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Sample GSM65394 Query DataSets for GSM65394
Status Public on Sep 13, 2005
Title DB4_728 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 20 46 1 1 1 1 0 51 12 820.353 558.417 261.936 710.804 148.511 442.917 8.073 267.887 708.333 89.092 574.5 16.898 133.833 1.001 2.002 0.927 12.802 9.991 133.833 1.545 0.627 0.228 -0.296 0.374 1.061 2.086 1.94 0.956
RP23-180K2_replicate2 2 33 46 1 1 2 1 0 52 12 900.769 568.667 332.103 797.538 168.012 453.833 6.043 343.705 761.327 101.661 598.75 28.085 162.577 1.08 2.114 0.931 14.711 9.997 162.577 1.538 0.621 0.273 -0.375 0.463 1.294 2.452 2.176 1.122
RP23-180K2_replicate3 3 46 46 1 1 3 1 0 52 11 937.423 572.818 364.605 764.231 135.425 450.182 11.864 314.049 738.981 89.76 583 31.74 155.981 1.01 2.013 0.944 16.427 9.934 155.981 1.424 0.51 0.293 -0.414 0.507 1.184 2.272 2.04 1.029
RP23-248G16_replicate1 4 59 46 1 1 4 1 0 52 9 1036.692 579.111 457.581 599.288 68.899 458.333 7.826 140.955 652.481 48.944 593.333 25.199 59.147 1.253 2.383 0.865 14.232 5.477 59.147 1.217 0.283 0.489 -0.958 1.076 1.33 2.514 1.89 0.919
RP23-248G16_replicate2 5 73 46 1 1 5 1 0 50 10 1013.18 583.5 429.68 599.5 60.25 456.6 10.7 142.9 656.66 42.645 594.1 27.36 62.56 1.192 2.284 0.894 15.587 5.932 62.56 1.263 0.336 0.447 -0.809 0.925 1.286 2.439 2.07 1.05
RP23-248G16_replicate3 6 86 46 1 1 6 1 0 51 15 1009.745 566.333 443.412 601.549 53.882 455.667 4.467 145.882 660.98 42.177 583.133 19.187 77.847 0.906 1.874 0.838 19.113 10.099 77.847 1.071 0.099 0.429 -0.75 0.864 1.065 2.092 1.796 0.845
RP23-327H7_replicate1 7 100 47 1 1 7 1 0 28 5 603.821 577.2 26.621 458.964 7.933 455.6 9.915 3.364 588.214 20.172 585 16.093 3.214 0.066 1.047 0.597 0.719 0.395 3.214 0.235 -2.09 0.776 -3.457 3.543 -1.767 0.294 0.15 -2.737
RP23-327H7_replicate2 8 113 47 1 1 8 1 -1
RP23-327H7_replicate3 9 126 47 1 1 9 1 0 20 5 603.3 578 25.3 466.45 7.944 457.4 4.722 9.05 598.3 23.47 582.6 15.11 15.7 -0.795 0.576 0.653 3.28 1.835 9.05 0.221 -2.178 0.617 -1.609 1.723 -1.378 0.385 0.341 -1.55
RP23-344O14_replicate1 10 139 46 1 1 10 1 0 51 9 815.569 577.444 238.124 677.588 111.761 456.889 4.885 220.699 703.294 63.511 584.667 18.695 118.627 0.896 1.86 0.94 14.027 10.924 118.627 1.654 0.726 0.111 -0.125 0.167 0.965 1.952 1.898 0.925
RP23-344O14_replicate2 11 152 46 1 1 11 1 0 52 10 919.538 580.8 338.738 757.654 122.821 457.3 5.982 300.354 742.596 83.506 585.5 22.057 157.096 0.935 1.912 0.937 17.527 11.621 157.096 1.379 0.463 0.279 -0.387 0.477 1.186 2.276 1.867 0.901
RP23-344O14_replicate3 12 165 46 1 1 12 1 0 52 12 933.058 578.417 354.641 757.462 134.181 465.75 6.917 291.712 749.404 82.514 600.5 17.702 148.904 0.97 1.959 0.914 15.588 11.882 148.904 1.487 0.572 0.241 -0.318 0.399 1.12 2.174 1.985 0.989
P1-5253_replicate1 13 179 47 1 1 13 1 0 25 4 602.64 576 26.64 463.68 9.818 460.5 9.747 3.18 593.48 26.912 593 31.948 0.48 2.728 6.625 0.558 0.605 0.028 0.48 0.203 -2.297 0.969 -31.569 31.583 -1.431 0.371 0.191 -2.387
P1-5253_replicate2 14 193 47 1 1 14 1 0 22 6 602.636 576.5 26.136 461.773 9.029 460 3.95 1.773 600.364 20.486 592 18.078 8.364 -2.238 0.212 0.358 0.706 0.975 1.773 0.158 -2.665 0.256 -0.344 0.429 -1.244 0.422 0.128 -2.963
P1-5253_replicate3 15 206 47 1 1 15 1 0 22 6 604.5 581.333 23.167 465.545 7.15 460 10.1 5.545 604.409 21.152 588 19.1 16.409 -1.565 0.338 0.497 1.262 1.822 5.545 0.168 -2.575 0.503 -1.013 1.131 -1.489 0.356 0.25 -2
RP23-6P7_replicate1 16 218 47 1 1 16 1 0 52 12 1123.25 585.167 538.083 689.942 124.953 461.75 8.572 228.192 706.327 70.866 594.167 21.833 112.16 1.025 2.035 0.936 13.037 9.607 112.16 1.651 0.723 0.189 -0.233 0.299 1.069 2.098 1.924 0.944
RP23-6P7_replicate2 17 232 47 1 1 17 1 0 51 15 1116 583.067 532.933 688.51 108.353 463.133 6.844 225.376 717.235 67.09 596.533 17.378 120.702 0.901 1.867 0.828 14.755 11.594 120.702 1.337 0.419 0.284 -0.396 0.487 0.966 1.953 1.863 0.898
RP23-6P7_replicate3 18 245 47 1 1 18 1 0 52 13 1123.173 581.231 541.942 690.692 109.2 464.231 7.907 226.462 712.423 66.796 594.769 28.534 117.654 0.945 1.925 0.927 14.8 9.657 117.654 1.516 0.6 0.212 -0.27 0.343 1.085 2.121 1.836 0.876
RP23-24C10_replicate1 19 19 60 1 1 1 2 0 51 10 1016.863 568.7 448.163 705.98 132.865 449 11.333 256.98 702.922 82.97 583.6 34.481 119.322 1.107 2.154 0.932 13.563 7.489 119.322 1.492 0.577 0.307 -0.443 0.539 1.231 2.347 1.931 0.949
RP23-24C10_replicate2 20 33 60 1 1 2 2 0 52 13 1120.038 574.462 545.577 748.346 122.292 453.538 6.827 294.808 728.673 77.17 585 21.268 143.673 1.037 2.052 0.913 17.276 11.758 143.673 1.447 0.533 0.295 -0.418 0.511 1.218 2.327 1.96 0.971

Total number of rows: 4032

Table truncated, full table size 898 Kbytes.




Supplementary data files not provided
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