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Sample GSM185087 Query DataSets for GSM185087
Status Public on May 08, 2007
Title Bone, NOS, Osteosarcoma, NOS (C40._, C41._) (12429852)
Sample type genomic
 
Channel 1
Source name TB0813DF1X10
Organism Homo sapiens
Characteristics Cell Line HOS
TB0813DF1X10
Growth protocol "Bone, NOS"; Osteosarcoma, NOS (C40._, C41._)
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was isolated from frozen tumors or cultured cells by overnight digestion, phenol-chloroform extraction and ethanol precipitation.
Label Cy5
Label protocol One µg of tumor and reference DNA were labeled with Cy3 or Cy5, respectively (Amersham, Piscataway, NJ) using the BioPrime random-primed labeling kit (Invitrogen, Carlsbad, CA). Labeled tumor and reference DNA were combined and precipitated with human Cot-1 DNA to reduce non-specific binding.
 
Channel 2
Source name pooled male
Organism Homo sapiens
Characteristics pooled male
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was isolated from frozen tumors or cultured cells by overnight digestion, phenol-chloroform extraction and ethanol precipitation.
Label Cy3
Label protocol One µg of tumor and reference DNA were labeled with Cy3 or Cy5, respectively (Amersham, Piscataway, NJ) using the BioPrime random-primed labeling kit (Invitrogen, Carlsbad, CA). Labeled tumor and reference DNA were combined and precipitated with human Cot-1 DNA to reduce non-specific binding.
 
 
Hybridization protocol DNA was resuspended and hybridized to the array for 72h at 37oC on a rotating platform. Additional details are found in: Greshock, J, Naylor, TL, Margolin, A, et al. 1-Mb resolution array-based comparative genomic hybridization using a BAC clone set optimized for cancer gene analysis. Genome Res 2004; 14: 179-87
Scan protocol Images were scanned with an Axon 4500 microarray scanner (Axon, Union City, CA) and analyzed with GenePix 3.0 software (Axon).
Description "Bone, NOS"; Osteosarcoma, NOS (C40._, C41._); University of Pennsylvania; 11/19/2002
Data processing All spots were subjected to a pin-tip normalization.
 
Submission date Apr 27, 2007
Last update date May 07, 2007
Contact name Joel Greshock
Organization name GlaxoSmithKline
Department Translational Medicine, Oncology
Street address 2301 Renaissance Blvd.
City King of Prussia
State/province PA
ZIP/Postal code 19406
Country USA
 
Platform ID GPL4894
Series (1)
GSE7692 Cancer cell lines as genetic models of their parent histology: analyses based on array comparative genomic hybridization

Data table header descriptions
ID_REF
SLIDE Slide/Exeriment Identifier
Dia Spot Diameter in Pixels
F635_Median Median foreground measurement of Cy5 channel
F635_Mean Mean foreground measurement of Cy5 channel
F635_SD Standard Deviation of foreground measurement of Cy5 channel
B635_Median Median background of Cy5 channel
B635_Mean Mean background of Cy5 channel
B635_SD Standard deviation of background of Cy5 channel
PCT_GT_B635_1SD Percent of pixels > 1 standard deviation above background for Cy5 channel
PCT_GT_B635_2SD Percent of pixels > 2 standard deviation above background for Cy5 channel
F635_PCT_Sat Percent of pixels that are saturated for Cy5 channel
F532_Median Median foreground measurement of Cy3 channel
F532_Mean Mean foreground measurement of Cy3 channel
F532_SD Standard Deviation of foreground measurement of Cy3 channel
B532_Median Median background of Cy3 channel
B532_Mean Mean background of Cy3 channel
B532_SD Standard deviation of background of Cy3 channel
PCT_GT_B532_1SD Percent of pixels > 1 standard deviation above background for Cy5 channel
PCT_GT_B532_2SD Percent of pixels > 2 standard deviation above background for Cy5 channel
F532_PCT_Sat Percent of pixels that are saturated for Cy3 channel
Ratio_of_Medians_532_635 Ratio of median pixel values (Cy3/Cy5)
Ratio_of_Means_532_635 Ratio of mean pixel values (Cy3/Cy5)
Median_of_Ratios_532_635 Median of all individual pixel ratios (Cy3/Cy5)
Mean_of_Ratios_532_635 Mean of all individual pixel ratios (Cy3/Cy5)
Ratios_SD_532_635 Standard deviation of all individual pixel ratios (Cy3/Cy5)
Rgn_Ratio_532_635 Red to green ratio
Rgn_R2_532_635 Red to green correlation
F_Pixels The number of pixels analyzed as foreground (both Cy3 and Cy5 uses same exact pixels)
B_Pixels The number of pixels analyzed as background (same for Cy3 and Cy5)
Sum_of_Medians Sum of Pixel intensity medians
Sum_of_Means Sum of Pixel intensity means
Log_Ratio_532_635 Log base 2 of the Cy3/Cy5 ratio
F635_Median_B635 Median Foreground intensity minus Background intensity, Cy5 channel
F532_Median_B532 Median Foreground intensity minus Background intensity, Cy3 channel
F635_Mean_B635 Mean Foreground intensity minus Background intensity, Cy5 channel
F532_Mean_B532 Mean Foreground intensity minus Background intensity, Cy3 channel
Ratio_Median Median Cy3/Cy5 ratio (using the Background corrected ratio of medians) for that specific print tip
Cy3_corrected Adjusted background corrected intensity (by print tip)= F532_Median_B532 / Ratio_Median_Tip
VALUE log(GREENsignal/REDsignal) per feature (processed signals used).
A mean log intensity
Sig_var_mean_Cy3 Signal variation from mean intsity for Cy3 channel
Sig_var_mean_Cy5 Signal variation from mean intsity for Cy5 channel
Mean_med_corr_Cy3 Mean-Median correlation for Cy3 channel
Mean_med_corr_Cy5 Mean-Median correlation for Cy5 channel

Data table
ID_REF SLIDE Dia F635_Median F635_Mean F635_SD B635_Median B635_Mean B635_SD PCT_GT_B635_1SD PCT_GT_B635_2SD F635_PCT_Sat F532_Median F532_Mean F532_SD B532_Median B532_Mean B532_SD PCT_GT_B532_1SD PCT_GT_B532_2SD F532_PCT_Sat Ratio_of_Medians_532_635 Ratio_of_Means_532_635 Median_of_Ratios_532_635 Mean_of_Ratios_532_635 Ratios_SD_532_635 Rgn_Ratio_532_635 Rgn_R2_532_635 F_Pixels B_Pixels Sum_of_Medians Sum_of_Means Log_Ratio_532_635 F635_Median_B635 F532_Median_B532 F635_Mean_B635 F532_Mean_B532 Ratio_Median Cy3_corrected VALUE A Sig_var_mean_Cy3 Sig_var_mean_Cy5 Mean_med_corr_Cy3 Mean_med_corr_Cy5
RP11-458D3 12429852 205 7290.5 7660.5 3287 241 320 409 100 99.5 0 7392 7914.5 3083 979 1032.5 480.5 99.5 99 0 0.9045 0.9305 0.921 0.9225 1.2585 0.947 0.924 316 1092.5 13462.5 14355 -0.1475 7049.5 6413 7419.5 6935.5 0.889 7213.72328458943 1.01749261297447 12.7036233829968 0.60871691034296 0.574361966533966 0.929628184446673 0.940188639575819
RP11-67E18 12429852 230 17039 17163 4193.5 384.5 533 834 100 100 0 14185 14516 3726.5 1310 1380 586.5 100 100 0 0.7675 0.7825 0.778 0.778 1.1715 0.794 0.955 392 1248 29529.5 29984.5 -0.386 16654.5 12875 16778.5 13206 0.747 17235.609103079 1.02742254239428 13.8239431158554 0.738161930337236 0.754546821579116 0.972674690200391 0.992586944202858
RP11-291C17 12429852 215 16598 16450.5 4598.5 326 486.5 1089.5 99 97.5 0 15821.5 16144 4576.5 1012 1079 626.5 100 99 0 0.913 0.937 0.9405 0.9385 1.174 0.944 0.97 354 1587.5 31081.5 31256.5 -0.1315 16272 14809.5 16124.5 15132 0.857 17280.6301050175 1.06502465520066 13.8720458894708 0.705272185038724 0.702740508997141 0.982127335763938 0.992253322007671
RP11-506N24 12429852 215 12050.5 12846.5 5071 315 484 964.5 99.5 99 0 10972 11807 4720 1091 1171.5 613.5 100 99 0 0.842 0.855 0.844 0.848 1.22 0.8655 0.946 354 1018.5 21616.5 23247.5 -0.2485 11735.5 9881 12531.5 10716 0.857 11529.7549591599 0.982472713329757 13.3945150971988 0.601810179135015 0.60494484252448 0.922221753832454 0.936479282130573
RP11-498J1 12429852 210 9142 8989 3363 260 331.5 443.5 100 100 0 8415.5 8443.5 2960 1002.5 1039.5 392.5 100 99.5 0 0.835 0.853 0.8525 0.848 1.2755 0.8585 0.941 316 1542 16295 16170 -0.26 8882 7413 8729 7441 0.866 8560.04618937644 0.96437961276858 12.9853457645642 0.649473805552165 0.626224122964356 0.985413741509416 0.982256206171573
RP11-335F1 12429852 215 9597.5 9783.5 4248.5 351 440.5 461.5 99 98.5 0 9071.5 9424 3526.5 1270.5 1309.5 375.5 99 98.5 0 0.8485 0.871 0.8675 0.865 1.2695 0.867 0.9395 354 1207 17047.5 17586 -0.2375 9246.5 7801 9432.5 8153.5 0.7735 10085.3264382676 1.09725057957753 13.0356346769118 0.625027025982138 0.569613738696833 0.958567808390791 0.980411957640121
RP11-501C13 12429852 215 5351.5 6030.5 3605.5 301.5 408.5 624 100 99.5 0 5401.5 6109 3508.5 1054 1094 437.5 100 99.5 0 0.856 0.88 0.8745 0.865 1.32 0.9395 0.914 354 1121.5 9397.5 10784 -0.224 5050 4347.5 5729 5055 0.857 5072.92882147024 0.999112748095054 12.1508074639454 0.388431851057374 0.357360150965047 0.846632662869776 0.870028352543725
RP11-367E10 12429852 210 15289 15413 3209 329 382 289 100 100 0 13665.5 14031 3230.5 1203.5 1229 343.5 100 100 0 0.8345 0.851 0.841 0.8485 1.162 0.864 0.959 316 1254 27422 27911.5 -0.262 14960 12462 15084 12827.5 0.7735 16111.1829347123 1.07868087521536 13.7355097636813 0.769903191076266 0.792054612646303 0.971680735864237 0.991451152145574
RP11-338J16 12429852 200 7230.5 7614 3195 310.5 491 1088.5 100 98.5 0 6164.5 6586.5 2590 1126 1246.5 922.5 99.5 95 0 0.7305 0.748 0.741 0.732 1.31 0.782 0.9255 316 1542 11958.5 12764 -0.454 6920 5038.5 7303.5 5460.5 0.849 5934.62897526502 0.860058821605336 12.5204581890926 0.606199442692539 0.576811709071827 0.922072148520474 0.924593012570736
RP11-490K2 12429852 210 11859.5 11637 4674.5 263.5 380 767.5 96 94.5 0 12037 11993 4505.5 971.5 1045 703 96.5 94.5 0 0.961 0.975 0.9725 0.9765 1.3025 0.9705 0.945 354 1219 22661.5 22395 -0.059 11596 11065.5 11373.5 11021.5 0.866 12777.7136258661 1.10960880611633 13.4564539590866 0.613239775971121 0.577520064815606 0.992950246725324 0.980739158008318
RP11-491P10 12429852 230 49205 49583.5 9865 396 538.5 789.5 100 100 5.5 36323 37158 8404.5 1276 1339.5 670 100 100 0 0.7185 0.729 0.7245 0.725 1.1945 0.735 0.967 392 1018 83856 85069.5 -0.477 48809 35047 49187.5 35882 0.747 46917.0013386881 0.961728489756128 15.3331770046814 0.774501072869245 0.801338174894019 0.977118603683449 0.986474445812949
RP11-492D3 12429852 215 10872 12363.5 5293.5 303 388 398 100 100 0 9842 10894.5 4607.5 1088.5 1135 391 100 99.5 0 0.827 0.813 0.801 0.8035 1.2025 0.837 0.9525 354 1031.5 19322.5 21866.5 -0.274 10569 8753.5 12060.5 9806 0.857 10214.1190198366 0.965111109395387 13.2268631433807 0.576043507376607 0.571716780400061 0.891101115830334 0.876073944620853
RP11-541N19 12429852 220 5757.5 6078.5 2935.5 348 464.5 610.5 98.5 95 0 7854 8145.5 3410 1299.5 1359.5 509 98.5 97.5 0 1.209 1.192 1.2045 1.2 1.38 1.1875 0.9235 392 1159 11964 12576.5 0.2735 5409.5 6554.5 5730.5 6846 0.7735 8473.82029734971 1.56247505026207 12.524672462559 0.57944425030706 0.51549468567584 0.954278906052077 0.940946774384398
RP11-25L9 12429852 210 20947.5 21424.5 5663.5 352 513.5 1011 100 100 0 17331.5 17652.5 5183.5 1278 1431 1650 100 100 0 0.779 0.7775 0.772 0.77 1.1465 0.794 0.9635 316 1068.5 36649 37447 -0.3615 20595.5 16053.5 21072.5 16374.5 0.8155 19685.4690374003 0.955271184611254 14.1491904508752 0.705444953828418 0.735664741508147 0.976312528180092 0.977368943871662
RP11-518H12 12429852 220 14260 13748 6838 264 330 310 100 99.5 0 6732.5 6435 2799 1016 1052.5 370.5 98.5 97 0 0.4085 0.4015 0.394 0.392 1.4505 0.3955 0.932 392 1069 19712.5 18903 -1.2915 13996 5716.5 13484 5419 0.889 6430.25871766029 0.459495713382155 13.1245002814138 0.564987886569897 0.503135216468186 0.948551942155531 0.964248549820091
RP11-35P20 12429852 205 20486 21079 7226 412 641 1191.5 100 100 0 16122 16966 6099.5 1341 1415 668.5 100 99.5 0 0.7315 0.7545 0.744 0.7445 1.1725 0.769 0.963 316 1006 34855 36292 -0.455 20074 14781 20667 15625 0.728 20303.5714285714 1.00526818206409 14.0612633917701 0.635834024134479 0.656409330438018 0.939339216144544 0.960816677365339
RP11-366L14 12429852 205 4744.5 5022.5 1733.5 263 334 303 100 100 0 6230.5 6706 2201 1038 1074.5 339 100 100 0 1.161 1.194 1.2175 1.1935 1.318 1.223 0.896 316 1153 9674 10427.5 0.212 4481.5 5192.5 4759.5 5668 0.866 5995.9584295612 1.34096060210897 12.2350536139479 0.670955558314058 0.654573565601726 0.915775624787846 0.942187678050328
RP11-568A9 12429852 215 11215.5 11672 4345 322.5 535 1065 100 99.5 0 10540 10953.5 3879 1051 1158.5 772.5 100 100 0 0.878 0.875 0.876 0.8785 1.208 0.88 0.9535 354 1533 20382 21252 -0.1895 10893 9489 11349.5 9902.5 0.857 11072.3453908985 1.02447431012497 13.29953335851 0.646795296907197 0.628817716799043 0.955831713155013 0.937047070083541
RP11-272A1 12429852 245 7555.5 9605 5916 419.5 711.5 1944 99 95 0 6039 8248 5696.5 1295 1443 1192.5 99.5 98 0 0.665 0.756 0.72 0.705 1.309 0.8335 0.9195 460 1342 11880 16138.5 -0.5895 7136 4744 9185.5 6953 0.747 6350.73627844712 0.890366521638665 12.5061057705025 0.312687789088565 0.38419672503665 0.685285853526235 0.777299586868474
RP11-542O22 12429852 240 21193 21063.5 5938.5 388.5 685 2146.5 100 99 0 14957.5 14979.5 4044.5 1353.5 1572 1949 99.5 97.5 0 0.6585 0.664 0.653 0.663 1.1875 0.67 0.9545 460 685 34408.5 34301 -0.6035 20804.5 13604 20675 13626 0.747 18211.5127175368 0.881628453849838 14.018482382912 0.731465706123641 0.723418686567977 0.99357239279764 0.994652222412665

Total number of rows: 2929

Table truncated, full table size 997 Kbytes.




Supplementary file Size Download File type/resource
GSM185087.gpr.gz 777.2 Kb (ftp)(http) GPR

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