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Sample GSM147957 Query DataSets for GSM147957
Status Public on Feb 15, 2007
Title BT474_replicate2
Sample type genomic
 
Channel 1
Source name BT474
Organism Homo sapiens
Characteristics breast ductal carcinoma cell line
Biomaterial provider ATCC (Cat# HTB-20D)
Extracted molecule genomic DNA
Extraction protocol DNA provided by ATCC Part Number HTB-20D
Label Cy5
Label protocol 0.5ug of DNA was labelled using standard agilent protocols from http://www.opengenomics.com/oligoaCGHLiterature.aspx (
Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis, Version 4.0. Part number is G4410-90010)
 
Channel 2
Source name Promega Human Male DNA
Organism Homo sapiens
Characteristics Normal Male DNA Promega
Extracted molecule genomic DNA
Extraction protocol DNA provided by Promega Part Number G1471
Label Cy3
Label protocol 0.5ug of DNA was labelled using standard agilent protocols from http://www.opengenomics.com/oligoaCGHLiterature.aspx (
Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis, Version 4.0. Part number is G4410-90010
 
 
Hybridization protocol Standard Agilent Protocols from http://www.opengenomics.com/oligoaCGHLiterature.aspx
Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis, Version 4.0. Part number is G4410-90010.
Scan protocol Agilent DNA Microarray Scanner p/n G2565BA.
Scan Region: 61x21.6 mm
Scan Resolution 5 micron
Dye Channel Red & Green
Red and Green PMT 100%
Description Part of a two entry flip fluor record
This Entry (BT474/Male)
Other Entry (Male/BT474) GSM147888
Data processing Value represent LOG10 Ratio (CH1/CH2) generated by Standard Agilent Protocols from http://www.opengenomics.com/oligoaCGHLiterature.aspx
 
Submission date Dec 01, 2006
Last update date Feb 14, 2007
Contact name Bradley P Coe
E-mail(s) [email protected]
Organization name BC Cancer Research Centre
Department Cancer Genetics and Developmental Biology
Lab Wan Lam Lab
Street address 675 West 10th Ave
City Vancouver
State/province BC
ZIP/Postal code V5Z1L3
Country Canada
 
Platform ID GPL4544
Series (1)
GSE6415 Resolving the resolution of array CGH

Data table header descriptions
ID_REF
VALUE Channel 1 (red) / Channel 2 (green) LOG10 Ratio
CH2_SIG_MEAN Channel 2 (green) Foreground Mean Signal
CH1_SIG_MEAN Channel 1 (red) Foreground Mean Signal
CH2_BKD_MEAN Channel 2 (green) Background Mean Signal
CH1_BKD_MEAN Channel 1 (red) Background Mean Signal
CH2_SATURATION Channel 2 (green) Saturation
CH1_SATURATION Channel 1 (red) Saturation
CH2_NONUNIFORM Channel 2 (green) Spot Non-Uniformity
CH1_NONUNIFORM Channel 1 (red) Spot Non-Uniformity

Data table
ID_REF VALUE CH2_SIG_MEAN CH1_SIG_MEAN CH2_BKD_MEAN CH1_BKD_MEAN CH2_SATURATION CH1_SATURATION CH2_NONUNIFORM CH1_NONUNIFORM
1 9.022993528e-003 1.151804e+003 1.686143e+003 3.951783e+001 4.811983e+001 0 0 0 0
2 0.000000000e+000 5.745313e+001 6.421875e+001 3.925581e+001 4.767829e+001 0 0 0 0
3 0.000000000e+000 5.456452e+001 6.504839e+001 3.862984e+001 4.735078e+001 0 0 0 0
4 -3.788285341e-003 2.323443e+002 3.188852e+002 3.861328e+001 4.792383e+001 0 0 0 0
5 -6.937609011e-002 2.090923e+002 2.543231e+002 3.844618e+001 4.908806e+001 0 0 0 0
6 1.732325397e-001 2.224462e+002 4.260615e+002 3.889901e+001 4.828911e+001 0 0 0 0
7 5.093510275e-001 3.203226e+002 1.307194e+003 3.919103e+001 4.881287e+001 0 0 0 0
8 -7.365857581e-002 2.691833e+002 3.256500e+002 3.935534e+001 4.822913e+001 0 0 0 0
9 1.507985901e-002 2.362308e+002 3.357846e+002 3.917939e+001 4.971565e+001 0 0 0 0
10 -2.546466773e-001 2.464462e+002 2.178308e+002 3.860742e+001 4.907813e+001 0 0 0 0
11 2.509337154e-001 1.930635e+002 4.211587e+002 3.828265e+001 4.793762e+001 0 0 0 0
12 -1.371459534e-001 2.655833e+002 2.859833e+002 3.868474e+001 4.776104e+001 0 0 0 0
13 7.094073059e-002 2.565873e+002 4.076349e+002 3.851440e+001 4.819770e+001 0 0 0 0
14 -1.558592573e-001 3.185873e+002 3.299683e+002 3.791502e+001 4.724506e+001 0 0 0 0
15 -1.669929770e-001 1.268871e+002 1.347419e+002 3.865437e+001 4.792816e+001 0 0 0 0
16 4.138792454e-001 2.599836e+002 8.344590e+002 3.904070e+001 4.792829e+001 0 0 0 0
17 2.227900004e-002 2.318413e+002 3.333492e+002 3.791211e+001 4.744141e+001 0 0 0 0
18 2.788238324e-002 2.509077e+002 3.661692e+002 3.786705e+001 4.771291e+001 0 0 0 0
19 3.068642368e-001 2.317742e+002 5.832903e+002 3.811456e+001 4.817282e+001 0 0 0 0
20 -1.260104461e-001 2.219375e+002 2.443906e+002 3.803333e+001 4.771373e+001 0 0 0 0

Total number of rows: 243351

Table truncated, full table size 20924 Kbytes.




Supplementary data files not provided
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