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Sample GSM161140 Query DataSets for GSM161140
Status Public on Feb 12, 2008
Title 7GRp_Blood_PNA_noHRT
Sample type RNA
 
Source name blood samples in PAXgene, globin reduction using PNA, no HRT user
Organism Homo sapiens
Characteristics postmenopausal women
Extracted molecule total RNA
Extraction protocol PAXgene Blood RNA Kit (PreAnalytiX, Hombrechtikon, Switzerland)
Label digoxigenin
Label protocol NanoAmp™ RT-IVT Labeling Kit from Applied Biosystems
 
Hybridization protocol Applied Biosystems Chemiluminescence Detection Kit
Scan protocol Applied Biosystems Chemiluminescence Detection Kit
Description Briefly, 10 μg of labeled cRNA targets from each sample were first fragmented, mixed with internal control target (24-mer oligo labeled with LIZ® fluorescent dye) and hybridized to a pre-hybridized microarray at 55°C for 16 hr. After washing to remove unhybridized DIG-labeled molecules, an alkaline phosphatase-antibody conjugate was added to bind to the DIG-labeled target. The addition of substrate and a chemiluminescence enhancer initiates the chemiluminescent reaction. Eight images were collected for each microarray using the 1700 analyzer including 2 “short” chemiluminescent images (5 seconds exposure length each) and 2 “long” chemiluminescent images (25 seconds exposure length each) for gene expression analysis, 2 fluorescent images for feature finding and spot normalization and 2 QC images for spectrum cross-talk correction. Applied Biosystems Expression System software was used to extract signal intensities, signal to noise ratios (S/N) and flagging values from the microarray images.
Data processing Using Applera package in R, we set the filtering criteria so that each gene had flagging value < 2 and a signal to noise ratio (S/N) ≥ 3 in at least 50% of the samples. After filtration, we proceed with quantile normalization of the log-intensities.
 
Submission date Feb 08, 2007
Last update date Feb 12, 2008
Contact name Vanessa Dumeaux
E-mail(s) vanessad@rr-research.no
Organization name "The Norwegian Women and Cancer project"
Street address University of Tromsoe
City Tromsoe
ZIP/Postal code 9037
Country Norway
 
Platform ID GPL2986
Series (1)
GSE7008 Comparison of globin RNA processing methods for genome-wide transcriptome analysis from whole-blood

Data table header descriptions
ID_REF
Signal_HB009IC_7/6/06_11:59_AM Signal
SDEV_HB009IC_7/6/06_11:59_AM Standard deviation
CV_HB009IC_7/6/06_11:59_AM Coefficient of variation
S_N_HB009IC_7/6/06_11:59_AM Signal to noise ratio
Flags_HB009IC_7/6/06_11:59_AM Flags
VALUE Quantile normalized log2 intensities

Data table
ID_REF Signal_HB009IC_7/6/06_11:59_AM SDEV_HB009IC_7/6/06_11:59_AM CV_HB009IC_7/6/06_11:59_AM S_N_HB009IC_7/6/06_11:59_AM Flags_HB009IC_7/6/06_11:59_AM VALUE
100002 18849.49 403.95 0.04 46.66 0 14.38
100003 196.07 196.07 1.54 -0.65 1
100027 189.5 189.5 1.12 -0.9 1
100036 1072.04 867.92 0.81 1.24 0
100037 6033.47 369.12 0.07 16.35 0 12.74
100039 1160.16 144.34 0.13 8.04 0 10.37
100044 175.71 175.71 2.77 0.36 1
100045 200.09 200.09 0.81 -1.24 1
100051 230.21 230.21 0.5 -2.01 1
100052 219.72 113.21 0.52 1.94 0
100057 777.65 777.65 1.09 0.92 1
100058 9765.73 305.09 0.05 32.01 0 13.44
100060 832.28 270.74 0.33 3.07 64
100062 706.69 276.97 0.39 2.55 0
100064 149.54 149.54 1.48 -0.68 1
100079 7599.22 375.35 0.06 20.25 0 13.08
100089 436.06 263.9 0.61 1.65 0
100093 148.78 148.78 1.61 0.62 1
100095 51.84 51.84 0.29 -3.43 131073
100100 7414.5 209.68 0.05 35.36 0 13.04

Total number of rows: 32878

Table truncated, full table size 1187 Kbytes.




Supplementary data files not provided

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