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Sample GSM186428 Query DataSets for GSM186428
Status Public on May 08, 2007
Title Bone, NOS, Osteosarcoma, NOS (C40._, C41._) (12409889)
Sample type genomic
 
Channel 1
Source name TB0829DF1X10
Organism Homo sapiens
Characteristics Cell Line KHOS-NP
TB0829DF1X10
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 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.
 
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 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.
 
 
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; 9/21/2002
Data processing All spots were subjected to a pin-tip normalization.
 
Submission date May 02, 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 12409889 200 1216.5 1306 584.5 233 266 189 89 78.5 0 1581 1666.5 560.5 443.5 479.5 227.5 97 88.5 0 1.3825 1.2755 1.3035 1.3585 2.044 1.2275 0.59 316 1109.5 2121 2296 0.408 983.5 1137.5 1073 1223 1.134 1003.08641975309 1.21927627308311 9.84974773617047 0 0 0 0
RP11-67E18 12409889 235 14380 15354.5 5492 483.5 580 624 100 99.5 0 10304.5 10833 3646.5 603.5 657 425 99.5 99.5 0 0.707 0.699 0.6935 0.702 1.1915 0.69 0.9645 426 1210.5 23597.5 25100.5 -0.507 13896.5 9701 14871 10229.5 0.793 12233.2912988651 0.891463136786965 13.4960244097242 0 0 0 0
RP11-291C17 12409889 225 7227 9011.5 4855.5 374.5 426.5 290 99.5 99.5 0 6420.5 8170.5 4280 542.5 574.5 252.5 100 99.5 0 0.8575 0.8835 0.877 0.884 1.341 0.8815 0.946 392 1456 12730.5 16265 -0.222 6852.5 5878 8637 7628 0.943 6233.29798515376 0.909113892688838 12.6254497074339 0 0 0 0
RP11-506N24 12409889 220 11746.5 13240 6357 323 379.5 283.5 100 100 0 10516.5 11551 5378.5 497.5 530.5 255.5 100 100 0 0.8975 0.8735 0.8715 0.875 1.219 0.8705 0.9615 392 929.5 21442.5 23970.5 -0.1615 11423.5 10019 12917 11053.5 0.943 10624.6023329799 0.951958331719556 13.3489632938687 0 0 0 0
RP11-498J1 12409889 210 4876.5 5534 2830.5 246 291.5 243 100 100 0 4714 5455.5 2704.5 454.5 487.5 264.5 100 100 0 0.926 0.9605 0.961 0.9505 1.3425 0.9805 0.9215 316 1521.5 8890 10289 -0.1115 4630.5 4259.5 5288 5001 1.0015 4253.12031952072 0.924899529879953 12.0952743432055 0 0 0 0
RP11-335F1 12409889 200 10035 10308 4262 410.5 460.5 285 100 100 0 8245.5 8511 3403.5 586 618.5 281 100 100 0 0.801 0.806 0.799 0.8095 1.2495 0.8025 0.9475 316 1316 17284 17822.5 -0.3215 9624.5 7659.5 9897.5 7925 0.8225 9312.46200607903 0.973670777230534 13.0512261977916 0 0 0 0
RP11-501C13 12409889 215 1310 1431 727 340 386 256 91.5 77.5 0 1490.5 1591 636 506.5 540 255.5 93.5 82 0 1.021 1 1.037 1.025 2.0435 0.943 0.5945 354 970 1954 2175.5 0.0285 970 984 1091 1084.5 0.943 1043.47826086957 1.08291916917754 9.92463861586386 0 0 0 0
RP11-367E10 12409889 195 16902.5 17751 5679.5 450 515.5 418 100 100 0 13541 14068.5 4073.5 572 626 395.5 100 100 0 0.803 0.7935 0.7945 0.7985 1.1745 0.783 0.9625 286 1286.5 29421.5 30797.5 -0.321 16452.5 12969 17301 13496.5 0.8225 15767.7811550152 0.976383383996841 13.8094010001172 0 0 0 0
RP11-338J16 12409889 155 1257.5 1342 551.5 345 395 260.5 94 78 0 1520 1618.5 622.5 525 563 251 95 83 0 1.0995 1.1015 1.118 1.0895 2.247 1.142 0.449 182 1137 1907.5 2090.5 0.134 912.5 995 997 1093.5 0.9015 1103.71602884082 1.21948187725432 9.88717288303529 0 0 0 0
RP11-490K2 12409889 205 8530.5 8892 2545 294 345 285 100 100 0 7946.5 8106.5 2158 466 502 271 100 100 0 0.915 0.9005 0.907 0.9035 1.2425 0.896 0.9385 316 1177.5 15717 16238.5 -0.1295 8236.5 7480.5 8598 7640.5 1.0015 7469.29605591613 0.91373852469953 12.9217729553003 0 0 0 0
RP11-491P10 12409889 220 44203.5 42379 12380 494 704 1245 99.5 99.5 8 31240.5 32547 10573 616.5 745 859.5 100 100 3 0.7075 0.759 0.722 0.763 1.349 0.7635 0.942 392 1178.5 74333.5 73815.5 -0.501 43709.5 30624 41885 31930.5 0.793 38617.9066834804 0.892125670226713 15.1372746991946 0 0 0 0
RP11-492D3 12409889 230 11163 13959.5 8487.5 334 384.5 268.5 100 100 0 10613 12578.5 7336 524 549 238.5 100 100 0 0.9565 0.906 0.914 0.9035 1.2415 0.899 0.954 392 937 20918 25680 -0.068 10829 10089 13625.5 12054.5 0.943 10698.8335100742 1.0143455031236 13.2786596609332 0 0 0 0
RP11-541N19 12409889 205 8530 8818.5 3902 431.5 486 315.5 100 100 0 6928.5 7215 3100.5 572.5 606.5 297.5 100 100 0 0.7825 0.7935 0.786 0.7915 1.2525 0.7905 0.945 316 1260 14454.5 15029.5 -0.3535 8098.5 6356 8387 6642.5 0.8225 7727.65957446809 0.9516524768819 12.7580802449246 0 0 0 0
RP11-25L9 12409889 220 16139 17283.5 6578 379 413.5 245 100 100 0 13253 14450.5 6639.5 582.5 603.5 238.5 100 100 0.5 0.8025 0.8165 0.7885 0.8135 1.235 0.8455 0.8985 392 856.5 28430.5 30772.5 -0.3175 15760 12670.5 16904.5 13868 0.858 14767.4825174825 0.935446862349007 13.7676793360842 0 0 0 0
RP11-518H12 12409889 220 3806.5 4532 2425.5 226.5 266 188 99 98.5 0 8297.5 10245 5297.5 449 473 216 99.5 99.5 0 2.2935 2.3745 2.3795 2.435 1.3915 2.3995 0.9355 392 1169 11428.5 14101.5 1.1825 3580 7848.5 4305.5 9796 1.134 6921.0758377425 2.02266123823497 12.3256276186629 0 0 0 0
RP11-35P20 12409889 210 19630 22705.5 10185 490.5 545 314 100 100 0 13748 15476.5 6684 573 604 247.5 100 100 0 0.694 0.6765 0.671 0.679 1.1915 0.6695 0.964 316 972 32314.5 37118.5 -0.531 19139.5 13175 22215 14903.5 0.7655 17210.9732201176 0.906765901924164 13.9502384460784 0 0 0 0
RP11-366L14 12409889 210 4740.5 4953 1882.5 247 291.5 230 100 100 0 5056 5343 1883 439.5 467.5 224.5 100 100 0 1.073 1.0825 1.0815 1.092 1.338 1.079 0.8995 316 1178 9110 9609.5 0.0905 4493.5 4616.5 4706 4903.5 1.0015 4609.58562156765 1.07140790166774 12.0894908458534 0 0 0 0
RP11-568A9 12409889 215 12556 12617 3715 355.5 416.5 324.5 100 100 0 11600 11747.5 2994.5 545 588 301.5 100 99.5 0 0.907 0.9155 0.9125 0.921 1.2175 0.9045 0.9555 354 1414.5 23255.5 23464 -0.1415 12200.5 11055 12261.5 11202.5 0.943 11723.2237539767 0.961664715763335 13.5027500307541 0 0 0 0
RP11-272A1 12409889 240 9879 12886 8519.5 535.5 654 672.5 99.5 99 0 7182.5 9631.5 7053.5 619.5 702.5 521 99 99 0 0.708 0.734 0.701 0.708 1.2775 0.768 0.935 460 1351.5 15906.5 21362.5 -0.5055 9343.5 6563 12350.5 9012 0.793 8276.16645649432 0.892879702339146 12.932534359906 0 0 0 0
RP11-542O22 12409889 235 15216 16427.5 7969.5 504 717.5 1093 99.5 99 0 14491.5 16023 7415 628 824.5 1131.5 100 99.5 0 0.9565 0.981 0.991 0.9915 1.1995 0.9825 0.9615 426 795 28575.5 31318.5 -0.0665 14712 13863.5 15923.5 15395 0.793 17482.3455233292 1.20677259705961 13.7731429989643 0 0 0 0

Total number of rows: 2941

Table truncated, full table size 806 Kbytes.




Supplementary file Size Download File type/resource
GSM186428.gpr.gz 1009.3 Kb (ftp)(http) GPR

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