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Sample GSM185249 Query DataSets for GSM185249
Status Public on May 08, 2007
Title Unknown primary site, Teratoma, malignant, NOS (13078131)
Sample type genomic
 
Channel 1
Source name TB3029DF1T10
Organism Homo sapiens
Characteristics Tissue
TB3029DF1T10
Growth protocol Unknown primary site; Teratoma, malignant, 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 Unknown primary site; Teratoma, malignant, NOS; University of Pennsylvania; 1/4/2005
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 13078131 150 59278.5 47752 20157 694.5 1550 4585.5 100 96.5 19.5 32385.5 27063.5 13376 285.5 796 3003 98.5 87 0 0.548 0.569 0.5765 0.533 1.5165 0.5955 0.9185 156 683.5 90684 73835.5 -0.868 58584 32100 47057.5 26778 0.5175 62028.9855072464 1.05876132857966 15.4041664222621 0.505302519947624 0.576954868258081 0.834015260623255 0.803100252215103
RP11-69E9 13078131 145 42469.5 41345 12100.5 579.5 902 2470.5 100 100 3.5 19722.5 19579.5 6618.5 254.5 408 1254 100 100 0 0.4655 0.474 0.4645 0.468 1.1515 0.488 0.9675 156 757.5 61358 60090.5 -1.1035 41890 19468 40765.5 19325 0.472 41245.7627118644 0.986230467265621 14.7928991899753 0.663261466124472 0.708847160357994 0.992158461273308 0.974427732392149
RP11-67E18 13078131 130 4856 4842 1317.5 639 714.5 480 100 99 0 3365 3253.5 874.5 261 289.5 198 100 100 0 0.7365 0.712 0.7185 0.716 1.21 0.695 0.938 120 630.5 7321 7195.5 -0.4415 4217 3104 4203 2992.5 0.454 6837.00440528634 1.62217974959492 11.820542809169 0.731962254679628 0.728584718679204 0.963825690964816 0.996662150156187
RP11-291C17 13078131 140 14407 14202.5 5328.5 520.5 648 912 99.5 99 0 6664.5 6765.5 2953 232 297.5 474.5 99 98.5 0 0.466 0.4795 0.4685 0.4655 1.1795 0.494 0.972 156 791.5 20319 20215.5 -1.103 13886.5 6432.5 13682 6533.5 0.468 13744.6581196581 0.995546663622535 13.1923874523335 0.569800749091079 0.629560408586348 0.980202661794702 0.984091672861902
RP11-506N24 13078131 140 19650.5 18884 4088.5 639 937 1937 99 99 0 9887 9522 2270.5 256 407.5 1061 98.5 97 0 0.5065 0.5075 0.506 0.498 1.1975 0.513 0.978 156 689 28642.5 27511 -0.9825 19011.5 9631 18245 9266 0.457 21074.3982494529 1.10760617143768 13.7191067773315 0.76409550192771 0.785044972201076 0.963045346523793 0.960670559407256
RP11-262N9 13078131 135 35842 34043 7118.5 778.5 1060 1483.5 100 99.5 0 16860.5 16004 3407.5 298.5 436.5 730 100 99.5 0 0.4725 0.472 0.4705 0.4695 1.1355 0.4735 0.9855 138 658 51625.5 48970 -1.0825 35063.5 16562 33264.5 15705.5 0.454 36480.1762114537 1.04043348439254 14.5564593534349 0.786868383794544 0.790700205756837 0.948167681462785 0.948520972462473
RP11-498J1 13078131 135 42700 41872.5 10386 610.5 1711.5 5296 100 100 0 22103.5 21615 6569 264.5 900.5 3214.5 100 99 0 0.519 0.517 0.5175 0.5065 1.325 0.53 0.9255 138 701 63928.5 62612.5 -0.9465 42089.5 21839 41262 21350.5 0.4845 45075.3353973168 1.07098870024532 14.8872692439092 0.69601339675581 0.752275011984854 0.970542685119433 0.97470598279021
RP11-335F1 13078131 145 15464.5 16294.5 4538.5 612 1426 4292.5 100 97 0 7887.5 8404.5 2682 257.5 686 2555 100 82.5 0 0.514 0.5195 0.5205 0.5145 1.132 0.538 0.9765 156 694 22482.5 23829.5 -0.9605 14852.5 7630 15682.5 8147 0.454 16806.1674008811 1.13170464231558 13.3769106378873 0.678639878976624 0.719083943662498 0.936242943166719 0.946717848524015
RP11-260B11 13078131 145 19444.5 17961.5 6475.5 653.5 833 1451.5 100 99 0 8078 7665 3088 251 345.5 1061 99.5 91.5 0 0.4165 0.4285 0.422 0.4215 1.2405 0.4445 0.91 156 702 26618 24722 -1.2635 18791 7827 17308 7414 0.4655 16814.1783029001 0.894916989764512 13.5651847046757 0.596899800857693 0.639412887920156 0.947736065558368 0.921710030653482
RP11-367E10 13078131 155 13107.5 14241.5 4821 741 1054.5 1759 100 99.5 0 6411 6863 2463 263.5 388 704 100 99.5 0 0.498 0.49 0.483 0.483 1.196 0.4925 0.9645 182 662 18514 20100 -1.0055 12366.5 6147.5 13500.5 6599.5 0.454 13540.7488986784 1.09741354473136 13.0826261449174 0.638091444004639 0.656626182234011 0.932829603928197 0.916812610874759
CTD-2341I10 13078131 140 53505.5 50172.5 10649.5 563 931.5 2260.5 100 99.5 23.5 23629.5 23034 6498.5 246 414 1129 99.5 99 0 0.441 0.457 0.4465 0.446 1.17 0.473 0.9735 156 679.5 76326 72397.5 -1.1815 52942.5 23383.5 49609.5 22788 0.472 49541.313559322 0.934086924725827 15.0661978790212 0.71647076261941 0.777754274983542 0.975215137309902 0.941902683867556
RP11-490K2 13078131 150 28640 28169 12855.5 696.5 778.5 529.5 100 100 0 14186.5 13546.5 6813.5 257 302.5 383 100 99 0 0.4965 0.4835 0.48 0.4645 1.3855 0.4925 0.935 156 686 41873 40762 -1.012 27943.5 13929.5 27472.5 13289.5 0.488 28544.0573770492 1.01706731957615 14.2580789574533 0.495617252510721 0.542867106468926 0.942622815861605 0.964757363597105
RP11-491P10 13078131 140 39375 38605.5 7800 738.5 910.5 1394.5 100 100 0 16160 16008.5 4127 271.5 336 511.5 99.5 99.5 0 0.4115 0.4155 0.4115 0.4055 1.189 0.4195 0.9775 156 672 54525 53604 -1.282 38636.5 15888.5 37867 15737 0.454 34996.6960352422 0.905889361239083 14.5965418006608 0.742206430762969 0.797956662493731 0.988427628368715 0.980325094466482
RP11-43H17 13078131 145 22040.5 21768.5 4729.5 557 938 2550 100 100 0 10849 10927 2512 242.5 428.5 1369 100 100 0 0.4925 0.5025 0.494 0.5015 1.1165 0.5105 0.9795 156 702.5 32090 31896 -1.0215 21483.5 10606.5 21211.5 10684.5 0.472 22471.3983050847 1.04373347701221 13.8737903198003 0.768647946062522 0.782268542537541 0.990664523592921 0.986521480329027
RP11-492D3 13078131 155 27520.5 27018.5 9073 761.5 1134.5 1949.5 99 98 0 12060.5 12103.5 4833.5 263.5 438 871.5 99 96.5 0 0.441 0.451 0.446 0.439 1.1695 0.4605 0.9725 182 656.5 38556 38097 -1.1815 26759 11797 26257 11840 0.454 25984.5814977974 0.971300986353103 14.1154258809394 0.599149751841447 0.662153286691773 0.974147891001149 0.980358382970981
RP11-97J12 13078131 140 38677 39242.5 7582 728 807.5 632 100 100 0 17265.5 17983 4475 271.5 304.5 252 100 100 0 0.449 0.4605 0.455 0.456 1.142 0.484 0.959 156 669.5 54943 56226 -1.156 37949 16994 38514.5 17711.5 0.454 37431.718061674 0.988554689147698 14.6279146532427 0.749864176430455 0.806701569804822 0.958836008018953 0.984436022407581
RP11-541N19 13078131 145 30376 30259 6319 678.5 1093.5 2753 99.5 99.5 0 12861 12678 2907 261 478 1440 99.5 99.5 0 0.4245 0.42 0.4185 0.4175 1.0985 0.429 0.9815 156 695 42297.5 41997.5 -1.2355 29697.5 12600 29580.5 12417 0.454 27753.3039647577 0.935366958833451 14.2363770692364 0.769194613537544 0.789311247803281 0.986153453228678 0.990053117979429
RP11-25L9 13078131 150 30594 30946.5 5975.5 702 783 447 100 100 0 13622 13912.5 2864 250 285.5 212.5 100 100 0 0.447 0.4515 0.449 0.45 1.0935 0.4585 0.9865 156 688.5 43264 43907 -1.1615 29892 13372 30244.5 13662.5 0.454 29453.744493392 0.984925681132413 14.2861440244464 0.794013625484472 0.806882746155221 0.978481190631827 0.988626331254212
RP11-347O8 13078131 145 26706.5 26007.5 6835 633 699 431 100 100 0 13296 13117 3861.5 252.5 280.5 203 100 100 0 0.5005 0.5075 0.5005 0.5025 1.1965 0.5165 0.9525 156 688 39117 38239 -0.999 26073.5 13043.5 25374.5 12864.5 0.4655 28020.4081632653 1.07464417517252 14.1704366228048 0.703881116211366 0.735480457580482 0.986137322312223 0.972817263349436
RP11-518H12 13078131 150 13125.5 16338 10043.5 717 923 1208 100 100 1.5 6270 8619 7019 273.5 388 838 99.5 97 0 0.4865 0.5285 0.5045 0.495 1.5015 0.5705 0.7945 156 704 18405 23966.5 -1.0405 12408.5 5996.5 15621 8345.5 0.5175 11587.4396135265 0.940442433005347 13.0619039716727 0.260662114965897 0.42765516392476 0.765184482999695 0.820282918659507

Total number of rows: 3856

Table truncated, full table size 1309 Kbytes.




Supplementary file Size Download File type/resource
GSM185249.gpr.gz 895.4 Kb (ftp)(http) GPR

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