NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM65380 Query DataSets for GSM65380
Status Public on Sep 13, 2005
Title DB4_6101 mouse breast tumor
Sample type genomic
 
Channel 1
Source name Mouse breast tumor
Organism Mus musculus
Characteristics Mouse strain FVB/N
Biomaterial provider William J Muller
Treatment protocol
Growth protocol
Extracted molecule genomic DNA
Extraction protocol Hodgson et al.(2001) Nat Genet, 29, 459-64.
Label Cy3
Label protocol Hodgson et al.(2001) Nat Genet, 29, 459-64.
 
Channel 2
Source name Normal mouse spleen
Organism Mus musculus
Characteristics Mouse strain FVB/N
Biomaterial provider J Graeme Hodgson
Treatment protocol
Growth protocol
Extracted molecule genomic DNA
Extraction protocol Hodgson et al.(2001) Nat Genet, 29, 459-64.
Label Cy5
Label protocol Hodgson et al.(2001) Nat Genet, 29, 459-64.
 
 
Hybridization protocol Hodgson et al.(2001) Nat Genet, 29, 459-64.
Scan protocol Hodgson et al.(2001) Nat Genet, 29, 459-64.
Description Mouse breast tumor
Data processing Hodgson et al.(2001) Nat Genet, 29, 459-64.
 
Submission date Jul 25, 2005
Last update date Jul 27, 2005
Contact name Graeme Hodgson
E-mail(s) ghodgson@cc.ucsf.edu
Phone 415-476-3630
Fax 415-476-8218
Organization name UCSF
Department Neurological Surgery
Street address Box0808
City San Francisco
State/province CA
ZIP/Postal code 94143
Country USA
 
Platform ID GPL2571
Series (1)
GSE3012 Copy number aberrations in mouse breast tumors reveal loci and genes important in tumorigenic RTK signaling

Data table header descriptions
ID_REF
SpotNum Unique integer for each spot.
Image-x X image coordinate of spot center.
Image-y Y image coordinate of spot center.
Arr-colx Subgrid column (1-based).
Arr-rowy Subgrid row.
Spot-colx Spot column (within subgrid).
Spot-rowy Spot row.
Flag Flag: 0 if spot is OK.
nfore Number of foreground pixels.
nback Number of background pixels.
DapiFore Dapi (or composite) channel foreground mean.
DapiBack Dapi background mean.
Dapi Dapi signal (fore - back).
TestFore Test foreground mean.
TestForeSD Test foreground standard deviation.
TestBack Test background mean.
TestBackSD Test background standard deviation.
Test Test signal (fore - back).
RefFore Reference foreground mean.
RefForeSD Reference foreground standard deviation.
RefBack Reference background mean.
RefBackSD Reference background standard deviation.
Ref Reference signal (fore - back).
VALUE log2(RawRat)
RawRat Test/Ref
SpotCorr Pearson's correlation of test to ref foreground pixels.
TestZstat Z-statistic of difference between test fore and back.
RefZstat Z-statistic of difference between ref fore and back.
MinF-B Minimum (fore-back) for all three channels.
Slope Slope of line fit to test/ref fore pixels
Log2Slope log2(Slope)
TestIntercept Normalized intercept.
RefIntercept Normalized intercept.
OriginDist Distance of intercept to origin.
MeanLog2Rat Mean of pixel by pixel log2(ratio)
MeanRat Corresponding non-logged ratio to MeanLog2Rat
MedianRatio Median pixel by pixel ratio.
Log2MedRat log2(MedianRatio)

Data table
ID_REF SpotNum Image-x Image-y Arr-colx Arr-rowy Spot-colx Spot-rowy Flag nfore nback DapiFore DapiBack Dapi TestFore TestForeSD TestBack TestBackSD Test RefFore RefForeSD RefBack RefBackSD Ref VALUE RawRat SpotCorr TestZstat RefZstat MinF-B Slope Log2Slope TestIntercept RefIntercept OriginDist MeanLog2Rat MeanRat MedianRatio Log2MedRat
RP23-180K2_replicate1 1 14 19 1 1 1 1 0 52 13 4451.288 1609.769 2841.519 572.192 202.804 323.923 12.285 248.269 644.25 138.946 492.538 21.93 151.712 0.711 1.636 0.937 8.764 7.508 151.712 1.368 0.452 0.164 -0.196 0.256 0.907 1.875 1.659 0.73
RP23-180K2_replicate2 2 28 19 1 1 2 1 0 52 11 4906.192 1801.727 3104.465 598.615 149.08 343.636 7.827 254.979 666.904 110.735 529.727 29.716 137.177 0.894 1.859 0.874 12.254 7.716 137.177 1.177 0.235 0.367 -0.579 0.685 1.048 2.068 1.744 0.803
RP23-248G16_replicate1 3 40 19 1 1 3 1 0 52 14 6120.981 1805.214 4315.766 758.577 277.903 356.857 54.054 401.72 751.942 184.607 515 24.763 236.942 0.762 1.695 0.97 9.761 8.961 236.942 1.461 0.547 0.139 -0.161 0.212 0.807 1.75 1.664 0.735
RP23-248G16_replicate2 4 54 20 1 1 4 1 0 52 14 6311.173 1814.786 4496.387 831 297.18 348.071 9.563 482.929 791.788 198.584 525.071 21.635 266.717 0.856 1.811 0.954 11.696 9.478 266.717 1.428 0.514 0.211 -0.268 0.341 1.104 2.149 1.775 0.828
RP23-327H7_replicate1 5 67 20 1 1 5 1 0 52 13 5256.712 1828.846 3427.865 819.596 402.576 354.692 8.43 464.904 792.135 272.567 533.231 25.272 258.904 0.845 1.796 0.941 8.32 6.735 258.904 1.39 0.475 0.226 -0.292 0.37 1.106 2.152 1.762 0.817
RP23-327H7_replicate2 6 80 20 1 1 6 1 0 52 11 5874.712 1851.727 4022.984 962.25 486.525 350.909 10.793 611.341 873.788 321.34 538.455 40.008 335.334 0.866 1.823 0.958 9.051 7.264 335.334 1.45 0.536 0.204 -0.257 0.328 1.279 2.427 1.725 0.787
RP23-344O14_replicate1 7 93 20 1 1 7 1 0 52 15 7187.846 1870.533 5317.313 660.365 96.925 354.933 9.231 305.432 705.038 79.195 549.667 24.453 155.372 0.975 1.966 0.848 22.375 12.265 155.372 1.038 0.054 0.472 -0.894 1.011 1.084 2.119 1.991 0.994
RP23-344O14_replicate2 8 107 20 1 1 8 1 0 52 15 7300.25 1886.8 5413.45 771.519 107.988 351.267 9.816 420.253 764.712 80.699 518.933 31.795 245.778 0.774 1.71 0.893 27.67 17.708 245.778 1.195 0.256 0.301 -0.431 0.526 0.837 1.787 1.716 0.779
P1-5253_replicate1 9 120 21 1 1 9 1 0 52 14 5292.135 1882.5 3409.635 577.981 68.693 348.786 8.107 229.195 657.25 50.259 529.429 25.096 127.821 0.842 1.793 0.803 23.461 13.215 127.821 1.097 0.134 0.388 -0.634 0.743 0.888 1.851 1.75 0.807
P1-5253_replicate2 10 134 20 1 1 10 1 0 52 14 5719.615 1884.286 3835.33 604 49.092 357.429 18.054 246.571 675.058 44.972 540.643 15.35 134.415 0.875 1.834 0.702 29.549 18.006 134.415 0.767 -0.383 0.582 -1.392 1.509 0.919 1.891 1.74 0.799
RP23-6P7_replicate1 11 147 20 1 1 11 1 0 51 12 3587.294 1891.167 1696.127 764.373 433.38 351.417 9.249 412.956 767.118 295.986 536.667 20.183 230.451 0.842 1.792 0.96 6.798 5.506 230.451 1.405 0.491 0.216 -0.275 0.35 1.205 2.306 1.856 0.892
RP23-6P7_replicate2 12 160 20 1 1 12 1 0 52 10 4143.635 1909.4 2234.235 904.712 596.277 355.2 7.239 549.512 846.423 390.375 539 18.85 307.423 0.838 1.787 0.968 6.643 5.645 307.423 1.479 0.564 0.173 -0.209 0.271 1.101 2.145 1.912 0.935
RP23-24C10_replicate1 13 173 21 1 1 13 1 0 52 11 5892.596 1924.273 3968.323 633.038 180.074 357.273 10.441 275.766 699.596 106.341 560.182 26.145 139.414 0.984 1.978 0.953 10.956 8.337 139.414 1.614 0.691 0.184 -0.225 0.291 1.236 2.356 1.926 0.945
RP23-24C10_replicate2 14 187 21 1 1 14 1 0 52 14 5614.25 1956.429 3657.821 868.25 888.211 355.786 7.007 512.464 693.827 110.899 546.571 14.238 147.255 1.799 3.48 0.443 4.16 9.295 147.255 3.545 1.826 -0.019 0.018 0.026 1.476 2.782 2.096 1.068
RP23-110G12_replicate1 15 200 21 1 1 15 1 0 52 14 7227.635 1972.786 5254.849 569.731 59.46 355.714 10.336 214.016 666.115 47.318 535.5 22.967 130.615 0.712 1.639 0.798 24.611 14.537 130.615 1.002 0.003 0.388 -0.635 0.744 0.783 1.721 1.668 0.738
RP23-110G12_replicate2 16 213 21 1 1 16 1 0 52 16 7584.154 1992.375 5591.779 567.154 48.39 357.188 7.53 209.966 660.558 40.365 551.313 23.779 109.245 0.943 1.922 0.846 30.126 13.379 109.245 1.014 0.02 0.473 -0.896 1.013 1.054 2.077 1.925 0.945
RP23-437G15_replicate1 17 226 21 1 1 17 1 0 52 13 7243.385 1981.846 5261.538 685.442 94.784 361.154 11.246 324.288 725.75 72.954 549.692 23.68 176.058 0.881 1.842 0.87 24.005 14.596 176.058 1.13 0.176 0.387 -0.63 0.739 0.988 1.984 1.867 0.9
RP23-437G15_replicate2 18 240 21 1 1 18 1 0 52 16 7889.923 1978.187 5911.736 697.904 76.568 357.5 9.43 340.404 732.058 54.047 555.813 28.058 176.245 0.95 1.931 0.896 31.297 17.169 176.245 1.269 0.343 0.343 -0.522 0.625 1.009 2.013 1.923 0.943
RP23-308G1_replicate1 19 13 33 1 1 1 2 0 52 15 6643.942 1784.4 4859.542 838.558 293.932 329.867 8.626 508.691 777.827 177.225 500.533 25.673 277.294 0.875 1.834 0.94 12.461 10.893 277.294 1.559 0.641 0.15 -0.176 0.231 0.974 1.965 1.784 0.835
RP23-308G1_replicate2 20 28 33 1 1 2 2 0 52 15 6912.269 1825.133 5087.136 862.385 280.898 337.4 10.391 524.985 799.981 187.727 517.933 34.392 282.047 0.896 1.861 0.934 13.445 10.254 282.047 1.398 0.483 0.249 -0.332 0.415 1.134 2.194 1.804 0.851

Total number of rows: 5184

Table truncated, full table size 1235 Kbytes.




Supplementary data files not provided
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap