protocol The sample and reference probes were mixed with GEx hybridization buffer and blocking solution (Agilent, Santa Clara, CA) and denatured by a 2-minute incubation at 95 degC. Probes were hybridized to Agilent 4x44K Whole Human Genome arrays and rotating over night at 65 degC.
Scan protocol Slide were scanned in an Agilent Microarray Scanner and the data were analyzed using Agilent Feature Extraction Software (v.9.1).
Description human grade 3 reactive stroma prostate cancer tissues, compared to universal reference RNA
Data processing LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Agilent and Bioconductor software was used.
 
Submission date Jun 04, 2008
Last update date Jan 16, 2009
Contact name Chad Creighton
E-mail(s) creighto@bcm.tmc.edu
Organization name Baylor College of Medicine
Department Biostatistics, Ducan Cancer Center
Street address One Baylor Plaza, Mail Stop: BCM305
City Houston
State/province TX
ZIP/Postal code 77030
Country USA
 
Platform ID GPL4133
Series (1)
GSE11682 Gene expression profiles of reactive stroma in prostate cancer

Data table header descriptions
ID_REF
VALUE signal' a measure of the ratio of transcript abundance of the sample versus a universal RNA reference.

Data table
ID_REF VALUE
1 5.551286963
2 0.680778391
3 0.132469317
4 0.01433094
5 -0.021651867
6 0.083567555
7 0.170599749
8 0.178588205
9 0.056140895
10 0.13753417
11 0.127528386
12 0.072519706
13 0.073965695
14 0.030256872
15 -0.030069422
16 -0.110093675
17 0.080067253
18 0.015977974
19 2.299184414
20 0.451535119

Total number of rows: 45015

Table truncated, full table size 798 Kbytes.




Supplementary file Size Download File type/resource
GSM296765.txt.gz 12.4 Mb (ftp)(http) TXT
Processed data included within Sample table

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