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Sample GSM161615 Query DataSets for GSM161615
Status Public on Feb 12, 2008
Title 33GRa_Blood_GlobinClear_noHRT
Sample type RNA
 
Source name blood samples in PAXgene, globin reduction using GlobinClear kit from ambion, non 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 12, 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_HB009HR_7/6/06_9:57_AM Raw siignal
SDEV_HB009HR_7/6/06_9:57_AM Standard deviation
CV_HB009HR_7/6/06_9:57_AM Coefficient of variation
S_N_HB009HR_7/6/06_9:57_AM Signal to noise ratio
Flags_HB009HR_7/6/06_9:57_AM Flags
VALUE Quantile normalized log2 intensities

Data table
ID_REF Signal_HB009HR_7/6/06_9:57_AM SDEV_HB009HR_7/6/06_9:57_AM CV_HB009HR_7/6/06_9:57_AM S_N_HB009HR_7/6/06_9:57_AM Flags_HB009HR_7/6/06_9:57_AM VALUE
100002 8213.12 203.84 0.05 40.29 0 13.26
100003 139.75 70.89 0.51 1.97 0
100027 79.55 79.55 1.44 -0.7 1
100036 494.02 166.81 0.34 2.96 0
100037 2005.51 185.72 0.1 10.8 0 11.52
100039 76.02 71.37 0.94 1.07 0 7.52
100044 73.72 73.72 1.28 -0.78 1
100045 139.51 139.51 0.89 -1.13 1
100051 181.12 181.12 4.68 -0.21 1
100052 175.08 77.91 0.45 2.25 0
100057 1136.57 1136.57 1.02 0.98 1
100058 15950.9 450.46 0.05 35.41 0 14.15
100060 656.62 230.5 0.35 2.85 0
100062 531.06 324.98 0.61 1.63 0
100064 55.21 53.88 0.98 1.02 0
100079 2561.07 143.6 0.07 17.83 0 11.8
100089 335.11 335.11 2.08 0.48 1
100093 290.87 79.83 0.28 3.64 0
100095 140.2 140.2 0.67 -1.5 1
100100 11394.5 177.45 0.05 64.21 0 13.68

Total number of rows: 32878

Table truncated, full table size 1173 Kbytes.




Supplementary data files not provided

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