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Sample GSM123033 Query DataSets for GSM123033
Status Public on Sep 08, 2006
Title MAQC_ABI_2_B4
Sample type RNA
 
Source name MAQC sample B, i.e., Ambion Human Brain Reference RNA (HBRR, Catalog #6050)
Organism Homo sapiens
Characteristics NA

Extracted molecule total RNA
Label Chemiluminescence - Digoxigenin
Label protocol Digoxigenin-UTP labeled cRNA was generated from 1 µg of total RNA for each MAQC sample (A, B, C, D) using Applied Biosystems NanoAmp RT-IVT Labeling Kit (P/N 4365715) according to the manufacturer’s protocol.
 
Hybridization protocol Array hybridization, array processing, chemiluminescence detection, image acquisition, and analysis were performed using Applied Biosystems Chemiluminescence Detection Kit and Applied Biosystems 1700 Chemiluminescent Microarray Analyzer following manufacturer’s protocol.
Scan protocol Chemiluminescent Detection Kit (P/N 4339627, http://docs.appliedbiosystems.com/pebiodocs/04339627.pdf) and Chemiluminescent Microarray Analyzer User Guide (P/N 4338852B).
Description NA
Data processing The Expression Array System Software suite performs the auto-gridding, feature extraction, fluorescence normalization, and signal data generation. The quantification data contain many distinct measurements for each probe, including the three basic measurements: Signal, S/N, and Flag values. The Signal value is the fully corrected, background subtracted measurement of chemiluminescent signal for gene expression values. The S/N value represents the ratio of signal above noise, or the measurement uncertainty of the probe signal, and can be used as a confidence level for the probe measurement. An S/N of 3 represents approximately a 99.95% confidence that the probe is detected above the background noise. In situations where the probe showed S/N < 1, the signal measurement is replaced with a 1 SDEV upper limit based on its probe signal SDEV.
 
Submission date Jul 24, 2006
Last update date Aug 17, 2006
Contact name Leming Shi
E-mail(s) lemingshi@fudan.edu.cn
Phone +86-18616827008
Organization name Fudan University
Department School of Life Sciences
Lab Center for Pharmacogenomics
Street address 2005 Songhu Road
City Shanghai
ZIP/Postal code 200438
Country China
 
Platform ID GPL2986
Series (1)
GSE5350 MicroArray Quality Control (MAQC) Project

Data table header descriptions
ID_REF Manufacturer's probe ID
VALUE The signal value is the fully corrected, background subtracted measurement of chemiluminescent signal for gene expression values. Data were quantile-normalized per test site (20 arrays).
Flag_Detection An S/N of 3 represents approximately a 99.95% confidence that the probe is detected above the background noise.

Data table
ID_REF VALUE Flag_Detection
100002 56219.32 49.85
100003 667.16 4.54
100027 236.913 1.87
100036 29137.119 60.13
100037 10561.569 31.84
100039 5368.343 27.25
100044 8386.963 30.96
100045 638.715 -0.1
100051 253.705 0.11
100052 4850.149 16.84
100057 3851.787 18.87
100058 44936.266 47.6
100060 1990.519 4.35
100062 901.201 -0.47
100064 247.304 -0.72
100079 66082.75 77.17
100089 20637.309 44.96
100093 2706.78 12.07
100095 174.832 1.19
100100 27198.033 51.49

Total number of rows: 32878

Table truncated, full table size 681 Kbytes.




Supplementary file Size Download File type/resource
GSM123033_ABI_2_B4.txt.gz 283.8 Kb (ftp)(http) TXT

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