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Sample GSM194481 Query DataSets for GSM194481
Status Public on Jun 04, 2007
Title Human skeletal muscle replicate 2 of 3
Sample type RNA
 
Source name Clontech Human skeletal muscle
Organism Homo sapiens
Characteristics Human skeletal muscle
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 skeletal muscle 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 47606.38021 46.56 P
100003 256.2611458 -0.45 P
100027 666.8573958 2.55 P
100036 23612.78771 23.58 P
100037 16286.44573 15.66 P
100039 9344.605833 16.29 P
100044 272.7360417 -0.33 P
100045 546.1839583 -0.64 P
100051 275.7697917 0.91 P
100052 657.8064583 1.48 P
100057 915.6714583 0.07 P
100058 266345.1141 90.05 P
100060 3504.079479 2.95 P
100062 1069.713125 0.13 P
100064 404.7117708 0.8 P
100079 30423.03719 66.98 P
100089 15877.33542 26.73 P
100093 3179.019479 5.73 P
100095 417.4569792 -0.78 P
100100 19130.18281 51.78 P

Total number of rows: 32878

Table truncated, full table size 841 Kbytes.




Supplementary file Size Download File type/resource
GSM194481.txt.gz 295.0 Kb (ftp)(http) TXT
Processed data included within Sample table

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