NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM262243 Query DataSets for GSM262243
Status Public on Mar 30, 2009
Title 5156T.tumor.Cy3
Sample type RNA
 
Channel 1
Source name Tumor epithelial tissue from murine mammary glands
Organism Mus musculus
Characteristics Sample identifier: 5156T; Diagnosis: erbb2-type carcinoma; Sex: Female; Strain: FVB/N
Extracted molecule total RNA
Extraction protocol Phenol-chloroform extraction
Label Cy3
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. Cy3-labeled cRNA was prepared from 4-5ug total RNA using Ambion's MessageAmp kit.
 
Channel 2
Source name Stratagene universal mouse reference
Organism Mus musculus
Characteristics None
Biomaterial provider Stratagene
Extracted molecule total RNA
Extraction protocol No extraction
Label Cy5
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. 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 -[INV_VALUE]
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
INV_VALUE log2 ratio of normalized Cy5 to Cy3 signal

Data table
ID_REF VALUE gMeanSignal gMedianSignal gBGMeanSignal gBGMedianSignal rMeanSignal rMedianSignal rBGMeanSignal rBGMedianSignal INV_VALUE
1 2.00457 1143.704 1125 41.29276 40 431.7037 431 45.17763 45 -2.00456644251298
2 -0.0689074 49.86207 49 40.13725 40 49.44828 50 44.78431 45 0.0689074185578953
3 -0.70101 1115.333 1103.5 39.79926 39 1927.767 1905 44.07435 44 0.701010276628768
4 -0.918259 55.75862 56 39.45683 39 175.8276 174 43.8777 44 0.918258506844364
5 -0.753205 470.6129 470 39.58909 39 824.1935 816 43.66182 44 0.753204529205785
6 0.27605 144.9 144.5 40.63799 40 131.2667 130.5 43.5448 44 -0.276050488230769
7 3.79686 929.4828 912 39.93066 40 134.3793 135 44.30292 44 -3.7968584440307
8 0.779025 695.9677 668 40.22807 40 533.1613 514 44.03158 44 -0.779025101858497
9 0.0657223 124.125 122 40 40 132.7813 132 43.46512 43.5 -0.0657223424625872
10 0.267482 3917.929 3853.5 40.13043 40 3239.321 3134 42.97233 43 -0.267482419162167
11 -0.393006 138.1379 139 39.96341 40 208.069 215 43.45122 44 0.39300578168964
12 0.0944733 124.4483 123 40.19549 40 131.069 127 42.87218 43 -0.0944732520194957
13 0.464981 218.1333 211 39.72993 39 201.1333 196 43.32847 43 -0.464980557874284
14 3.97302 972 919 39.70313 39.5 124.7586 125 43.31641 43 -3.9730235627443
15 -0.123046 76.36667 75 40.5977 40 100.0667 101 44.44061 44 0.123046101695241
16 0.289148 213.7241 219 40.58571 40 217.5517 219 43.56429 44 -0.289148418295104
17 -0.794374 982.7742 994 40.30216 40 1875.387 1838 43.03237 43 0.794373533560432
18 0.401888 639.9259 643 39.63258 39 614.037 613 43.52652 44 -0.401887900020629
19 -0.136171 64.13793 66 39.83972 40 88.82759 89 42.90941 43 0.136171021178786
20 -0.717053 8398.586 8284 41.01132 41 11270.34 11174 43.68679 44 0.717053024322993

Total number of rows: 43790

Table truncated, full table size 3575 Kbytes.




Supplementary file Size Download File type/resource
GSM262243.txt.gz 11.3 Mb (ftp)(http) TXT
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap