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Sample GSM262224 Query DataSets for GSM262224
Status Public on Mar 30, 2009
Title 562T.tumor.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 4-5 ug total RNA using Ambion's MessageAmp kit.
 
Channel 2
Source name Tumor epithelial tissue from murine mammary glands
Organism Mus musculus
Characteristics Sample identifier: 562T; Diagnosis: MIN with solid, nodular intra lobular polyps; 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 4-5ug 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 -2.2207276537171 1100.033 1082.5 42.06918 42 305.1 295.5 43.56604 43.5
2 -0.143606470408175 87.2069 87 42.9542 43 49.13793 49 43.12977 43
3 -0.597191760769931 1543.69 1572 43.47872 43 956.1379 977 43.26241 43
4 -1.00570690641580 237.0385 237 43.32184 43 59.30769 60 43.16475 43
5 -0.7075436752101 1062.719 1074 43.29091 44 610.1563 604.5 43.30182 43
6 0.30602420234923 217.0345 217 43.18008 43 182.8621 181 42.63985 43
7 -3.45850759184873 871.6207 856 43.48921 44 113.2414 115 42.3741 42
8 -0.434203875839588 502.5313 499 43.93141 44 322.5625 322 43.04693 43
9 0.0203723073417041 180.8438 182.5 43.71174 44 126.3125 125 42.38434 42
10 -0.0977614482826255 2948.133 2935.5 42.92578 43 2562.1 2563 42.97266 43
11 -0.261606620327475 160 160 43.24188 43 77.74194 78 43.15162 43
12 -0.0796457844296885 135.7586 136 43.59191 44 80.31034 80 42.80882 43
13 0.0763945647203812 162.069 163 43.48014 43 115.4828 114 42.50903 43
14 -3.27811656246053 949.2069 932 43.85448 43 145 146 42.73507 43
15 -0.0433307809837657 162.9655 159 43.67647 43 101.1724 103 42.33824 42
16 0.730709270021505 320.4375 315.5 43.85769 43 310.7188 310 42.53462 42
17 -1.17230018711172 1978.759 1973 45.121 45 804.7241 802 42.73665 43
18 0.379811010941701 970.2188 979.5 44.69288 44 977.5625 975 42.73408 43
19 -0.141482212693067 126.4667 126.5 44.18947 44 59.23333 60 42.53333 42
20 -0.510762249478006 9893.419 10186 44.94007 45 7093.452 7312 42.41199 42

Total number of rows: 43790

Table truncated, full table size 3183 Kbytes.




Supplementary file Size Download File type/resource
GSM262224.txt.gz 11.3 Mb (ftp)(http) TXT
Processed data included within Sample table
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