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Sample GSM185218 Query DataSets for GSM185218
Status Public on May 08, 2007
Title Tibia, Chondroblastic osteosarcoma (C40._, C41._) (12432597)
Sample type genomic
 
Channel 1
Source name TB1160DF1T20
Organism Homo sapiens
Characteristics Tissue
TB1160DF1T20
Growth protocol Tibia; Chondroblastic osteosarcoma (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 female
Organism Homo sapiens
Characteristics pooled female
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 Tibia; Chondroblastic osteosarcoma (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 12432597 215 5333 5784.5 2516 99.5 182 543.5 99 97.5 0 5524 5950.5 2379.5 637.5 714.5 604.5 98 93.5 0 0.901 0.9175 0.903 0.879 1.41 0.9305 0.9315 354 1033.5 10120 10998 -0.1535 5233.5 4886.5 5685 5313 1.01 4838.11881188119 0.892144590476684 12.0534960827907 0.527431057104135 0.474754649639105 0.863027207889407 0.877269374834387
RP11-67E18 12432597 245 17922.5 19602.5 10143 127.5 258 1183 99.5 99 0 14499 15830 7500.5 853 943.5 650 99.5 99.5 0 0.7665 0.7675 0.793 0.7835 1.2795 0.7465 0.916 460 1238.5 31441 34452 -0.3845 17795 13646 19475 14977 0.812 16805.4187192118 0.943451850925904 13.9132150142347 0.543160019568548 0.501408532262213 0.923244756129078 0.924570742875049
RP11-291C17 12432597 205 28949 29525.5 9974 122 175.5 300.5 100 100 0 26449 26947.5 8765 707 746.5 340 100 100 0 0.8925 0.8935 0.8945 0.897 1.1675 0.893 0.9715 316 1581.5 54569 55644 -0.164 28827 25742 29403.5 26240.5 0.9085 28334.6175013759 0.982208033094891 14.7230401134761 0.677663216260827 0.66262539415328 0.981362077507457 0.982234576016753
RP11-506N24 12432597 210 22922.5 25013 9953.5 112 160 488 100 100 0 19238.5 20961 8039.5 679.5 708.5 252.5 100 100 0 0.8135 0.8145 0.818 0.816 1.167 0.811 0.9615 316 1056.5 41369.5 45182.5 -0.2975 22810.5 18559 24901 20281.5 0.9085 20428.1783159054 0.895531992677477 14.3285649271615 0.616433661845212 0.60206657212949 0.915044368065604 0.916046788133503
RP11-498J1 12432597 205 9136 9794 4525.5 99 165 455 100 100 0 10601 11035 4882 635 699.5 615 100 100 0 1.1075 1.0795 1.069 1.077 1.2455 1.096 0.937 316 1554.5 19003 20095 0.146 9037 9966 9695 10400 0.966 10316.7701863354 1.14614633305873 13.2075025706353 0.55846361684266 0.541036354859673 0.96059220945431 0.936258818858809
RP11-335F1 12432597 215 7818 9805 7187.5 140.5 242.5 529.5 100 99.5 0 7254 8251 4707.5 894.5 959.5 483 99 98.5 0 0.829 0.7665 0.793 0.786 1.3825 0.7085 0.855 354 1245.5 14037 17021 -0.271 7677.5 6359.5 9664.5 7356.5 0.832 7643.6298076923 0.995986880155717 12.7695945508951 0.432256813302689 0.278621425866723 0.865481576701266 0.801213991472642
RP11-501C13 12432597 225 4764.5 5640 3542 125 187 303 99.5 99 0 4749.5 5387.5 3127.5 685 733 371 99 99 0 0.872 0.8505 0.8475 0.8355 1.3725 0.862 0.9095 392 1072.5 8704 10217.5 -0.2 4639.5 4064.5 5515 4702.5 0.9085 4473.85800770501 0.959865844598931 12.0750497251904 0.417146792601338 0.372319663804353 0.864651259204154 0.845235198968169
RP11-367E10 12432597 205 20461.5 22037.5 10649 138 175.5 268.5 100 100 0 15850.5 17319.5 8140 842.5 874.5 295.5 100 100 0 0.7385 0.7525 0.7495 0.762 1.303 0.746 0.904 316 1222.5 35331.5 38376.5 -0.437 20323.5 15008 21899.5 16477 0.832 18038.4615384616 0.88772531008611 14.0917022240344 0.530050279635838 0.516981725480141 0.910749848916013 0.927895221518315
RP11-338J16 12432597 215 15441 17350.5 9761 136.5 260.5 932 96.5 87.5 1.5 15150 16913.5 9163 764.5 868.5 958 93 85 0.5 0.936 0.9435 0.937 0.9225 1.373 0.963 0.94 354 1558 29690 33363 -0.0955 15304.5 14385.5 17214 16149 0.889 16181.664791901 1.05277323603495 13.4030178820663 0.372036346189827 0.348711394246262 0.840781293665914 0.846337681048577
RP11-490K2 12432597 200 16498.5 17508 6278 114.5 168 248 100 100 0 14591 15786.5 5479.5 635 682 333 100 100 0 0.8525 0.8705 0.8685 0.874 1.191 0.87 0.9595 316 1221 30340 32545 -0.233 16384 13956 17393.5 15151.5 0.966 14447.2049689441 0.882840393311374 13.8833397860565 0.65345039404567 0.641420682602306 0.920763593343074 0.942178369056838
RP11-491P10 12432597 235 40376 42638.5 15532 147 210 399.5 100 100 9 33540 36472.5 14746.5 882.5 939 459.5 100 100 3 0.812 0.8375 0.803 0.826 1.2905 0.8545 0.951 426 854.5 72886.5 78081.5 -0.301 40229 32657.5 42491.5 35590 0.812 40218.5960591133 0.999682444768785 15.1442604994298 0.594190279871408 0.633698523130056 0.917610024602478 0.946792743875206
RP11-492D3 12432597 215 16966 19012.5 11070.5 120.5 153.5 175.5 100 100 0 15982.5 17265 8682.5 691.5 726.5 304.5 100 100 0 0.909 0.8775 0.9105 0.9035 1.2585 0.842 0.925 354 1088 32136.5 35465.5 -0.1385 16845.5 15291 18892 16573.5 0.9085 16831.0401761144 1.00040418317411 13.9693382662448 0.496768674335462 0.418377153890729 0.922555304006979 0.892159185859894
RP11-541N19 12432597 210 10156.5 11287 7008 144.5 227.5 552.5 100 100 0 9556 10066 5470 866 965.5 757 100 99.5 0 0.868 0.8335 0.8565 0.8345 1.3 0.8385 0.8775 316 1162.5 18702 20342.5 -0.205 10012 8690 11142.5 9200 0.832 10444.7115384616 1.0433562375261 13.1869655168315 0.456547992318528 0.393137000412497 0.944920953070187 0.907561216787286
RP11-25L9 12432597 215 21348 23288 12606 142 224.5 388 99.5 99 1 17216 18716.5 9644 853 894 359.5 100 99.5 0.5 0.776 0.776 0.7905 0.7945 1.319 0.765 0.9065 354 1034 37569 41009.5 -0.368 21206 16363 23146 17863.5 0.879 18615.4721274175 0.883031835587419 14.1813328173623 0.489400874033816 0.462295532986084 0.917772091227439 0.918146451102252
RP11-518H12 12432597 215 6918 7539.5 4071.5 99 154 288 100 99.5 0 7267.5 7749 3601.5 659.5 710 363 99.5 99.5 0 0.974 0.9565 0.962 0.955 1.2945 0.943 0.9285 354 1116 13427 14530 -0.04 6819 6608 7440.5 7089.5 1.01 6542.57425742575 0.963962711563493 12.7075385393097 0.533924570194316 0.457154504379016 0.939007084467785 0.922281023757636
RP11-35P20 12432597 205 24080.5 26461 12361.5 149.5 241 667.5 100 100 0 19945.5 21747 9720.5 930.5 1007.5 711 100 100 0 0.8015 0.795 0.8145 0.8075 1.2255 0.7835 0.9285 316 1020 42946 47128 -0.3235 23931 19015 26311.5 20816.5 0.7915 24024.0050536955 1.01320868986227 14.3759614640431 0.552441267345725 0.52742443622005 0.913282032225119 0.90710211890601
RP11-366L14 12432597 215 6645.5 7340 3811.5 111.5 176.5 329 99 98 0 7550 8254.5 3919.5 633.5 701.5 421.5 97.5 97 0 1.053 1.053 1.0625 1.0505 1.3825 1.0555 0.9165 354 1113 13450.5 14849.5 0.074 6534 6916.5 7228.5 7621 0.966 7159.93788819876 1.09029720908474 12.689141813337 0.518920618453254 0.475029935207853 0.902233497828359 0.902075847245773
RP11-568A9 12432597 210 17616 17881 8039 114 174 297.5 100 100 0 16008 15923 5998 678.5 725.5 356 100 100 0 0.876 0.858 0.871 0.8785 1.2375 0.831 0.9475 354 1522.5 32831.5 33011.5 -0.191 17502 15329.5 17767 15244.5 0.9085 16873.417721519 0.964217584622282 13.9995776235778 0.623673639271027 0.549623727250661 0.993868747012497 0.985060529393376
RP11-272A1 12432597 245 8433 11796 9117.5 152 226 470.5 100 100 0 8306 11187 8270 876.5 923.5 401.5 100 99.5 0 0.8935 0.8875 0.8845 0.868 1.265 0.8945 0.914 460 1348 15710.5 21954.5 -0.1695 8281 7429.5 11644 10310.5 0.812 9149.63054187193 1.10063767401559 12.929873080054 0.255839382745312 0.228019736478517 0.717273547267578 0.712298181450682
RP11-542O22 12432597 235 14173 15939 8259 150 315.5 1059 100 100 0 13106 14066.5 6520 927 1090 1279.5 100 100 0 0.87 0.835 0.845 0.8415 1.2365 0.8235 0.913 426 687 26202 28928.5 -0.202 14023 12179 15789 13139.5 0.812 14998.7684729064 1.07090644637753 13.6724305595176 0.541031635145659 0.491092319744284 0.928926427909589 0.892454488647717

Total number of rows: 2863

Table truncated, full table size 968 Kbytes.




Supplementary file Size Download File type/resource
GSM185218.gpr.gz 771.8 Kb (ftp)(http) GPR

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