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Sample GSM67679 Query DataSets for GSM67679
Status Public on Nov 30, 2005
Title MicMa065_AB_REP2
Sample type RNA
 
Source name biopy of breast carcinoma
Organism Homo sapiens
Characteristics early stage, breast carcinoma
Extracted molecule total RNA
Extraction protocol Biopy samples were fresh frozen immediately after surgery and stored at -80oC. All specimens analyzed contained more than 40% tumor cells (of the total number of cells counted). The majority of tumors were invasive ductal carcinomas, tumor status T1-T2 and histological grade 2 and 3 (Table S1). Total RNA was isolated by phenol-chloroform extraction (TRIzol reagent, Invitrogen), the quality and integrity of the total RNA was evaluated on the 2100 Bioanalyzer (Agilent Technologies) and the concentration was measured using a NanoDrop spectrophotometer (NanoDrop Technologies).
Label DIG-UTP
Label protocol Digoxigenin-UTP labeled cRNA was generated and amplified from 2 ?g of total RNA from each sample using Applied Biosystems Chemiluminescent RT-IVT Labeling Kit v 1.0 (P/N 4340472) according to the manufacturer’s protocol (P/N 4339629).
 
Hybridization protocol Array hybridization was performed for 16 hrs at 55 oC. Chemiluminescence detection, image acquisition and analysis were performed using Applied Biosystems Chemiluminescence Detection Kit (P/N 4342142) and Applied Biosystems 1700 Chemiluminescent Microarray Analyzer (P/N 4338036) following the manufacturer’s protocol (P/N 4339629).
Scan protocol image acquisition and analysis were performed using Applied Biosystems Chemiluminescence Detection Kit (P/N 4342142) and Applied Biosystems 1700 Chemiluminescent Microarray Analyzer (P/N 4338036) following the manufacturer’s protocol (P/N 4339629).
Description biopy of breast carcinoma
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 v 1.1 (P/N 4336391).
 
Submission date Aug 08, 2005
Last update date Oct 28, 2005
Contact name Yulei Wang
E-mail(s) wangyy@appliedbiosystems.com
Organization name Applied Biosystems
Street address 850 Lincoln Centre Dr
City Foster City
State/province CA
ZIP/Postal code 94404
Country USA
 
Platform ID GPL1426
Series (1)
GSE3155 Gene expression profiling of the 20 human early breast carcinomas by three miaroarray platforms

Data table header descriptions
ID_REF Probe ID
VALUE Signal intensity normalized by median signal intensity of the array
SIGNAL_RAW Raw signal intensity
STDEV Noise/background signal intensity
S2N Signal to noise ratio is equal to SIGNAL_RAW/ STDEV
CV Coefficient of variation of signal intensity based on error model built in the Applied Biosystem image analysis software
DETECTION_FLAG Detectable : 1 (S/N >3 and Flag < 5000) ; Not detectable: 0 (S/N < 3 or Flag > 5000)
FLAG Quality flag of spot

Data table
ID_REF VALUE SIGNAL_RAW STDEV S2N CV DETECTION_FLAG FLAG
100002 38.58869116 13444.3 272.5 49.3 0.103 1 0
100003 0.336107922 117.1 117.1 -0.3 3.693 0 65
100027 0.262055109 91.3 91.3 -1.8 0.573 0 1
100036 6.998851894 2438.4 149.6 16.3 0.089 1 0
100037 7.06228473 2460.5 176.9 13.9 0.124 1 0
100039 6.133754305 2137 197 10.9 0.113 1 0
100043 0.962399541 335.3 335.3 0 21.615 0 1
100044 0.545063146 189.9 189.9 -0.8 1.212 0 1
100045 0.302525832 105.4 105.4 0.7 1.395 0 1
100051 0.403559127 140.6 117.4 1.2 0.838 0 0
100052 0.256601607 89.4 89.4 -1 1.023 0 1
100057 0.387485649 135 135 0.5 1.92 0 1
100058 34.06917336 11869.7 257.9 46 0.103 1 0
100060 1.825774971 636.1 211.9 3 0.348 1 0
100062 0.458668197 159.8 159.8 0.1 8.514 0 1
100064 0.496268657 172.9 172.9 -1.9 0.531 0 1
100079 45.34931114 15799.7 267.5 59.1 0.067 1 0
100089 9.674799082 3370.7 135.1 25 0.076 1 0
100093 11.73450057 4088.3 211.2 19.4 0.113 1 0
100095 0.492250287 171.5 171.5 -1.3 0.775 0 1

Total number of rows: 33096

Table truncated, full table size 1453 Kbytes.




Supplementary data files not provided

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