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Sample GSM262228 Query DataSets for GSM262228
Status Public on Mar 30, 2009
Title 5156N.normal.Cy5
Sample type RNA
 
Channel 1
Source name Stratagene universal mouse reference
Organism Mus musculus
Characteristics None
Biomaterial provider Stratagene
Extracted molecule total RNA
Extraction protocol No extraction
Label Cy3
Label protocol 4ng of extracted RNA was subjected to one round of linear T7 RNA amplification (Amino Allyl MessageAmp kit, Ambion) according to manufacturer's protocol. Cy3-labeled cRNA was prepared from 4-5ug total RNA using Ambion's MessageAmp kit.
 
Channel 2
Source name Normal epithelial tissue from murine mammary glands
Organism Mus musculus
Characteristics Sample identifier: 5156N; Diagnosis: normal; Sex: Female; Strain: FVB/N
Extracted molecule total RNA
Extraction protocol Phenol-chloroform extraction
Label Cy5
Label protocol 4ng of extracted RNA was subjected to two rounds of linear T7 RNA amplification (Amino Allyl MessageAmp kit, Ambion) according to manufacturer's protocol. Cy5-labeled cRNA was prepared from 4-5 ug total RNA using Ambion's MessageAmp kit.
 
 
Hybridization protocol Following fragmentation, 750ng of cRNA was hybridized to Agilent's Whole Mouse Genome expression array (G4122A) according to the protocols provided by the manufacturer.
Scan protocol Array was scanned using Agilent's dual-laser microarray scanner (Model G2505B), and Cy5/Cy3-signals were quantified using Agilent's Feature Extraction software (Palo Alto, CA).
Description RNA isolated from laser capture microdissected mammary tissue.
Data processing Raw Cy5 and Cy3 intensities were background corrected using the RMA background correction algorithm. Data was transformed to log2 ratios and within array normalization was performed using spatial and intensity-dependent loess.
 
Submission date Feb 04, 2008
Last update date Mar 30, 2009
Contact name Robert Lesurf
Organization name Washington University in St. Louis
Department McDonnell Genome Institute
Lab Griffith Lab
Street address 4444 Forest Park Ave
City St. Louis
State/province MO
ZIP/Postal code 63112
Country USA
 
Platform ID GPL2872
Series (1)
GSE10450 Met induces mammary tumors with diverse histologies and is associated with poor outcome and human basal breast cancer

Data table header descriptions
ID_REF
VALUE log2 ratio of normalized Cy5 to Cy3 signal
gMeanSignal The mean foreground signal in the Cy3 channel
gMedianSignal The median foreground signal in the Cy3 channel
gBGMeanSignal The mean background signal in the Cy3 channel
gBGMedianSignal The median background signal in the Cy3 channel
rMeanSignal The mean foreground signal in the Cy5 channel
rMedianSignal The median foreground signal in the Cy5 channel
rBGMeanSignal The mean background signal in the Cy5 channel
rBGMedianSignal The median background signal in the Cy5 channel

Data table
ID_REF VALUE gMeanSignal gMedianSignal gBGMeanSignal gBGMedianSignal rMeanSignal rMedianSignal rBGMeanSignal rBGMedianSignal
1 -1.490556025421 1136.593 1117 39.19205 39 435.6667 409 42.83113 43
2 0.0552685540214242 54.58065 55 38.49035 39 48.3871 48 42.99228 43
3 -0.705014278527674 1519.2 1486 39.16791 39 885.6667 879.5 42.90672 43
4 -0.730931064593507 189.8 192 39.30651 39 61.16667 61 43.22989 43
5 -0.287123508925742 755.8214 756.5 38.80586 38 558.0714 537.5 42.95604 43
6 0.56017116955007 136.08 135 38.80297 39 169.8 174 43.27138 43
7 -3.54979476799963 930.7692 912.5 39.16917 39 123.0769 125 43.10902 43
8 1.02388827052246 485.8276 490 38.81295 38 705.5517 713 42.6295 42
9 0.580338108442692 150.7931 148 39.25623 39 182.6552 183 42.19217 42
10 0.74608535699998 2584.935 2535 41.45769 41 4142.484 4137 45.50769 45
11 -0.241318716328498 179.7931 175 40.00389 39 113.7931 114 43.1323 43
12 0.243742812852220 114.3571 114.5 38.46538 38 118.3929 118 43.00769 43
13 0.489263741716801 151.7037 146 38.99259 38 173.3704 174 42.93704 43
14 -3.58349871904505 870.4333 870 38.97727 39 103.7667 102.5 42.375 42
15 0.144865544365272 89.48276 87 39.17121 39 87.27586 87 42.61089 43
16 0.317589812800531 166.6 159 39.3861 39 165.8 163.5 42.76448 43
17 -1.25291978427292 1950.733 1974 40.12268 40 813.4 818 43.19331 43
18 1.40259690583866 1138.179 1154.5 39.92222 39.5 2526.607 2507.5 42.77778 43
19 0.119334368069012 89.65517 90 39.64 39 83.75862 83 42.91273 43
20 -0.0736624024999735 9228.966 9347 40.28625 40 9432.862 9410 43.41264 43

Total number of rows: 43790

Table truncated, full table size 3181 Kbytes.




Supplementary file Size Download File type/resource
GSM262228.txt.gz 11.3 Mb (ftp)(http) TXT
Processed data included within Sample table

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