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Sample GSM185285 Query DataSets for GSM185285
Status Public on May 08, 2007
Title Humerus, Leiomyosarcoma, NOS (13074677)
Sample type genomic
 
Channel 1
Source name TB2705DF1T10
Organism Homo sapiens
Characteristics Tissue
TB2705DF1T10
Growth protocol Humerus; Leiomyosarcoma, NOS
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 reference
Organism Homo sapiens
Characteristics pooled reference
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 Humerus; Leiomyosarcoma, NOS; University of Pennsylvania; 11/19/2004
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 13074677 150 28918.5 27886.5 6776 441.5 875.5 2269.5 99 97.5 0 15072.5 14511.5 4036 695.5 1097.5 2310.5 98 92 0 0.505 0.5035 0.4965 0.494 1.1675 0.5265 0.941 156 591 42854 41261 -0.9865 28477 14377 27445 13816 0.635 22640.9448818898 0.795037630083876 14.3043574024354 0.721262037417016 0.756189644057979 0.961710234273894 0.963799076357714
RP11-69E9 13074677 150 32564.5 32503.5 8106 481.5 641 1149.5 100 100 0 19712.5 21081.5 8278.5 736.5 874.5 1203 100 100 0 0.597 0.6425 0.609 0.618 1.2115 0.7235 0.922 156 734.5 51059 52367 -0.748 32083 18976 32022 20345 0.7025 27012.0996441281 0.850016470785204 14.5840386493695 0.608401345748967 0.753151439632687 0.933568259824284 0.986065515682897
RP11-67E18 13074677 125 2368 2355.5 662.5 532.5 571.5 360.5 98.5 95.5 0 1853 1858 565.5 844 880 390 88 62.5 0 0.5495 0.5555 0.564 0.5075 2.1155 0.6025 0.4435 120 588 2844.5 2837 -0.864 1835.5 1009 1823 1014 0.742 1359.83827493262 0.740457322694516 10.4076609249318 0.69518403672739 0.717867362095996 0.979708989128749 0.993489013426612
RP11-291C17 13074677 145 14565 14339.5 4428.5 446.5 487.5 448 100 100 0 8584 8818.5 3622.5 752.5 790.5 361.5 99.5 99 0 0.5645 0.5885 0.5715 0.5575 1.3235 0.682 0.912 156 818 21950 21959 -0.8275 14118.5 7831.5 13893 8066 0.699 11203.8626609442 0.807634144872266 13.3170932534641 0.59423769148866 0.696648827009958 0.972978654821282 0.985771139518975
RP11-506N24 13074677 145 16019.5 15917.5 2821.5 479.5 543 518 100 100 0 8765.5 8623 1996.5 740.5 855 1046.5 99 98 0 0.5155 0.51 0.5025 0.498 1.2465 0.523 0.875 156 677 23565 23320.5 -0.955 15540 8025 15438 7882.5 0.649 12365.1771956857 0.794894591830736 13.4439766615524 0.766998726556948 0.823080823084209 0.981822155894206 0.993155350915046
RP11-262N9 13074677 140 22840 21773 4603 516.5 574 389 100 100 0 19208 18319 4105.5 858.5 940.5 1013.5 100 99 0 0.825 0.826 0.8335 0.816 1.316 0.828 0.9395 156 658 40673 38717 -0.2795 22323.5 18349.5 21256.5 17460.5 0.742 24729.7843665768 1.111441657325 14.3012302074421 0.776092308047764 0.787057106280719 0.95215007305056 0.951373456071561
RP11-498J1 13074677 140 14189 13946.5 4159.5 436 650.5 1651.5 100 99 0 10994.5 11018 4215 746 889.5 1227.5 98.5 97 0 0.7495 0.768 0.748 0.7325 1.2995 0.8225 0.9395 156 676.5 24001.5 23782.5 -0.4175 13753 10248.5 13510.5 10272 0.717 14293.5843793584 1.04533188625513 13.5278969858859 0.619430365033698 0.701931442086399 0.997829479910539 0.979704104981632
RP11-335F1 13074677 150 8421.5 8665 2991.5 523.5 712 1012.5 98 90 0 6116 6767 3318.5 767.5 991 1289 83.5 61.5 0 0.665 0.73 0.7025 0.6595 1.5645 0.945 0.839 156 659.5 13246.5 14141 -0.5895 7898 5348.5 8141.5 5999.5 0.742 7208.22102425879 0.896278279637936 12.4510378682234 0.499478114413492 0.656111527689633 0.881597802535722 0.968036755387925
RP11-260B11 13074677 150 10082.5 9300.5 3757 458 807 2338 99 77.5 0 6462.5 6412.5 3211 730.5 982.5 1951.5 91 64.5 0 0.5955 0.6425 0.621 0.5985 1.412 0.7665 0.883 156 653 15356.5 14524.5 -0.7475 9624.5 5732 8842.5 5682 0.6405 8949.25839188134 0.929767874732111 12.8585184733668 0.498984985268987 0.595974618091303 0.991290289433122 0.918699716521388
RP11-367E10 13074677 155 13941.5 14841 3928.5 539 941.5 1910.5 100 100 0 10589 12778.5 6153 803.5 1351 2627 99 81.5 0 0.7305 0.839 0.751 0.7745 1.41 1.012 0.814 182 598 23188 26277 -0.453 13402.5 9785.5 14302 11975 0.742 13188.0053908355 0.984670168537215 13.4816017391893 0.51812830759678 0.73335161395119 0.817079582962938 0.936600753721538
CTD-2341I10 13074677 145 13693.5 13432 4088.5 467 563.5 595 100 100 0 8035.5 8110 3283.5 732.5 798 603 100 99 0 0.555 0.57 0.547 0.542 1.312 0.6375 0.8915 156 679 20529.5 20342.5 -0.8505 13226.5 7303 12965 7377.5 0.7025 10395.7295373665 0.789545262764675 13.2175478273341 0.606241883466951 0.698425798168311 0.99082317154307 0.982409011522614
RP11-490K2 13074677 150 15411.5 15558.5 7048.5 450.5 607.5 1119 100 100 0 9063.5 9645.5 5112.5 686 809.5 1107 99.5 95.5 0 0.5595 0.5925 0.5715 0.555 1.272 0.663 0.9415 156 696 23338.5 24067.5 -0.838 14961 8377.5 15108 8959.5 0.65 12888.4615384616 0.860792567335422 13.4464497108873 0.467494678074913 0.545369666886335 0.934399513026786 0.978813189931599
RP11-491P10 13074677 140 23113.5 22727.5 4148.5 540 739.5 1645.5 100 100 0 18102 17854 3523.5 825 1057 2111 100 99 0 0.765 0.7675 0.752 0.7665 1.306 0.7695 0.9195 156 671 39850.5 39216.5 -0.386 22573.5 17277 22187.5 17029 0.742 23284.3665768194 1.0314879865145 14.2694471325731 0.802679959331509 0.817189645886544 0.985648631133507 0.982886166061815
RP11-43H17 13074677 150 16424 15409 5017.5 468 619 1058.5 100 100 0 12766 12151 4743.5 729.5 917 1450 99.5 97 0 0.761 0.771 0.7625 0.739 1.244 0.8455 0.926 156 701 27992.5 26362.5 -0.397 15956 12036.5 14941 11421.5 0.7025 17133.8078291815 1.08350278618903 13.7512913661757 0.612214606778462 0.680496180422852 0.948496392427832 0.935827376541343
RP11-492D3 13074677 155 18235 17914 5418 551 940 2484.5 100 98 0 14269 14276.5 5847.5 804 1217.5 2616 98 90 0 0.762 0.776 0.741 0.729 1.4135 0.8535 0.8935 182 628 31149 30835.5 -0.3945 17684 13465 17363 13472.5 0.742 18146.9002695418 1.02653254673532 13.9129482111865 0.590652049604631 0.697562171439778 0.999093456260741 0.981851174426705
RP11-97J12 13074677 155 23085.5 24227 8056.5 549.5 622 494.5 100 99.5 0 17924 18879 7498.5 843 910 624 99 98 0 0.758 0.7615 0.7675 0.719 1.6125 0.789 0.867 182 702 39617 41713.5 -0.4 22536 17081 23677.5 18036 0.742 23020.2156334231 1.02130464853605 14.2590884515457 0.60376841443054 0.668099121132594 0.946715036338447 0.951540231244113
RP11-541N19 13074677 155 11744 11832 3509 539 831 2120.5 98.5 97.5 0 7549 7965 3053 800 1127 2427.5 94.5 75.5 0 0.6035 0.6245 0.599 0.5925 1.46 0.685 0.8565 182 624 17954 18458 -0.7285 11205 6749 11293 7165 0.742 9095.68733153638 0.813566678975703 12.9783707157598 0.638098626655603 0.71873918110017 0.93986142033635 0.985807340386037
RP11-25L9 13074677 150 22883 23802.5 5830 534.5 829.5 1755.5 100 100 0 11602 12194.5 4167.5 777 1048.5 1948 100 98.5 0 0.4845 0.4905 0.477 0.4745 1.2125 0.529 0.923 156 654 33173.5 34685.5 -1.0455 22348.5 10825 23268 11417.5 0.742 14588.948787062 0.65281952495824 13.9249496394818 0.658633886520446 0.755094408459668 0.948384652597972 0.960533755694557
RP11-347O8 13074677 150 14137.5 12949 4655.5 480 921 2292.5 97 90 0 9410.5 9013 3880.5 719.5 1096 2253.5 91 83 0 0.6355 0.665 0.6485 0.632 1.314 0.7455 0.9225 156 694.5 22348.5 20762.5 -0.6545 13657.5 8691 12469 8293.5 0.6405 13569.0866510539 0.992441819100099 13.40918431264 0.570923638347484 0.641068202467294 0.955508234437143 0.913431026369873
RP11-518H12 13074677 155 13477 13259 5098 426.5 925.5 2544.5 99 90.5 0 10441.5 11157.5 6393.5 660.5 1104 2546 92 79.5 0 0.749 0.817 0.744 0.733 1.3985 0.9545 0.8965 182 646.5 22831.5 23329.5 -0.416 13050.5 9781 12832.5 10497 0.635 15403.1496062992 1.17998369992773 13.4581886013103 0.431437325871255 0.617801903137958 0.936196728799477 0.975168486378061

Total number of rows: 3857

Table truncated, full table size 1306 Kbytes.




Supplementary file Size Download File type/resource
GSM185285.gpr.gz 870.4 Kb (ftp)(http) GPR

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