NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM185094 Query DataSets for GSM185094
Status Public on May 08, 2007
Title Breast, NOS (excludes Skin of breast C44.5), Carcinoma, NOS (12933423)
Sample type genomic
 
Channel 1
Source name TB1190DF1X21
Organism Homo sapiens
Characteristics Cell Line MDA-MB-231
TB1190DF1X21
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 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 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; 9/3/2004
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 12933423 140 3736 3626 1044 374.5 403.5 236.5 98.5 97.5 0 3777.5 3755 934.5 398 429.5 237.5 99.5 98.5 0 1.0055 1.033 1.026 1.0585 1.514 1.014 0.823 156 676 6741 6608.5 0.008 3361.5 3379.5 3251.5 3357 0.804 4203.35820895523 1.25048420034079 11.7187306448011 0.751130139920329 0.712244251059489 0.993339908347893 0.967192021834903
RP11-69E9 12933423 135 4796.5 4973 1230 355.5 427.5 420 100 100 0 4372 4498 1157 383 447.5 377.5 99.5 99 0 0.8965 0.889 0.8995 0.889 1.3625 1.099 0.777 138 640.5 8430 8732.5 -0.158 4441 3989 4617.5 4115 0.81 4924.69135802469 1.1068000759255 12.0281118190029 0.738152705241313 0.747959440910293 0.971903196879026 0.964094088264077
RP11-67E18 12933423 130 713 761.5 406.5 444.5 490 300 46 16.5 0 570 644 408 433.5 470.5 264 34.5 9.5 0 0.477 0.677 0.8075 0.6785 3.376 0.865 0.1235 130 626 405 527.5 -1.0865 268.5 136.5 317 210.5 0.732 186.475409836066 0.651896624197359 7.39692698505923 0.362374950271204 0.451089744270043 0.60114200850105 0.84078022492971
RP11-291C17 12933423 130 3610.5 3520 892.5 365.5 402 240 100 100 0 2433 2465 774 389.5 426 253 99.5 98.5 0 0.6265 0.6525 0.6385 0.6285 1.5815 0.671 0.743 120 719.5 5288.5 5230 -0.676 3245 2043.5 3154.5 2075.5 0.7845 2604.84384958572 0.798659022047948 11.3171031940637 0.683985351219548 0.74649067318625 0.9750842945874 0.973128725071011
RP11-506N24 12933423 140 2501.5 2496.5 767.5 346.5 389.5 277.5 98.5 97.5 0 1898.5 1908 747.5 360.5 402 264.5 94 88 0 0.716 0.7185 0.709 0.7 1.834 0.7515 0.7305 156 725.5 3693 3697.5 -0.4825 2155 1538 2150 1547.5 0.772 1992.22797927461 0.927481592811128 10.8194690783043 0.606974948951641 0.69081483983594 0.993483860071358 0.952966886857233
RP11-262N9 12933423 130 4314.5 4292 1000 461.5 508 328.5 100 99.5 0 2812.5 2813.5 723.5 418.5 441 247.5 99.5 98.5 0 0.6255 0.6275 0.631 0.6185 1.4105 0.6385 0.8175 120 682 6247 6225.5 -0.6775 3853 2394 3830.5 2395 0.732 3270.49180327869 0.854540518428755 11.5489081106132 0.74187777405443 0.764536609291615 0.994953392463903 0.99077395647783
RP11-498J1 12933423 125 2072.5 2107 590 362.5 393.5 207 100 99.5 0 2103.5 2119.5 613.5 388 413.5 204 99.5 98.5 0 1.0015 0.989 0.995 0.98 1.561 1.0355 0.6855 120 636 3425.5 3476 0.002 1710 1715.5 1744.5 1731.5 0.8135 2108.78918254456 1.23104635691212 10.733042841514 0.709889412923642 0.720100852895402 0.991807475678444 0.979230295076752
RP11-335F1 12933423 140 2119.5 2149 613 369.5 417 281 99.5 97 0 1592 1644 605.5 409 441 251.5 98 91 0 0.6725 0.6885 0.678 0.658 1.79 0.718 0.5915 156 682.5 2933 3014.5 -0.573 1750 1183 1779.5 1235 0.732 1616.12021857923 0.918389311406898 10.451795244454 0.633066898907527 0.715304308923999 0.957011927390758 0.980195727675336
RP11-260B11 12933423 135 1960 2000 584 398 428.5 228 100 97.5 0 1629 1666.5 576.5 390 424 228 97 93.5 0 0.7935 0.7975 0.809 0.763 1.8025 0.817 0.631 138 634 2801 2878.5 -0.334 1562 1239 1602 1276.5 0.785 1578.34394904458 1.01041658892138 10.4390136670815 0.655441812675752 0.708407004898925 0.970675800955673 0.975630652070443
RP11-367E10 12933423 145 1624.5 1662.5 599 406.5 495.5 399.5 93 78 0 1134.5 1223 546.5 386 469 397 78.5 49 0 0.617 0.67 0.665 0.6175 2.2135 0.746 0.489 156 716.5 1966.5 2093 -0.701 1218 748.5 1256 837 0.732 1022.54098360656 0.843217519560873 9.89776504587094 0.555253731682852 0.637767971335187 0.895178871837127 0.969544437665243
CTD-2341I10 12933423 140 2897 3039 1248 355 380 227 100 99 0 2641 2697 931 371 401 193 99 98 0 0.893 0.867 0.841 0.858 1.63 0.822 0.758 156 684 4812 5010 -0.163 2542 2270 2684 2326 0.81 2802.46913580247 1.10246622179483 11.2301124485916 0.654801631442343 0.5893385982231 0.975924333619948 0.947093889716841
RP11-490K2 12933423 135 2199 2182.5 584 333 361 197 98.5 98.5 0 2166.5 2184.5 575.5 367 398 212.5 99.5 99 0 0.9645 0.984 0.961 0.9825 1.652 0.998 0.7225 138 654.5 3665.5 3667 -0.0525 1866 1799.5 1849.5 1817.5 0.793 2269.23076923077 1.2165160101474 10.839436815684 0.736557111843154 0.731798871588674 0.990102855468329 0.982451272210118
RP11-491P10 12933423 125 3351.5 3451.5 1196.5 458.5 493.5 278 100 98 0 2422 2501.5 919.5 420.5 460.5 291 98.5 96.5 0 0.691 0.695 0.689 0.6755 1.604 0.699 0.7665 120 633.5 4894.5 5074 -0.533 2893 2001.5 2993 2081 0.732 2734.28961748634 0.944286747527438 11.2283710378124 0.632242988710122 0.650677755841484 0.960160688139879 0.96544970390844
RP11-43H17 12933423 130 3355.5 3352 706 348 440.5 522.5 100 100 0 2853.5 2802.5 622.5 393.5 466.5 385 100 99 0 0.816 0.8005 0.797 0.7945 1.411 0.8635 0.736 120 666.5 5467.5 5413 -0.2995 3007.5 2460 3004 2409 0.81 3037.03703703704 1.007195004181 11.4039441142418 0.777706654211265 0.789755028029725 0.980238650420739 0.993559260743663
RP11-492D3 12933423 140 2078 2113 734 399 443 261.5 99 94.5 0 1501.5 1523 612 411 442 261.5 92 79.5 0 0.646 0.648 0.651 0.6045 1.8825 0.674 0.6295 156 657 2769.5 2826 -0.633 1679 1090.5 1714 1112 0.732 1489.75409836066 0.882292766352506 10.3886635986599 0.595151247190598 0.651519094845662 0.948678327405765 0.978538575420424
RP11-97J12 12933423 130 2849.5 2918.5 764.5 481.5 529.5 346 99.5 99 0 2200 2267 767.5 431 465.5 260 100 98.5 0 0.745 0.7515 0.7625 0.7265 1.5385 0.8055 0.734 120 615.5 4137 4273 -0.4255 2368 1769 2437 1836 0.732 2416.66666666667 1.01757717682788 10.9895277254993 0.664956963526333 0.737309693023873 0.963886302132778 0.972467579537243
RP11-541N19 12933423 140 2005 2034.5 585 393.5 441 320.5 96.5 86 0 1803.5 1839 550.5 413.5 450.5 257 98 92 0 0.8505 0.8595 0.867 0.8545 1.882 0.81 0.5725 156 691 3001.5 3066.5 -0.235 1611.5 1390 1641 1425.5 0.732 1898.90710382514 1.16223038849159 10.4844688454144 0.696430159091143 0.70658212590651 0.967862016687443 0.978160437123852
RP11-25L9 12933423 145 2423 2487 741.5 405 498 509 98.5 85.5 0 1989 2122 713.5 406 476 410.5 98.5 87 0 0.786 0.8305 0.837 0.8145 1.6145 0.8065 0.689 156 674 3601 3798 -0.347 2018 1583 2082 1716 0.732 2162.56830601093 1.07413026805238 10.7976533382158 0.662615656837297 0.699552290930743 0.92122442099815 0.970989860061364
RP11-347O8 12933423 140 2339 2371 635 334 373.5 284 99.5 99.5 0 1983 1981.5 648.5 368 398.5 209 97.5 96.5 0 0.8045 0.7915 0.798 0.7715 1.688 0.785 0.668 156 673.5 3620 3650.5 -0.3145 2005 1615 2037 1613.5 0.785 2057.32484076433 1.02489561004028 10.8102403760479 0.6721623644151 0.732715137229209 0.966139265590653 0.979342407768203
RP11-518H12 12933423 150 2470.5 2523.5 665.5 352.5 388.5 208 100 100 0 1798.5 1801.5 624 389 428.5 234 97.5 94.5 0 0.665 0.65 0.653 0.6185 1.725 0.675 0.6465 156 721 3527.5 3583.5 -0.5895 2118 1409.5 2171 1412.5 0.804 1753.10945273632 0.827275355180896 10.7536506640304 0.653163541469473 0.736263905377479 0.983709655378656 0.9755672335554

Total number of rows: 3854

Table truncated, full table size 1260 Kbytes.




Supplementary file Size Download File type/resource
GSM185094.gpr.gz 834.6 Kb (ftp)(http) GPR

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap