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Sample GSM65395 Query DataSets for GSM65395
Status Public on Sep 13, 2005
Title DB4_925 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 18 50 1 1 1 1 0 52 16 5678.096 765.063 4913.034 2803.404 988.487 458.25 23.57 2345.154 2731.577 1300.037 483.938 25.204 2247.639 0.061 1.043 0.979 17.092 12.46 2247.639 0.745 -0.425 0.286 -0.401 0.493 0.234 1.176 1.066 0.092
RP23-180K2_replicate2 2 33 50 1 1 2 1 0 52 17 3960.654 783.588 3177.066 2152.788 749.403 466.588 13.019 1686.2 2134.096 1009.195 490.353 17.557 1643.743 0.037 1.026 0.983 16.218 11.74 1643.743 0.73 -0.454 0.288 -0.405 0.497 0.248 1.188 1.053 0.075
RP23-180K2_replicate3 3 46 51 1 1 3 1 0 50 13 3840.66 788.308 3052.352 2174.5 688.865 459.385 6.358 1715.115 2157.74 950.775 480.769 19.297 1676.971 0.032 1.023 0.977 17.602 12.462 1676.971 0.708 -0.499 0.308 -0.445 0.541 0.183 1.135 0.989 -0.015
RP23-248G16_replicate1 4 59 51 1 1 4 1 0 52 15 1390.885 795 595.885 663.346 76.372 454.067 7.713 209.279 638.096 71.36 479.933 18.211 158.163 0.404 1.323 0.947 19.42 14.436 158.163 1.013 0.019 0.234 -0.306 0.385 0.481 1.395 1.354 0.437
RP23-248G16_replicate2 5 72 51 1 1 5 1 0 51 17 1464.02 804.176 659.843 670.706 79.772 458 8.993 212.706 642.333 75.75 483.412 18.422 158.922 0.421 1.338 0.953 18.689 13.808 158.922 1.004 0.006 0.25 -0.333 0.416 0.523 1.437 1.322 0.402
RP23-248G16_replicate3 6 86 51 1 1 6 1 0 49 14 1424.878 808.643 616.235 670.102 74.768 455.857 9.844 214.245 644.612 69.631 481.643 30.318 162.969 0.395 1.315 0.932 19.476 12.702 162.969 1 0 0.239 -0.314 0.395 0.462 1.377 1.341 0.424
RP23-327H7_replicate1 7 99 51 1 1 7 1 -1
RP23-327H7_replicate2 8 112 51 1 1 8 1 0 26 10 850.423 813.4 37.023 473.5 10.312 463.4 7.919 10.1 496.5 22.628 488.2 17.687 8.3 0.283 1.217 0.584 3.138 1.162 8.3 0.266 -1.909 0.781 -3.57 3.654 -1.075 0.475 0.182 -2.459
RP23-327H7_replicate3 9 125 51 1 1 9 1 0 23 6 850.826 809.5 41.326 466.043 9.975 460 9.529 6.043 487.261 19.208 483.833 25.872 3.428 0.818 1.763 0.668 1.37 0.303 3.428 0.347 -1.528 0.803 -4.086 4.164 -1.066 0.478 0.289 -1.79
RP23-344O14_replicate1 10 139 51 1 1 10 1 0 52 14 1592.019 836.786 755.234 807.846 137.691 468.286 13.094 339.56 806.385 158.95 487.286 24.879 319.099 0.09 1.064 0.984 17.492 13.86 319.099 0.853 -0.23 0.199 -0.248 0.318 0.182 1.134 1.07 0.097
RP23-344O14_replicate2 11 152 51 1 1 11 1 0 52 14 1588.135 841.714 746.42 810.115 144.799 462.5 10.625 347.615 798.981 168.441 472.429 22.463 326.552 0.09 1.065 0.982 17.141 13.54 326.552 0.844 -0.244 0.207 -0.261 0.333 0.191 1.142 1.046 0.065
RP23-344O14_replicate3 12 165 51 1 1 12 1 0 51 14 1593.039 850.714 742.325 810.059 143.211 462.214 5.618 347.845 806.059 161.188 485.571 18.952 320.487 0.118 1.085 0.975 17.297 13.855 320.487 0.867 -0.207 0.202 -0.252 0.323 0.217 1.162 1.092 0.126
P1-5253_replicate1 13 178 51 1 1 13 1 0 32 7 897.969 845.714 52.254 503.281 29.386 450.143 8.009 53.138 518.625 31.587 483.143 23.427 35.482 0.583 1.498 0.829 8.838 3.39 35.482 0.771 -0.375 0.485 -0.942 1.06 0.61 1.526 1.223 0.29
P1-5253_replicate2 14 192 51 1 1 14 1 0 32 5 910.188 852 58.187 504.781 35.048 459.2 4.087 45.581 518.781 38.544 487 9.772 31.781 0.52 1.434 0.857 7.056 3.926 31.781 0.779 -0.36 0.457 -0.841 0.957 0.663 1.584 1.148 0.2
P1-5253_replicate3 15 205 51 1 1 15 1 0 36 7 915.5 865 50.5 510.25 39.306 454 6.807 56.25 530.861 31.968 483.429 25.683 47.433 0.246 1.186 0.829 7.992 4.283 47.433 1.019 0.027 0.141 -0.164 0.216 0.045 1.031 1.085 0.117
RP23-6P7_replicate1 16 218 51 1 1 16 1 0 52 12 1529.442 878.75 650.692 740.442 109.13 458.917 10.492 281.526 717.827 112.462 484.833 26.849 232.994 0.273 1.208 0.976 18.241 13.379 232.994 0.947 -0.079 0.216 -0.276 0.351 0.35 1.275 1.196 0.258
RP23-6P7_replicate2 17 231 51 1 1 17 1 0 52 17 2327.192 890.412 1436.781 827.058 151.137 463.353 8.514 363.705 824.538 175.003 496.059 23.36 328.48 0.147 1.107 0.986 17.27 13.181 328.48 0.852 -0.231 0.231 -0.3 0.378 0.248 1.188 1.131 0.177
RP23-6P7_replicate3 18 245 51 1 1 18 1 0 48 14 2557.438 904.5 1652.937 878.021 163.509 464.714 8.033 413.307 872.292 185.806 495.357 17.977 376.935 0.133 1.096 0.984 17.441 13.835 376.935 0.866 -0.208 0.21 -0.266 0.34 0.218 1.163 1.106 0.145
RP23-24C10_replicate1 19 18 64 1 1 1 2 0 52 16 2196.635 767.25 1429.385 992.385 209.703 455.75 14.866 536.635 984.173 242.269 485.813 17.833 498.361 0.107 1.077 0.981 18.304 14.705 498.361 0.849 -0.236 0.211 -0.268 0.342 0.22 1.165 1.08 0.111
RP23-24C10_replicate2 20 33 64 1 1 2 2 0 51 17 2307.176 785.529 1521.647 1021.745 213.937 458.882 12.732 562.863 1023.882 256.521 477.588 20.485 546.294 0.043 1.03 0.986 18.69 15.065 546.294 0.822 -0.283 0.202 -0.253 0.324 0.135 1.098 1.023 0.033

Total number of rows: 4032

Table truncated, full table size 931 Kbytes.




Supplementary data files not provided
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