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Sample GSM259440 Query DataSets for GSM259440
Status Public on Jul 01, 2010
Title MicMa 031
Sample type genomic
 
Channel 1
Source name primary breast carcinoma, MicMa 031
Organism Homo sapiens
Characteristics Tissue: breast carcinoma, part of a larger cohort of stage I and II primary tumors.
Gender: female
Extracted molecule genomic DNA
Extraction protocol Tumor DNA was extracted at The Norwegian Radium Hospital using an ABI 341 Nucleic Acid Purification System (Applied Biosystems) according to manufacturer’s protocol. Fresh frozen tumor tissue were homogenized and digested before phenol chloroform extraction on the ABI 341 system. DNA was stored at 4ºC until use.
Label Cy5
Label protocol 100 ng genomic DNA was amplified using phi29 DNA polymerase at 30ºC, 16 hours over night. Amplified DNA was digested using 50 units AluI and 50 units RsaI nucleases, 2 hours incubation at 37ºC. The amplified and digested DNA was purified using QIAprep Miniprep Kit (QIAGEN) according to manufacturer's protocol, and quantified using a NanoDrop ND-1000 UV-Vis Spectrophotometer (NanoDrop Technologies). 10 μg amplified and digested DNA was labeled with Cy5-dUTP (PerkinElmer) using the BioPrime Labeling System (Invitrogen). Cy3 and Cy5 reactions were combined and purified using Microcon YM-30 Filters (Amicon).
 
Channel 2
Source name Human Male Genomic DNA
Organism Homo sapiens
Characteristics Purified human genomic DNA from multiple anonymous donors. Promega Cat.# G1471
Biomaterial provider Promega
Extracted molecule genomic DNA
Extraction protocol Genomic DNA are purified (extraction method unknown), and greater than 90% of the DNA is longer than 50kb in size as measured by pulsed-field gel electrophoresis. The DNA is stored in 10mM Tris-HCl (pH 8.0), 1mM EDTA.
Label Cy3
Label protocol 100 ng genomic DNA was amplified using phi29 DNA polymerase at 30ºC, 16 hours over night. Amplified DNA was digested using 50 units AluI and 50 units RsaI nucleases, 2 hours incubation at 37ºC. The amplified and digested DNA was purified using QIAprep Miniprep Kit (QIAGEN) according to manufacturer's protocol, and quantified using a NanoDrop ND-1000 UV-Vis Spectrophotometer (NanoDrop Technologies). 10 μg amplified and digested DNA was labeled with Cy3-dUTP (PerkinElmer) using the BioPrime Labeling System (Invitrogen). Cy3 and Cy5 reactions were combined and purified using Microcon YM-30 Filters (Amicon).
 
 
Hybridization protocol For each experiment, 10 μg labeled tumor DNA, 10 μg labeled reference DNA, Agilent blocking agent, Cot-1 DNA and Agilent hybridization buffer were loaded onto the arrays and assembled in hybridization chambers according to manufacturer’s protocol.Arrays were incubated at 65ºC for 40 hours in a Robbins Scientific oven with rotary motion (20 rpm).Hybridization chambers were taken out of the oven, arrays quickly disassembled in washing solution 1 (0.5 x SSPE, 0.005% N-lauroylsarcosine) and placed in slide-rack submerged in fresh washing solution 1.Arrays were manually washed in batches of four; five minutes in washing solution 1, one minute in washing solution 2 (0.1 x SSPE 0.005% N-lauroylsarcosine) at 37ºC, one minute in 100% acetonitrile (Merck) and 30 seconds in Stabilization & Drying solution (Agilent Technologies).Arrays were protected from light until scanning.
Scan protocol ScannerName: Agilent Technologies Scanner G2505B US22502513
NumChannels: 2
MicronsPerPixel: 10
FeatureExtractor_ScanFileGUID: e4fe23c9-8c99-4157-b681-88b0ff1d7e7a
Description The arrays were scanned within 30 minutes after washing, using an Agilent Microarray Scanner. Data extraction, filtering and normalization were conducted using the Feature Extraction software version A.7.5.1 from Agilent Technologies
Data processing VALUE = LogRatio (base 10): (REDsignal/GREENsignal) per feature (processed signals used).
Processed signals: Raw intensities are background corrected using local background subtraction. A linear normalization is applied to correct for dye bias.
 
Submission date Jan 25, 2008
Last update date Jan 22, 2010
Contact name Jørgen Mømb Aarøe
E-mail(s) jorgen.aaroe@rr-research.no
Phone +4791774653
Fax +4722934440
Organization name The Norwegian Radium Hospital
Department Genetics
Lab Genetics
Street address Montebello
City Oslo
ZIP/Postal code N-0310
Country Norway
 
Platform ID GPL2873
Series (1)
GSE10583 Genome-wide analysis of in-trans correlations between copy number and expression with application to human breast cancer

Data table header descriptions
ID_REF Agilent feature number
VALUE LogRatio (base 10): (REDsignal/GREENsignal) per feature (processed signals used)
gProcessedSignal green (Cy3) preprossed signal
rProcessedSignal red (Cy5) preprossed signal
gMeanSignal Raw mean signal of feature in green channel (inlier pixels)
rMeanSignal Raw mean signal of feature in red channel (inlier pixels)
gBGSubSignal green background-subtracted signal
rBGSubSignal red background-subtracted signal

Data table
ID_REF VALUE gProcessedSignal rProcessedSignal gMeanSignal rMeanSignal gBGSubSignal rBGSubSignal
1 -2.00E+00 1.72E+04 1.21E+02 3.05E+03 8.79E+01 2967.33 25.3373
2 1.02E+00 4.28E+00 4.46E+01 8.01E+01 7.18E+01 -4.965 9.30398
3 5.57E-02 1.07E+03 1.21E+03 2.69E+02 3.16E+02 184.281 253.377
4 -7.35E-02 1.34E+03 1.14E+03 3.17E+02 2.99E+02 231.936 236.825
5 -1.35E-02 1.14E+03 1.10E+03 2.81E+02 2.92E+02 195.936 229.729
6 -9.34E-03 7.96E+02 7.79E+02 2.22E+02 2.25E+02 137.235 162.437
7 -2.00E+00 1.73E+04 1.73E+02 3.07E+03 9.87E+01 2982.7 36.1706
8 1.66E-01 4.11E+02 6.02E+02 1.56E+02 1.88E+02 70.8529 125.509
9 2.21E-02 3.04E+02 3.20E+02 1.37E+02 1.29E+02 52.4326 66.7206
10 -1.14E-01 1.40E+03 1.08E+03 3.27E+02 2.87E+02 241.79 224.828
11 -5.48E-02 1.20E+03 1.06E+03 2.92E+02 2.83E+02 207.04 220.721
12 -2.19E-02 6.50E+02 6.18E+02 1.97E+02 1.91E+02 112.079 128.878
13 3.79E-02 1.85E+03 2.02E+03 4.04E+02 4.84E+02 319.004 420.971
14 -2.00E+00 1.88E+04 1.54E+02 3.32E+03 9.46E+01 3239.53 32.0373
15 2.30E-01 1.70E+02 2.89E+02 1.14E+02 1.23E+02 29.3612 60.3278
16 -1.59E-01 1.91E+03 1.32E+03 4.14E+02 3.39E+02 329.244 276.229
17 -1.43E-01 4.08E+02 2.94E+02 1.55E+02 1.24E+02 70.3969 61.2206
18 4.14E-02 3.85E+02 4.24E+02 1.51E+02 1.51E+02 66.4522 88.4061
19 7.15E-02 9.79E+02 1.15E+03 2.54E+02 3.03E+02 168.802 240.704
20 -1.84E-01 1.22E+03 7.98E+02 2.95E+02 2.29E+02 210.433 166.542

Total number of rows: 42633

Table truncated, full table size 2794 Kbytes.




Supplementary file Size Download File type/resource
GSM259440.txt.gz 9.9 Mb (ftp)(http) TXT
Processed data included within Sample table

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