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Sample GSM185158 Query DataSets for GSM185158
Status Public on May 08, 2007
Title Bone, NOS, Osteosarcoma, NOS (C40._, C41._) (12457588)
Sample type genomic
 
Channel 1
Source name TB0937DF1X10
Organism Homo sapiens
Characteristics Cell Line TI-73
TB0937DF1X10
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; 12/6/2002
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 12457588 200 2035.5 2054 818 315 461 726.5 86.5 58.5 0 2460 2490 872 592.5 673 502.5 94.5 83 0 1.0865 1.0935 1.1255 1.113 1.7895 0.981 0.705 316 1015.5 3588 3636.5 0.119 1720.5 1867.5 1739 1897.5 1.0935 1707.81893004115 0.993517578084525 10.8073517829398 0.650205694926192 0.598493011684444 0.953172867463289 0.989245342152441
RP11-67E18 12457588 240 19790 20055 5769 402 493 576 100 100 0 16465 16784.5 4711.5 666 712 336 100 100 0 0.8145 0.82 0.817 0.8215 1.168 0.8175 0.9715 460 1257 35187 35771.5 -0.298 19388 15799 19653 16118.5 0.875 18056 0.930791429527828 14.0939638700591 0.719341091425656 0.712360136340682 0.980735703741257 0.986482071609995
RP11-291C17 12457588 220 9986.5 11275.5 5451.5 462.5 582.5 802 99.5 99 0 10100.5 11730.5 5564.5 706.5 774.5 534 99.5 99.5 0 0.986 1.02 1.0195 1.0235 1.245 1.0205 0.9365 392 1432.5 18918 21837 -0.02 9524 9394 10813 11024 1.032 9102.71317829457 0.955632562217899 13.2045619195893 0.523636896229355 0.515298234015838 0.854451205593816 0.883926205269578
RP11-506N24 12457588 220 8989.5 9618 4105.5 484.5 722 941 98 96.5 0 8979 9665 3852 672 867.5 816 99 97.5 0 0.9705 0.981 0.9905 0.9955 1.266 0.9705 0.949 392 901.5 16812 18126.5 -0.0445 8505 8307 9133.5 8993 1.032 8049.41860465117 0.940420952971055 13.0165056819043 0.597578346996854 0.57275192017887 0.917184941145194 0.927373363851537
RP11-498J1 12457588 210 6579.5 7339.5 4055 309.5 373.5 429 100 99.5 0 7134.5 8491 4819 589.5 629.5 348.5 100 100 0 1.036 1.1225 1.1115 1.0955 1.297 1.1505 0.942 316 1539 12815 14931.5 0.0455 6270 6545 7030 7901.5 1.0725 6102.5641025641 0.966193600203804 12.6322057837348 0.426748227103799 0.445278946239215 0.822303356902891 0.890495849982606
RP11-335F1 12457588 210 6632 7916 4668 481 739 2012 99 76 0 6596 8104 4353 748 882 1101 100 96 0 0.951 0.989 0.976 0.98 1.348 0.937 0.856 316 1109 11999 14791 -0.073 6151 5848 7435 7356 0.899 6505.00556173526 1.05755252182332 12.550166428278 0.462857847976308 0.410308236483072 0.79499728113105 0.827303295225286
RP11-501C13 12457588 230 3030 4305 3900 459 925 2034 57 32 0 3862 5756 5340 687 998 1401 77 55 0 1.235 1.318 1.294 1.384 1.747 1.333 0.827 392 1003 5746 8915 0.304 2571 3175 3846 5069 1.032 3076.5503875969 1.19663570112676 11.4803273856903 0.0722724113968033 0.0940766550522648 0.62635628329059 0.668486739469579
RP11-367E10 12457588 215 10460.5 10969.5 3893.5 496 637 1222 98.5 96.5 0 9520.5 10238 3696 739 837 888 99 98 0 0.878 0.907 0.898 0.908 1.265 0.909 0.943 354 1139 18746 19972.5 -0.1885 9964.5 8781.5 10473.5 9499 0.899 9768.07563959957 0.976756547426074 13.1815983408558 0.631331386223835 0.63732083661604 0.922539048343574 0.953700019241764
RP11-338J16 12457588 165 3045 3798.5 2459.5 474.5 659.5 1195 86.5 48 0 2920.5 3501 1735 717 829.5 796 91 65.5 0 0.863 0.872 0.88 0.8815 1.756 0.8275 0.732 206 1194 4774 6108 -0.2125 2570.5 2203.5 3324 2784 0.986 2234.78701825558 0.875623322307209 11.1065455295102 0.535258459726008 0.422824523121005 0.814038500994007 0.824725721695606
RP11-490K2 12457588 205 8225.5 8913.5 4215 399.5 448 295 100 100 0 8940.5 9414 4002.5 601 631.5 262.5 100 100 0 1.0665 1.034 1.05 1.0545 1.2375 1.0145 0.9505 316 1232.5 16165.5 17327 0.0865 7826 8339.5 8514 8813 1.0725 7775.75757575758 0.994142499954695 12.977201485165 0.577088123802179 0.527534123973261 0.945382571679925 0.91946526838722
RP11-491P10 12457588 245 20202 25550.5 14995 499.5 679.5 947.5 99.5 99.5 0 17171.5 22036.5 13104 736 842 629.5 99.5 99.5 0 0.835 0.8515 0.845 0.848 1.231 0.856 0.9615 460 843 36138 46351.5 -0.2605 19702.5 16435.5 25051 21300.5 0.875 18783.4285714286 0.954248094501775 14.1310613756632 0.404954478446 0.412550164825247 0.770650773146804 0.78536690684606
RP11-492D3 12457588 220 7335 8286 3886 462 611.5 837.5 99.5 98 0 8094 8969.5 4185 669.5 755 516.5 100 99.5 0 1.0765 1.0605 1.044 1.0545 1.3175 1.0625 0.9185 392 954.5 14297.5 16124 0.1055 6873 7424.5 7824 8300 1.032 7194.28294573644 1.04333747557238 12.7940916881976 0.529030421605735 0.528548476211738 0.891560122875251 0.877951868851595
RP11-541N19 12457588 215 9086.5 10507 6802 510 713 1338 99 94.5 0 7938 9447.5 5667 769 868 712.5 99.5 99 0 0.8455 0.881 0.895 0.889 1.2665 0.8585 0.9215 354 1130 15745.5 18675.5 -0.244 8576.5 7169 9997 8678.5 0.899 7974.41601779756 0.940587492048645 12.9111644762401 0.398809085237793 0.35710884580365 0.82776486539761 0.862433366890565
RP11-25L9 12457588 215 13168 14598.5 5661.5 489.5 595 568 99.5 99.5 0 12481.5 13808 4847.5 743 813.5 461.5 100 99.5 0 0.933 0.9315 0.9375 0.944 1.1955 0.9255 0.9595 354 990 24417 27174 -0.102 12678.5 11738.5 14109 13065 0.9545 12298.0618124673 0.976985336853835 13.558696034963 0.646719824551867 0.611514587084103 0.900357963071429 0.899751786448823
RP11-518H12 12457588 225 4481.5 4639 2897 289.5 384 482 96.5 90.5 0 5721 5708.5 3074 586.5 663 466 98 94 0 1.2245 1.1755 1.1955 1.211 1.4945 1.1365 0.897 392 1048 9326.5 9471.5 0.2905 4192 5134.5 4349.5 5122 1.0935 4695.47325102881 1.11954197383967 12.1785669948835 0.46060557754287 0.375308437205625 0.973263787662901 0.964654218967272
RP11-35P20 12457588 210 20398 21472 8691 597.5 907.5 1360.5 100 100 0 16155.5 16950 6451.5 746.5 908 709.5 100 100 0 0.7795 0.7765 0.7835 0.7825 1.162 0.7675 0.973 316 959.5 35209.5 37078 -0.365 19800.5 15409 20874.5 16203.5 0.8165 18872.0146968769 0.955104239645824 14.0903854847374 0.621866568967388 0.595205804568583 0.95166100803202 0.94850683151494
RP11-366L14 12457588 205 3875.5 4589 2386 394.5 483.5 402 99.5 96 0 4538 5410.5 2718.5 662 717.5 397 99.5 96.5 0 1.102 1.1275 1.1135 1.1185 1.4255 1.1405 0.9065 316 1164.5 7357 8943 0.134 3481 3876 4194.5 4748.5 1.0725 3613.98601398601 1.02748273273706 11.8229210781136 0.489534956945014 0.475697703830696 0.810489080437011 0.8317460113715
RP11-568A9 12457588 220 10229.5 10829.5 5229 415.5 493 482.5 99.5 98.5 0 11489 11861.5 4705.5 813.5 1216.5 1553.5 98.5 95 0 1.101 1.069 1.071 1.109 1.3705 1.024 0.9035 392 1406.5 20489.5 21462 0.1235 9814 10675.5 10414 11048 1.032 10344.4767441861 1.0667269648955 13.3174975980365 0.603491521070401 0.513025542053532 0.965661124279641 0.941308269618303
RP11-272A1 12457588 250 9354 10788.5 6151.5 431 754 2274 96.5 78.5 0 7957.5 10465 7535.5 674 872.5 1780.5 95.5 77 0 0.8205 0.9505 0.8685 0.8715 1.364 1.0435 0.911 460 1234 16206.5 20148.5 -0.2955 8923 7283.5 10357.5 9791 0.875 8324 0.937698462076925 12.9742603739875 0.279795912141297 0.428190750073614 0.743618278598051 0.863228471390857
RP11-542O22 12457588 250 9409 10717.5 6122.5 500.5 635.5 760 100 99 0 9268.5 10487 5851.5 731 818 609 100 99.5 0 0.9585 0.9545 0.951 0.952 1.2525 0.954 0.9575 460 645 17446 19973 -0.0605 8908.5 8537.5 10217 9756 0.875 9757.14285714286 1.09588026331951 13.0897180587366 0.441789260196357 0.428544399759257 0.876842810343081 0.872586352228047

Total number of rows: 2901

Table truncated, full table size 975 Kbytes.




Supplementary file Size Download File type/resource
GSM185158.gpr.gz 769.8 Kb (ftp)(http) GPR

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