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Sample GSM65393 Query DataSets for GSM65393
Status Public on Sep 13, 2005
Title DB4_5707 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 16 44 1 1 1 1 0 52 17 3036.019 1909.824 1126.196 1288.423 211.054 585.941 15.75 702.482 1155.865 254.188 529.235 23.077 626.63 0.165 1.121 0.968 23.8 17.557 626.63 0.803 -0.316 0.283 -0.395 0.486 0.231 1.173 1.108 0.148
RP23-180K2_replicate2 2 30 44 1 1 2 1 0 52 17 3943.827 1986 1957.827 1691.058 318.77 610.765 17.031 1080.293 1520.846 431.946 545 24.985 975.846 0.147 1.107 0.983 24.332 16.208 975.846 0.725 -0.464 0.345 -0.527 0.63 0.25 1.19 1.103 0.141
RP23-180K2_replicate3 3 43 44 1 1 3 1 0 52 17 3288.846 2022.118 1266.729 1265.365 196.57 623.706 17.971 641.66 1120.635 233.235 549.882 23.704 570.752 0.169 1.124 0.968 23.244 17.374 570.752 0.816 -0.294 0.275 -0.378 0.467 0.232 1.174 1.129 0.175
RP23-248G16_replicate1 4 56 44 1 1 4 1 0 52 17 3036.654 2023.647 1013.007 836.712 65.204 605.176 14.006 231.535 722.385 67.654 532.235 26.162 190.149 0.284 1.218 0.937 23.97 16.789 190.149 0.903 -0.147 0.258 -0.348 0.433 0.327 1.254 1.229 0.298
RP23-248G16_replicate2 5 70 44 1 1 5 1 0 52 16 3074.25 2029.625 1044.625 852.212 76.476 610.125 13.351 242.087 740.327 77.748 539.313 25.881 201.014 0.268 1.204 0.941 21.774 15.986 201.014 0.925 -0.112 0.232 -0.302 0.38 0.303 1.234 1.218 0.285
RP23-248G16_replicate3 6 83 44 1 1 6 1 0 51 14 3071.078 2023.071 1048.007 862.706 70.382 618.429 6.572 244.277 748 71.979 539 21.53 209 0.225 1.169 0.931 24.401 18.008 209 0.91 -0.136 0.221 -0.285 0.361 0.255 1.193 1.188 0.248
RP23-327H7_replicate1 7 97 46 1 1 7 1 0 21 7 2058.143 1987.857 70.286 616.714 9.509 610.286 10.843 6.429 543 23.354 542.286 14.233 0.714 3.17 9 0.432 1.399 0.096 0.714 0.176 -2.508 0.98 -50.211 50.221 -1.183 0.44 0.239 -2.064
RP23-327H7_replicate2 8 110 46 1 1 8 1 0 23 7 2056.391 1976.429 79.963 631.217 9.055 617.143 8.194 14.075 547.217 22.191 518.571 13.879 28.646 -1.025 0.491 0.202 3.88 4.095 14.075 0.082 -3.604 0.833 -4.975 5.044 -1.223 0.428 0.314 -1.669
RP23-327H7_replicate3 9 123 46 1 1 9 1 -1
RP23-344O14_replicate1 10 136 44 1 1 10 1 0 52 17 3890.115 1986.706 1903.409 1292.904 213.416 632.176 14.196 660.727 1133.231 233.532 546.059 21.431 587.172 0.17 1.125 0.98 22.176 17.902 587.172 0.895 -0.16 0.204 -0.257 0.328 0.207 1.155 1.14 0.188
RP23-344O14_replicate2 11 150 44 1 1 11 1 0 52 17 4019.327 2008.706 2010.621 1357.481 229.098 640.765 14.648 716.716 1186 242.817 557.882 21.257 628.118 0.19 1.141 0.975 22.42 18.439 628.118 0.919 -0.121 0.194 -0.241 0.31 0.224 1.168 1.145 0.195
RP23-344O14_replicate3 12 162 44 1 1 12 1 0 52 15 4146.942 2011.467 2135.476 1417.808 257.358 637.4 11.873 780.408 1237.288 279.772 554.2 29.17 683.088 0.192 1.142 0.977 21.787 17.284 683.088 0.899 -0.154 0.213 -0.271 0.345 0.236 1.178 1.157 0.211
P1-5253_replicate1 13 176 46 1 1 13 1 0 39 9 2053.359 1982.333 71.026 670.667 32.391 634.556 12.621 36.111 575.487 52.186 563.667 19.59 11.821 1.611 3.055 0.753 5.407 1.115 11.821 0.467 -1.098 0.847 -5.538 5.603 1.041 2.058 0.975 -0.037
P1-5253_replicate2 14 190 46 1 1 14 1 0 32 9 2065 1983.556 81.444 678.781 28.304 631.778 9.189 47.003 584.938 40.211 534.667 20.062 50.271 -0.097 0.935 0.794 8.012 5.151 47.003 0.559 -0.839 0.402 -0.672 0.783 -0.446 0.734 0.784 -0.35
P1-5253_replicate3 15 203 46 1 1 15 1 0 28 9 2068.821 1988.222 80.599 662.571 23.45 635.333 15.851 27.238 569.25 31.29 545.778 17.676 23.472 0.215 1.16 0.695 3.95 2.812 23.472 0.521 -0.941 0.551 -1.227 1.345 0.363 1.286 0.872 -0.198
RP23-6P7_replicate1 16 216 46 1 1 16 1 0 51 14 3708.765 2025.571 1683.193 1053.176 137.374 641.643 11.843 411.534 903.275 149.954 557.286 30.633 345.989 0.25 1.189 0.974 21.11 15.352 345.989 0.892 -0.165 0.25 -0.333 0.416 0.314 1.243 1.198 0.26
RP23-6P7_replicate2 17 229 46 1 1 17 1 0 52 15 3549.673 2026.667 1523.006 1026.173 130.185 637.4 9.085 388.773 885.077 146.657 546.333 18.5 338.744 0.199 1.148 0.963 21.355 16.215 338.744 0.855 -0.227 0.255 -0.343 0.428 0.262 1.199 1.169 0.225
RP23-6P7_replicate3 18 241 45 1 1 18 1 0 52 16 3628.365 2013.813 1614.553 1041.135 138.209 646.438 15.862 394.697 899.019 148.427 560.5 21.869 338.519 0.222 1.166 0.988 20.166 15.895 338.519 0.92 -0.12 0.211 -0.267 0.34 0.29 1.222 1.167 0.222
RP23-24C10_replicate1 19 16 58 1 1 1 2 0 52 17 3374.077 1984.529 1389.548 1235.423 193.774 599.353 18.993 636.07 1095.481 221.482 521.118 26.528 574.363 0.147 1.107 0.959 23.33 18.303 574.363 0.839 -0.253 0.242 -0.319 0.401 0.194 1.144 1.107 0.147
RP23-24C10_replicate2 20 31 59 1 1 2 2 0 50 14 3317.96 2073.857 1244.103 1196.64 167.598 634.143 25.666 562.497 1046.44 181.68 546.214 17.638 500.226 0.169 1.124 0.968 22.797 19.149 500.226 0.893 -0.163 0.206 -0.259 0.33 0.2 1.149 1.126 0.172

Total number of rows: 4032

Table truncated, full table size 938 Kbytes.




Supplementary data files not provided
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