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Sample GSM186713 Query DataSets for GSM186713
Status Public on May 08, 2007
Title Breast, NOS (excludes Skin of breast C44.5), Carcinoma, NOS (12410062)
Sample type genomic
 
Channel 1
Source name TB1173DF1X10
Organism Homo sapiens
Characteristics Cell Line HCC1187
TB1173DF1X10
Growth protocol "Breast, NOS (excludes Skin of breast C44.5)"; Carcinoma, 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 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 "Breast, NOS (excludes Skin of breast C44.5)"; Carcinoma, NOS; University of Pennsylvania; 9/11/2002
Data processing All spots were subjected to a pin-tip normalization.
 
Submission date May 02, 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 12410062 200 3769.5 4100 2026.5 461 559 291 98.5 96 0 4927.5 5352 2117 644 707 242 100 99.5 0 1.354 1.3415 1.3545 1.4485 1.6265 1.285 0.826 316 1099 7592 8347 0.411 3308.5 4283.5 3639 4708 1.1715 3656.42338881776 1.15565510996421 11.8577096260396 0.604349295837606 0.501097309400072 0.909489869936164 0.90232990175288
RP11-67E18 12410062 225 18380.5 19109.5 5085 819.5 2310 440 100 100 0 24805 26011.5 6924.5 872.5 2647 313.5 100 100 0 1.3675 1.3825 1.367 1.382 1.2045 1.393 0.9435 392 1169 41493.5 43429 0.45 17561 23932.5 18290 25139 1.031 23212.9000969932 1.32612315953923 14.3198618820596 0.733310449208119 0.733089029493685 0.951632329204899 0.961211043147583
RP11-291C17 12410062 220 11392.5 13914.5 7293 773 867 412.5 100 99.5 0 9515.5 11964.5 6247.5 843 892.5 285 99.5 99 0 0.818 0.8465 0.8385 0.8455 1.308 0.8465 0.941 392 1445 19292 24263 -0.2905 10619.5 8672.5 13141.5 11121.5 1.05 8259.52380952381 0.779120510443414 13.2259401775296 0.477585405440252 0.475546712510764 0.779503526589654 0.807212738402597
RP11-506N24 12410062 225 15112.5 17360.5 7420.5 625 712 370.5 100 100 0 14470.5 16408 6178 703.5 745 267 100 100 0 0.9575 0.95 0.959 0.966 1.2155 0.927 0.948 392 921.5 28254.5 32440 -0.0675 14487.5 13767 16735.5 15704.5 1.05 13111.4285714286 0.912297190042185 13.7827586264156 0.624071401323681 0.577955680749427 0.876913030138531 0.868641588576804
RP11-498J1 12410062 210 6249.5 7305 3671.5 578.5 653.5 339.5 100 100 0 8955.5 11010.5 5363.5 692 739 258.5 100 100 0 1.462 1.549 1.564 1.587 1.357 1.567 0.9125 316 1501 13934.5 17045 0.5435 5671 8263.5 6726.5 10318.5 1.115 7411.21076233184 1.3115261152035 12.7397738796471 0.512734838963043 0.501521961184882 0.800601014908374 0.847023476186998
RP11-335F1 12410062 200 15499.5 16290.5 5224 758 840.5 410 100 100 0 12494 13312.5 4133.5 829 873.5 293 100 100 0 0.791 0.8035 0.8 0.8075 1.2325 0.793 0.9375 316 1264.5 26406.5 28016 -0.338 14741.5 11665 15532.5 12483.5 1.0525 11083.135391924 0.751761782276225 13.6785836566651 0.69026753877889 0.679133063258643 0.934930377508026 0.949063862758063
RP11-501C13 12410062 215 1534.5 1631.5 767 698 801.5 382 74.5 54 0 1988.5 2027 576 741.5 867.5 276 97.5 90 0 1.498 1.385 1.335 1.487 2.6515 0.998 0.2565 354 979.5 2083.5 2219 0.5775 836.5 1247 933.5 1285.5 1.05 1187.61904761905 1.4263889093628 9.99478246401761 0.715783107164979 0.525980756831821 0.970201083596961 0.896488833603999
RP11-367E10 12410062 210 16984.5 17834 5310 841 947 439 100 100 0 18106.5 19049.5 5110.5 869.5 931 306 100 100 0 1.075 1.0795 1.0895 1.0875 1.226 1.0745 0.9385 316 1238.5 33380.5 35173 0.102 16143.5 17237 16993 18180 1.0525 16377.1971496437 1.0216404480364 14.0199281604628 0.731729679492663 0.703373300010733 0.948319928133909 0.951686149364994
RP11-338J16 12410062 260 932 1030 669 809 902 420 32 14 0 965 1073 781 771 828 268 43 26 0 1.577 1.367 0.844 0.841 3.66 0.732 0.133 540 1700 317 523 0.657 123 194 221 302 1.055 183.886255924171 1.49501021076561 7.27121367376318 0.272134203168686 0.350485436893204 0.642384105960265 0.556561085972851
RP11-490K2 12410062 205 9301.5 9968.5 3643 598.5 686 349 100 100 0 15258 16499.5 5307 742.5 785.5 271.5 100 100 0 1.6935 1.7005 1.71 1.735 1.267 1.695 0.925 316 1152 23218.5 25127 0.748 8703 14515.5 9370 15757 1.115 13018.3856502242 1.51892380315936 13.4512635844586 0.678301618231858 0.633413652575054 0.921329404395559 0.927943339556713
RP11-491P10 12410062 220 36247 37533 14139.5 814 970.5 437 99.5 99 2 41417 42728.5 14596.5 854.5 980.5 299.5 100 100 7.5 1.1405 1.1385 1.1055 1.154 1.7035 1.1315 0.876 392 1167.5 75995.5 78593 0.1885 35433 40562.5 36719 41874 1.031 39342.87099903 1.10634361802478 15.2025223485503 0.657474576196738 0.624309867231752 0.965906350452084 0.964266046725171
RP11-492D3 12410062 230 13514.5 15568.5 7262.5 638 745 368.5 100 100 0 11553 13334 6396 761 813.5 278 100 100 0 0.8395 0.8445 0.8265 0.834 1.267 0.853 0.9335 392 864.5 23668.5 27503.5 -0.253 12876.5 10792 14930.5 12573 1.05 10278.0952380953 0.799495786094952 13.5243799741558 0.520474176233616 0.534688283963961 0.858352619800566 0.86325475047008
RP11-541N19 12410062 210 14347 15262.5 5509.5 648 748.5 360 100 100 0 14293 15061 5222 795.5 845 287.5 100 100 0 0.9845 0.9755 0.983 0.982 1.2335 0.972 0.9445 316 1130 27196.5 28880 -0.0215 13699 13497.5 14614.5 14265.5 1.0525 12824.2280285035 0.935797523658613 13.728546673932 0.654871015839873 0.641040074023123 0.948111726718047 0.938832962117694
RP11-25L9 12410062 220 20090 21233 6088.5 776 886 405.5 100 100 0 27529.5 28920 7429.5 836.5 887 297 100 100 0 1.3825 1.3745 1.3745 1.3965 1.2135 1.366 0.952 392 795.5 46007 48540.5 0.4675 19314 26693 20457 28083.5 1.0495 25434.0161981896 1.31728345976526 14.4704082405495 0.743141627798838 0.712814015870182 0.950571248180413 0.944302996680612
RP11-518H12 12410062 220 6738 7966.5 4250.5 411.5 535 273.5 99 98.5 0 7050.5 8394.5 4368.5 667 784.5 265.5 99 98.5 0 1.042 1.063 1.0605 1.069 1.395 1.0825 0.8895 392 1164 12710 15282.5 0.0445 6326.5 6383.5 7555 7727.5 1.1715 5448.99701237729 0.889748734866483 12.6137553562821 0.482832168774372 0.470666177079032 0.831709694666367 0.848369048965284
RP11-35P20 12410062 210 31200.5 33948.5 10447 826.5 928 423.5 100 100 0 23442 25861.5 7905 801 835 270 100 100 0 0.747 0.76 0.749 0.763 1.268 0.754 0.948 316 874 53015 58182.5 -0.4215 30374 22641 33122 25060.5 0.996 22731.9277108434 0.750024797055666 14.674287876125 0.694873222381249 0.693172307077571 0.903835707604461 0.919238207531295
RP11-366L14 12410062 215 9289 10298 4533 559.5 640.5 324 99 99 0 9429.5 10520 4638.5 714 750 265 99.5 99.5 0 1.01 1.023 1.035 1.0295 1.296 1.032 0.9325 354 1103 17445 19544.5 0.00700000000000001 8729.5 8715.5 9738.5 9806 1.115 7816.59192825112 0.905645130106957 13.0859284454619 0.558780113019008 0.556482643833422 0.893107922199539 0.904888739867542
RP11-568A9 12410062 220 13763.5 13974.5 4891.5 705.5 782 389 99.5 99 0 18329 18973 6166 774.5 810.5 281 100 100 0 1.3525 1.3805 1.384 1.407 1.244 1.372 0.9505 392 1394.5 30612.5 31467.5 0.4335 13058 17554.5 13269 18198.5 1.05 16718.5714285714 1.28819352922183 13.880496440056 0.675182838076279 0.650446243560243 0.963897850681881 0.983076852148334
RP11-272A1 12410062 235 12502 17567 12143 858.5 1118 457 100 100 0 15159.5 22855.5 16120 858.5 1003 295.5 99.5 99 1 1.232 1.328 1.3045 1.309 1.5565 1.3555 0.8735 426 1355.5 25944.5 38705.5 0.3005 11643.5 14301 16708.5 21997 1.031 13870.9990300679 1.1949852160695 13.6388032337635 0.291589375834168 0.308368424249876 0.647373278986327 0.696189337220097
RP11-542O22 12410062 235 13582.5 15678.5 7039 797.5 1116 425 99.5 99.5 0 14445 16609 7241.5 840.5 1084.5 297 100 99.5 0 1.062 1.0595 1.0725 1.0645 1.2625 1.048 0.93 426 755 26389.5 30649.5 0.0865 12785 13604.5 14881 15768.5 1.031 13195.4413191076 1.03005381902461 13.6812702954267 0.564772281459131 0.551632124816593 0.865074683690449 0.864154130709845

Total number of rows: 2923

Table truncated, full table size 989 Kbytes.




Supplementary file Size Download File type/resource
GSM186713.gpr.gz 780.8 Kb (ftp)(http) GPR

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