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Sample GSM65384 Query DataSets for GSM65384
Status Public on Sep 13, 2005
Title MT_8413 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 20 23 1 1 1 1 0 52 12 3028.212 1402.5 1625.712 637.731 284.143 339.583 9.366 298.147 698.519 189.272 526.833 23.269 171.686 0.796 1.737 0.964 7.549 6.337 171.686 1.447 0.533 0.167 -0.2 0.261 1.357 2.562 1.602 0.68
RP23-180K2_replicate2 2 33 23 1 1 2 1 0 49 12 3234.755 1422.083 1812.672 654.816 273.24 349.833 6.767 304.983 707.98 191.01 524.5 27.665 183.48 0.733 1.662 0.949 7.803 6.453 183.48 1.357 0.44 0.184 -0.225 0.29 0.901 1.867 1.495 0.58
RP23-248G16_replicate1 3 47 24 1 1 3 1 0 52 12 3738.654 1417.5 2321.154 695.423 217.498 355.5 9.405 339.923 754.442 177.179 536 20.167 218.442 0.638 1.556 0.933 11.225 8.651 218.442 1.146 0.196 0.264 -0.358 0.445 0.973 1.962 1.52 0.604
RP23-248G16_replicate2 4 61 24 1 1 4 1 0 52 15 3806.327 1424.067 2382.26 728.058 241.588 363.867 15.999 364.191 785.231 189.436 552 34.736 233.231 0.643 1.562 0.946 10.789 8.402 233.231 1.206 0.27 0.228 -0.295 0.373 0.855 1.809 1.524 0.608
RP23-327H7_replicate1 5 73 24 1 1 5 1 0 52 13 3778.962 1425.385 2353.577 898.346 461.395 360.385 11.102 537.962 910.154 340.838 522.385 38.875 387.769 0.472 1.387 0.965 8.398 7.999 387.769 1.306 0.386 0.058 -0.062 0.085 0.547 1.461 1.378 0.463
RP23-327H7_replicate2 6 87 24 1 1 6 1 0 52 12 4062.327 1428.25 2634.077 968.538 481.137 361.417 9.995 607.122 953.135 364.268 538.667 24.399 414.468 0.551 1.465 0.962 9.091 8.126 414.468 1.271 0.345 0.133 -0.153 0.202 0.863 1.819 1.446 0.532
RP23-344O14_replicate1 7 100 24 1 1 7 1 0 52 15 4153.942 1424.733 2729.209 636.538 106.875 365.667 7.017 270.872 707.673 81.641 553.667 14.544 154.006 0.815 1.759 0.887 18.141 12.911 154.006 1.161 0.216 0.34 -0.514 0.616 1.011 2.015 1.748 0.805
RP23-344O14_replicate2 8 114 24 1 1 8 1 0 52 15 4362.038 1426.067 2935.972 665.731 91.767 365 10.61 300.731 724.269 79.306 546.2 21.91 178.069 0.756 1.689 0.814 23.102 14.398 178.069 0.942 -0.087 0.442 -0.793 0.908 0.978 1.97 1.671 0.741
P1-5253_replicate1 9 127 24 1 1 9 1 0 52 13 3170.288 1412.231 1758.058 550.519 59.098 366.538 11.794 183.981 665.596 57.379 558.462 34.854 107.135 0.78 1.717 0.877 20.85 8.557 107.135 0.903 -0.148 0.474 -0.902 1.019 0.886 1.847 1.558 0.64
P1-5253_replicate2 10 140 24 1 1 10 1 0 52 16 3267.442 1416.625 1850.817 568.942 48.212 365 9.121 203.942 684.712 50.667 541 16.17 143.712 0.505 1.419 0.822 28.871 17.729 143.712 0.782 -0.355 0.449 -0.815 0.931 0.581 1.496 1.411 0.496
RP23-6P7_replicate1 11 154 24 1 1 11 1 0 45 11 2306.756 1405 901.756 724.733 406.045 368 11.207 356.733 792.578 334.175 541.091 23.42 251.487 0.504 1.418 0.942 5.884 4.998 251.487 1.145 0.196 0.193 -0.239 0.307 0.691 1.614 1.478 0.563
RP23-6P7_replicate2 12 167 25 1 1 12 1 0 50 6 2772.14 1391 1381.14 903.2 674.226 372.833 10.572 530.367 923.1 524.398 562.5 12.613 360.6 0.557 1.471 0.969 5.557 4.851 360.6 1.246 0.317 0.153 -0.181 0.237 0.69 1.613 1.288 0.366
RP23-24C10_replicate1 13 179 25 1 1 13 1 0 51 12 3105.804 1386.25 1719.554 714 329.038 362.917 7.597 351.083 764.804 227.373 543.917 18.338 220.887 0.669 1.589 0.969 7.611 6.844 220.887 1.402 0.488 0.118 -0.134 0.178 0.949 1.931 1.586 0.666
RP23-24C10_replicate2 14 193 25 1 1 14 1 0 52 10 3082.115 1393.7 1688.415 671.538 295.748 362.6 8.54 308.938 735.5 202.503 545.6 18.106 189.9 0.702 1.627 0.966 7.516 6.626 189.9 1.41 0.496 0.133 -0.154 0.203 0.874 1.832 1.591 0.67
RP23-110G12_replicate1 15 206 25 1 1 15 1 0 52 10 3820.231 1394.2 2426.031 535.788 64.217 358.7 6.43 177.088 664.058 55.313 529.4 20.222 134.658 0.395 1.315 0.873 19.387 13.484 134.658 1.014 0.02 0.229 -0.297 0.375 0.451 1.367 1.356 0.44
RP23-110G12_replicate2 16 220 25 1 1 16 1 0 52 13 4029.923 1394.923 2635 541.923 55.749 365.385 8.088 176.538 676.115 54.946 556.462 19.26 119.654 0.561 1.475 0.833 21.931 12.858 119.654 0.845 -0.243 0.427 -0.747 0.86 0.821 1.767 1.502 0.587
RP23-437G15_replicate1 17 233 25 1 1 17 1 0 52 14 3877.423 1397.786 2479.637 628.942 98.501 366.643 6.698 262.299 728.769 85.824 559.143 18.025 169.626 0.629 1.546 0.869 19.04 13.211 169.626 0.997 -0.004 0.355 -0.551 0.655 0.675 1.597 1.463 0.549
RP23-437G15_replicate2 18 247 25 1 1 18 1 0 52 16 4198.212 1386.5 2811.712 647.173 80.954 362.563 8.132 284.611 736.596 73.743 555.5 16.673 181.096 0.652 1.572 0.887 24.947 16.399 181.096 0.974 -0.038 0.38 -0.614 0.722 0.705 1.63 1.552 0.634
RP23-308G1_replicate1 19 20 38 1 1 1 2 0 52 14 4030.077 1415.357 2614.72 801.827 289.012 344.5 10.783 457.327 811.865 221.905 510.214 25.679 301.651 0.6 1.516 0.956 11.381 9.567 301.651 1.246 0.317 0.178 -0.217 0.281 1.026 2.036 1.53 0.614
RP23-308G1_replicate2 20 33 38 1 1 2 2 0 51 11 4046.941 1420.091 2626.85 788.529 267.539 355 6.618 433.529 813.373 205.461 529.545 23.205 283.827 0.611 1.527 0.949 11.556 9.586 283.827 1.235 0.305 0.191 -0.236 0.304 1.05 2.07 1.529 0.613

Total number of rows: 5184

Table truncated, full table size 1231 Kbytes.




Supplementary data files not provided
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