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Sample GSM262230 Query DataSets for GSM262230
Status Public on Mar 30, 2009
Title 4691N.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: 4691N; 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 -0.677942990117497 1547.034 1530 40.05431 40 986.8966 981 43.377 43
2 -0.124608820920969 51.89286 52 40.36364 40 47.60714 47 43.78409 44
3 -0.590420181583081 2174.9 2168 40.46182 40 1452.567 1446.5 43.52364 44
4 -0.867084496490005 197.3913 188 39.6332 39 68.52174 69 43.20463 43
5 -0.226117040909458 912.5172 914 40.16667 40 745.6552 728 43.35816 43
6 0.626562948675042 186.6774 184 40.14118 40 230.7742 229 43.19608 43
7 -3.37460903167212 887.931 876 40.28523 40 137.1034 137 42.98658 43
8 1.84491884143367 478.5357 471.5 39.70803 40 1200.643 1196.5 42.80292 43
9 0.138889483940371 159.5862 160 39.38869 39 154.2414 154 43.51943 43
10 -0.450217195204292 2600.429 2536 39.65098 39 1860.214 1850.5 43.49412 43
11 -0.440466251007983 211.1333 208 40.22826 40 127.5667 129.5 43.69928 43
12 0.267658043423552 160.3103 162 39.96863 40 166.8966 167 43.51373 43
13 0.667732993409933 253.6667 255 39.38328 40 290.2593 289 43.26481 43
14 -3.50297381930089 1031.897 994 40.40809 40 148.2414 145 42.94118 43
15 0.0209637454571929 124.5 121 40.04362 40 110.1538 110 43.01007 43
16 0.585679258804273 276.6897 274 40.28315 40 300.0345 300 43.10394 43
17 -1.49268826215113 2002.897 1995 40.57037 41 732.0345 738 43.07778 43
18 0.95787524390867 947.4643 932.5 39.74627 39 1532.107 1520 42.59701 43
19 -0.0387091058584996 91.25 88.5 40.39286 40 74.5625 74 43.09286 43
20 -0.688255453750635 9817.321 9894.5 40.65789 41 6461.536 6289.5 42.96617 43

Total number of rows: 43790

Table truncated, full table size 3182 Kbytes.




Supplementary file Size Download File type/resource
GSM262230.txt.gz 11.3 Mb (ftp)(http) TXT
Processed data included within Sample table

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