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Sample GSM185450 Query DataSets for GSM185450
Status Public on May 08, 2007
Title Unknown primary site, Melanoma, NOS (12933611)
Sample type genomic
 
Channel 1
Source name TB2664DF1T10
Organism Homo sapiens
Characteristics Tissue
TB2664DF1T10
Growth protocol Unknown primary site; Melanoma, 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; Melanoma, NOS; University of Pennsylvania; 8/13/2004
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 12933611 170 728 969.5 854.5 81 128 171 65.5 60 0 362 612.5 555 81.5 138.5 192 57.5 50 0 0.393 0.5965 0.632 0.61 2.8225 0.614 0.805 208 516 927.5 1419.5 -1.4575 647 280.5 888.5 531 0.924 303.571428571429 0.425221114308146 8.55202109312831 0.0820256776034235 0.105048548333094 0.489202718503362 0.714510534095286
RP11-69E9 12933611 170 1344 1076 754.5 73 94.5 109 78 74.5 0 1314.5 1081.5 805 78 98.5 112 73 71.5 0 0.9795 1.0065 0.9745 0.9085 2.3125 1.052 0.8645 208 516 2507.5 2006.5 -0.0305 1271 1236.5 1003 1003.5 0.907 1363.2855567806 1.08038917664024 10.270613412179 0.263983331469807 0.311005709228093 0.820534082923401 0.798744160377843
RP11-67E18 12933611 170 101.5 125 69.5 78 89.5 59.5 34.5 18.5 0 99.5 113 52.5 81 95 75 21 4.5 0 0.8215 0.6895 0.771 0.8005 2.758 0.8205 0.476 208 516 42 79 -0.3425 23.5 18.5 47 32 0.895 20.6703910614525 0.917649493068488 4.3672832549574 0.535188087774295 0.443967725409836 0.575490196078431 0.497264021887824
RP11-291C17 12933611 170 403 426 316 70.5 73 29 75.5 69 0 353 386.5 298 74.5 76.5 22 74 66 0 0.8395 0.89 0.8875 0.8005 2.6575 0.9135 0.7735 208 818 611 667.5 -0.2525 332.5 278.5 355.5 312 0.952 292.542016806723 0.881746705576419 8.17284618956759 0.259497067082225 0.29011904835835 0.90774849158463 0.927534150675833
RP11-506N24 12933611 170 630.5 553 430 78.5 84 72 64 60 0 440 463 366.5 77.5 81 24 67 60.5 0 0.685 0.8135 0.827 0.7505 2.4645 0.797 0.816 208 472 914.5 860 -0.5735 552 362.5 474.5 385.5 0.9295 389.994620763852 0.736934002863991 8.78848610710108 0.208497246262785 0.222637764223368 0.943637261000081 0.880372358073972
RP11-262N9 12933611 170 377 622 571 77 86 51 60 55 0 260 635 611 81 89 50 55 52 0 0.597 1.017 1.002 0.928 2.185 1.059 0.939 208 516 479 1099 -0.745 300 179 545 554 0.895 200 0.666666666666667 7.85631723388007 0.0377952755905512 0.0819935691318328 0.323104693140794 0.55045871559633
RP11-498J1 12933611 170 311 472 396 78.5 84 41 65 57 0 183 477 433 81.5 87 44 59 49 0 0.511 1.0045 0.9895 0.903 2.647 1.0945 0.8 208 516 334 789 -1.015 232.5 101.5 393.5 395.5 0.63 161.111111111111 0.811370977496034 7.05430561525745 0.0881027290723982 0.156998556998557 0.249826064549379 0.566273913100022
RP11-335F1 12933611 170 480 402 223 79 85 42 76 72 0 362 308 175 79 89 150 66 44 0 0.706 0.709 0.713 0.64 2.409 0.966 0.54 208 516 684 552 -0.503 401 283 323 229 0.895 316.201117318436 0.788531464634503 8.3960583346434 0.431818181818182 0.445273631840796 0.809187279151943 0.805486284289277
RP11-260B11 12933611 170 434.5 388 297 79 90.5 54.5 63 59 0 383 352 264.5 80.5 93 63.5 58.5 55 0 0.8505 0.8785 0.9185 0.8275 2.3985 0.897 0.778 208 516 658 580.5 -0.234 355.5 302.5 309 271.5 0.8585 352.358765288294 0.990580371999401 8.3550219657911 0.248197023170171 0.234920212765957 0.898353516739064 0.869366403858052
RP11-367E10 12933611 170 392 359.5 202 78.5 89 77 73 69.5 0 286 280.5 160.5 76 85.5 51 73.5 67.5 0 0.668 0.727 0.73 0.699 2.0645 0.736 0.7755 208 427 523.5 485.5 -0.583 313.5 210 281 204.5 0.895 234.63687150838 0.746404505475519 7.99706834255724 0.4264375159724 0.436248445273632 0.974283353606757 0.895219685812469
CTD-2341I10 12933611 170 443.5 422 304.5 80 115 165 71.5 62.5 0 439 434.5 326.5 80.5 105 101 70.5 67 0 0.9575 1.064 1.0565 0.9435 2.2495 1.1255 0.746 208 494 722 696 -0.0645 363.5 358.5 342 354 0.907 395.259095920617 1.05571573437248 8.20222836165573 0.288647846406467 0.326965111391341 0.846078652530265 0.938717834300163
RP11-490K2 12933611 170 723 646.5 494.5 79.5 87.5 67 66.5 62 0 725.5 676.5 542 80 92.5 84 61.5 58.5 0 1.003 1.0515 1.046 0.897 2.7735 1.112 0.814 208 516 1289 1163.5 0.004 643.5 645.5 567 596.5 0.894 722.035794183445 1.12204479867852 9.33202395788132 0.198549711651387 0.234812563759933 0.92432271566538 0.8812589655289
RP11-491P10 12933611 170 164 501.5 484.5 75.5 79 28 62.5 54.5 0 134 426 408.5 78 82.5 30.5 57 49 0 0.643 0.8175 0.8 0.7685 2.4245 0.8295 0.932 208 516 144.5 774 -0.6445 88.5 56 426 348 0.895 62.5698324022347 0.718003896395174 6.12582105164045 0.0411562432839028 0.0338742393509128 0.16080866807611 0.208459197847992
RP11-43H17 12933611 170 572 503 345 77 95.5 82.5 73.5 69 0 464.5 435 306 79 95.5 86 69.5 65.5 0 0.798 0.8415 0.853 0.8125 2.1845 0.872 0.8225 208 516 880.5 782 -0.3295 495 385.5 426 356 0.907 425.02756339581 0.879644414131533 8.70781715713873 0.324547620254448 0.341692051291938 0.915092305037957 0.864829073831367
RP11-492D3 12933611 170 471 424.5 288 78.5 90 60 71 65 0 327.5 319.5 214 79 91 65.5 66 58.5 0 0.63 0.6955 0.6905 0.6875 2.242 0.687 0.7725 208 516 641 586.5 -0.669 392.5 248.5 346 240.5 0.895 277.653631284917 0.703577836262815 8.27313792112745 0.328072877830541 0.319076750089063 0.908888888888889 0.885344102415815
RP11-97J12 12933611 170 675.5 589.5 480 78 87 53.5 63 58.5 0 636 611.5 525 80.5 90.5 85 56.5 54.5 0 0.8935 1.0395 1.038 0.9335 2.198 1.0825 0.9015 208 516 1153 1042.5 -0.191 597.5 555.5 511.5 531 0.895 620.670391061453 0.998501901906829 9.09675207208842 0.135986471555232 0.181437461505386 0.737312477878516 0.872579212491672
RP11-541N19 12933611 170 486 410.5 226.5 75.5 79 35.5 77.5 73.5 0 554 452 259.5 78.5 82 36.5 73.5 71 0 1.157 1.1125 1.1255 1.042 2.32 1.133 0.852 208 516 886 708.5 0.211 410.5 475.5 335 373.5 0.895 531.284916201117 1.29296502687297 8.78078990092976 0.422635961796511 0.445476392085774 0.784599989278247 0.816249745779947
RP11-25L9 12933611 170 791 608 458 79.5 87.5 41.5 67.5 62 0 869 722 592 81.5 92.5 64 64 58 0 1.099 1.2125 1.2215 1.098 2.173 1.308 0.8995 208 494 1499 1169 0.121 711.5 787.5 528.5 640.5 0.895 879.888268156423 1.22801778596477 9.53347703669209 0.180118170656845 0.246992973681077 0.838195553780618 0.745333061408754
RP11-347O8 12933611 170 496 549.5 434.5 82 99.5 87 63.5 60.5 0 444 547 465 82.5 103.5 115 59 55 0 0.876 0.994 1.004 0.9045 2.2945 1.067 0.8505 208 516 775.5 932 -0.1925 414 361.5 467.5 464.5 0.8585 421.083284799068 1.02032634702262 8.59346609962097 0.149975402347319 0.209247949978142 0.778590925549397 0.885929993136582
RP11-518H12 12933611 170 692 617.5 413.5 79 101 103 70.5 66 0 495 443 302 77 97 95.5 66.5 60.5 0 0.685 0.683 0.7075 0.6495 2.5415 0.6865 0.787 208 516 1031 904.5 -0.5455 613 418 538.5 366 0.924 452.380952380953 0.741471902342738 8.94759488789266 0.306936678252985 0.314523326572008 0.881422924901185 0.884157375354044

Total number of rows: 3788

Table truncated, full table size 1178 Kbytes.




Supplementary file Size Download File type/resource
GSM185450.gpr.gz 742.1 Kb (ftp)(http) GPR

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