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Sample GSM65390 Query DataSets for GSM65390
Status Public on Sep 13, 2005
Title DB4_1249 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 GPL2642
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 15 40 1 1 1 1 0 49 7 1820.898 1210.143 610.755 529.469 85.211 339.571 10.147 189.898 604.857 74.336 462.143 27.661 142.714 0.412 1.331 0.918 14.879 9.577 142.714 1.052 0.074 0.209 -0.264 0.337 0.514 1.428 1.324 0.405
RP23-180K2_replicate2 2 29 38 1 1 2 1 0 45 14 2670.022 1281.643 1388.379 542.689 93.576 358.714 23.727 183.975 617.6 82.238 488.571 26.717 129.029 0.512 1.426 0.937 12.006 9.095 129.029 1.067 0.093 0.252 -0.337 0.42 0.586 1.501 1.422 0.508
RP23-180K2_replicate3 3 42 40 1 1 3 1 0 43 12 2027.465 1280.417 747.048 596.186 91.771 352.167 10.878 244.019 647.907 77.377 482.083 25.949 165.824 0.557 1.472 0.931 17.013 11.864 165.824 1.104 0.143 0.25 -0.333 0.416 0.66 1.58 1.489 0.574
RP23-248G16_replicate1 4 55 40 1 1 4 1 0 47 14 2082.681 1253.5 829.181 453.021 41.77 356.714 7.205 96.307 558.17 45.803 489.429 22.016 68.742 0.486 1.401 0.89 15.072 7.721 68.742 0.812 -0.3 0.42 -0.725 0.838 0.683 1.606 1.309 0.389
RP23-248G16_replicate2 5 69 40 1 1 5 1 0 50 13 2033.98 1238.462 795.518 465.82 39.308 359.846 12.902 105.974 576.32 41.851 494.692 24.978 81.628 0.377 1.298 0.817 16.029 8.959 81.628 0.767 -0.382 0.409 -0.692 0.804 0.489 1.403 1.331 0.413
RP23-248G16_replicate3 6 82 40 1 1 6 1 0 52 15 2131.077 1253.4 877.677 470.173 43.275 364.133 6.749 106.04 579.692 47.404 500.133 24.328 79.559 0.415 1.333 0.848 16.969 8.75 79.559 0.774 -0.37 0.419 -0.722 0.835 0.562 1.476 1.315 0.395
RP23-327H7_replicate1 7 95 38 1 1 7 1 -1
RP23-327H7_replicate2 8 108 40 1 1 8 1 0 25 7 1337.68 1217.571 120.109 360.88 8.715 358.857 9.281 2.023 492.16 20.599 488.571 16.216 3.589 -0.827 0.564 0.458 0.516 0.486 2.023 0.194 -2.369 0.657 -1.912 2.021 -1.831 0.281 0.008 -6.931
RP23-327H7_replicate3 9 122 40 1 1 9 1 -1
RP23-344O14_replicate1 10 136 39 1 1 10 1 0 50 12 2088.76 1243.083 845.677 678.82 163.097 362.417 8.66 316.403 738.56 277.041 495.917 20.007 242.643 0.383 1.304 0.799 13.638 6.127 242.643 0.47 -1.088 0.639 -1.773 1.884 0.775 1.711 1.451 0.537
RP23-344O14_replicate2 11 149 39 1 1 11 1 0 52 15 2229.923 1248.867 981.056 711.808 132.045 367.4 11.012 344.408 739.481 104.623 505.667 19.208 233.814 0.559 1.473 0.95 18.586 15.249 233.814 1.2 0.263 0.186 -0.228 0.294 0.627 1.544 1.49 0.575
RP23-344O14_replicate3 12 162 39 1 1 12 1 0 52 12 1813.5 1240.833 572.667 576.692 88.568 362.25 8.17 214.442 648.404 75.244 495.083 16.747 153.321 0.484 1.399 0.924 17.146 13.332 153.321 1.088 0.122 0.222 -0.286 0.362 0.579 1.494 1.403 0.489
P1-5253_replicate1 13 173 40 1 1 13 1 0 20 7 1432 1234.143 197.857 363.25 11.616 352.286 6.751 10.964 501.6 26.769 479.286 16.859 22.314 -1.025 0.491 0.724 3.011 2.552 10.964 0.314 -1.669 0.36 -0.563 0.668 -0.591 0.664 0.492 -1.023
P1-5253_replicate2 14 186 38 1 1 14 1 0 41 10 1770.927 1234.9 536.027 365.171 9.227 358.7 7.499 6.471 504.756 27.975 494.3 25.743 10.456 -0.692 0.619 0.614 2.332 1.132 6.471 0.203 -2.303 0.672 -2.053 2.161 -1.593 0.332 0.228 -2.132
P1-5253_replicate3 15 201 40 1 1 15 1 0 32 7 1556 1248.857 307.143 360.063 9.214 358.714 8.48 1.348 504 22.774 495.429 23.23 8.571 -2.668 0.157 0.735 0.375 0.887 1.348 0.297 -1.75 -0.891 0.471 1.007 -1.462 0.363 0.3 -1.739
RP23-6P7_replicate1 16 215 40 1 1 16 1 0 48 14 2481.187 1255.429 1225.759 541.188 79.943 357.214 7.149 183.973 637.021 74.444 504.5 25.267 132.521 0.473 1.388 0.954 15.73 10.442 132.521 1.024 0.034 0.262 -0.355 0.442 0.598 1.513 1.363 0.447
RP23-6P7_replicate2 17 228 40 1 1 17 1 0 51 14 2254.784 1245.286 1009.499 526.961 71.294 358.071 4.393 168.889 627.922 64.642 487.643 17.981 140.279 0.268 1.204 0.922 16.802 13.688 140.279 1.017 0.025 0.155 -0.183 0.24 0.302 1.233 1.225 0.293
RP23-6P7_replicate3 18 241 40 1 1 18 1 0 47 11 2449.404 1248.727 1200.677 551.085 75.005 359.636 7.865 191.449 654.745 70.002 500.818 29.02 153.926 0.315 1.244 0.911 17.102 11.447 153.926 0.976 -0.035 0.215 -0.274 0.349 0.401 1.321 1.308 0.387
RP23-24C10_replicate1 19 15 53 1 1 1 2 0 50 12 2122.96 1243.333 879.627 511.8 78.276 343.5 6.829 168.3 603.4 91.712 481 24.409 122.4 0.459 1.375 0.885 14.968 8.292 122.4 0.755 -0.405 0.451 -0.821 0.936 0.639 1.558 1.313 0.392
RP23-24C10_replicate2 20 29 53 1 1 2 2 0 50 13 2323.5 1265.231 1058.269 572.76 85.735 348.769 13.761 223.991 646.42 73.242 484.385 24.673 162.035 0.467 1.382 0.928 17.621 13.052 162.035 1.086 0.119 0.214 -0.273 0.347 0.545 1.459 1.411 0.497

Total number of rows: 4032

Table truncated, full table size 884 Kbytes.




Supplementary data files not provided
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