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Sample GSM194461 Query DataSets for GSM194461
Status Public on Jun 04, 2007
Title Human fetal liver replicate 3 of 3
Sample type RNA
 
Source name Clontech Human fetal liver
Organism Homo sapiens
Characteristics Human fetal liver
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 fetal liver replicate 3 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 85945.84708 82.61 P
100003 218.7022917 -2.07 P
100027 527.4946875 -1.42 P
100036 2398.958229 1.07 P
100037 23071.75583 24.63 P
100039 7800.685313 14.82 P
100044 275.7477083 -0.18 P
100045 506.1305208 -0.7 P
100051 265.5228125 -0.6 P
100052 171.38875 -2.52 P
100057 2685.336771 5.71 P
100058 101247.301 77.12 P
100060 2073.925104 2.34 P
100062 1262.092083 0.66 P
100064 735.3078125 2.6 P
100079 33847.51083 47.59 P
100089 9975.877396 18.89 P
100093 2537.01375 4.13 P
100095 576.2708333 -0.72 P
100100 27608.03219 64.16 P

Total number of rows: 32878

Table truncated, full table size 842 Kbytes.




Supplementary file Size Download File type/resource
GSM194461.txt.gz 297.6 Kb (ftp)(http) TXT
Processed data included within Sample table

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