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Sample GSM194478 Query DataSets for GSM194478
Status Public on Jun 04, 2007
Title Human prostate replicate 2 of 3
Sample type RNA
 
Source name Clontech Human prostate
Organism Homo sapiens
Characteristics Human prostate
Biomaterial provider Clontech
Extracted molecule total RNA
Extraction protocol Clontech's Total RNAs are prepared by the methods referenced in the following: Chomczynski & Sacchi (1987) Anal. Biochem. 162:156-159 Guanidinium thiocyanate method in Maniatis, Sambrook, J. et al (1989) Molecular Cloning: A Laboratory Manual, 2nd edition
Label Digoxigenin-UTP
Label protocol Digoxigenin-UTP-labeled cRNA was generated and linearly amplified from 1 µg of total RNA with three replicates per tissue, using the Applied Biosystems Chemiluminescent RT-IVT Labeling Kit v 2.0 and kit protocol.
 
Hybridization protocol Microarray hybridization, chemiluminescence detection, image acquisition, and analysis were performed on the on the Applied Biosystems 1700 Chemiluminescent Microarray Analyzer using the Applied Biosystems Chemiluminescence Detection Kit and kit protocol. Each microarray was pre-hybridized at 55oC for 1 hr in hybridization buffer with a blocking reagent. Next, 15 µg of labeled cRNA targets were fragmented by incubating them at 60oC for 30 min with fragmentation buffer and the internal control target (a 24-mer oligo labeled with the LIZ® fluorescent dye), and then hybridized to each microarray in a 1.5-mL volume at 55oC for 16 hr. After hybridization the arrays were washed with hybridization wash buffer and chemiluminescence rinse buffer. Enhanced chemiluminescent signals were generated by incubating the arrays with anti-digoxigenin-alkaline phosphatase and chemiluminescence enhancing solution, followed by chemiluminescence substrate.
Scan protocol Images from each microarray were collected on the Applied Biosystems 1700 Microarray Analyzer. The images were auto-gridded and the chemiluminescent signals were quantified, corrected for background and spot quality, and spatially normalized.
Description Human prostate replicate 2 of 3
Data processing Images were auto-gridded and the chemiluminescent signals were quantified, corrected for background, and finally, spot- and spatially-normalized using the Applied Biosystems 1700 Chemiluminescent Microarray Analyzer software. The raw data was globally normalized using quantle normalization.
 
Submission date May 25, 2007
Last update date May 25, 2007
Contact name Julie Blake
E-mail(s) blakejj@appliedbiosystems.com
Phone 706-855-0103
Fax 706-855-0103
Organization name Applied Biosystems
Department SDS/Arrays
Street address 850 Lincoln Centre Dr
City Foster City
State/province CA
ZIP/Postal code 94404
Country USA
 
Platform ID GPL2986
Series (1)
GSE7905 Whole genome survey of 32 Human Tissues

Data table header descriptions
ID_REF ProbeID
VALUE Quantile normalized signal intensity
S/N Signal-to-noise ratio. Used for probe detectability. A probe with S/N >=3 is generally considered detected. This threshold can be changed for a given experiment.
FLAG Quality flag of the feature spot. P indicates good spot, F indicates that the spot may have quantification issues

Data table
ID_REF VALUE S/N FLAG
100002 132468.857 84.25 P
100003 483.2077083 -0.68 P
100027 367.086875 1.35 P
100036 64380.72313 43.01 P
100037 16687.41438 22.48 P
100039 8957.006667 20.14 P
100044 249.1810417 -1.52 P
100045 294.7777083 -0.63 P
100051 307.6401563 -1.06 P
100052 1049.331979 2.01 P
100057 3127.645104 9.49 P
100058 59223.84667 76.87 P
100060 9164.359479 28.61 P
100062 504.1269792 0.85 P
100064 295.4279167 0.91 P
100079 43973.37969 44.63 P
100089 23827.36813 46.15 P
100093 20375.10521 36.48 P
100095 629.4970833 -0.14 P
100100 28732.13938 58.71 P

Total number of rows: 32878

Table truncated, full table size 842 Kbytes.




Supplementary file Size Download File type/resource
GSM194478.txt.gz 299.4 Kb (ftp)(http) TXT
Processed data included within Sample table

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