NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM185432 Query DataSets for GSM185432
Status Public on May 08, 2007
Title Ovary, Carcinoma, NOS (13077967)
Sample type genomic
 
Channel 1
Source name TB2649DF1T10
Organism Homo sapiens
Characteristics Tissue
TB2649DF1T10
Growth protocol Ovary; 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 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 Ovary; Carcinoma, NOS; University of Pennsylvania; 11/30/2004
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 13077967 140 9024.5 8101 3243 217.5 241.5 141 100 100 0 7250 6524 2772 333.5 360.5 498.5 99 94.5 0 0.7855 0.785 0.777 0.7595 1.2305 0.815 0.9355 156 664 15723.5 14074 -0.3485 8807 6916.5 7883.5 6190.5 0.793 8721.94199243379 0.990373985307846 12.9299176892583 0.575034396707051 0.599397066595582 0.895172851550003 0.895117318524519
RP11-69E9 13077967 140 16142 16219 4138 205.5 239.5 284 100 100 0 13452.5 13936.5 4396 298 323 259.5 100 100 0 0.824 0.8495 0.8325 0.834 1.1405 0.886 0.9765 156 696.5 29091 29652 -0.284 15936.5 13154.5 16013.5 13638.5 0.8335 15782.2435512898 0.988347029250422 13.8177095661357 0.68863698595965 0.745596866315984 0.966151117527888 0.995252896339305
RP11-67E18 13077967 125 683.5 706.5 214.5 180 231.5 356 62 49.5 0 744.5 752.5 260.5 278.5 329 383 59 44 0 0.9255 0.901 0.914 0.8435 1.8835 0.9965 0.6135 120 610.5 969.5 1000.5 -0.1125 503.5 466 526.5 474 0.845 551.479289940828 1.09550527310325 8.91958272383413 0.653826184623209 0.696771949101904 0.968425692805699 0.957214983242806
RP11-291C17 13077967 145 6946.5 7107 2076.5 201 218 133 100 100 0 6042 6217 2206.5 283 297.5 133 100 100 0 0.852 0.8575 0.8575 0.841 1.1805 0.8965 0.961 156 837 12504.5 12840 -0.2355 6745.5 5759 6906 5934 0.823 6997.56986634264 1.03534057435317 12.6015263469839 0.644145142216902 0.707604460732022 0.969314812916571 0.976894734360277
RP11-506N24 13077967 140 5293 5110 1075.5 199 208 88.5 100 99.5 0 4272 4153.5 885.5 294.5 303 108.5 99.5 99 0 0.7825 0.787 0.7905 0.786 1.2425 0.7895 0.961 156 696 9071.5 8770 -0.355 5094 3977.5 4911 3859 0.7945 5006.29326620516 0.984937843235161 12.1350813094171 0.786972967943159 0.789216660795292 0.969995796114725 0.96382164816472
RP11-262N9 13077967 135 6583.5 6094 1649 184 200 106 100 100 0 5775 5367 1511 284.5 301 136 100 99.5 0 0.8575 0.8595 0.8695 0.8465 1.3695 0.8675 0.9465 138 633 11890 10992.5 -0.2215 6399.5 5490.5 5910 5082.5 0.845 6497.63313609468 1.01502337592837 12.5306185172016 0.720409160631529 0.730960408797681 0.927415375075225 0.925322814062157
RP11-498J1 13077967 135 5872.5 5985 1542.5 231 471.5 1035.5 100 96 0 5027.5 5173.5 1519 317 540.5 994.5 100 94.5 0 0.8335 0.843 0.829 0.8325 1.1855 0.873 0.9605 138 671 10352 10610.5 -0.2635 5641.5 4710.5 5754 4856.5 0.841 5601.07015457788 0.991007742901261 12.3277966520524 0.704005175485724 0.739676315105295 0.968713501802027 0.980271664640242
RP11-335F1 13077967 145 3386.5 3398.5 948.5 210.5 286 486.5 100 99 0 3009.5 3146.5 1144.5 269 345 522.5 99.5 96.5 0 0.8605 0.903 0.8755 0.8725 1.2735 0.9955 0.9165 156 694 5916.5 6065.5 -0.2165 3176 2740.5 3188 2877.5 0.845 3243.19526627219 1.01876467806229 11.5150713718678 0.631675102346835 0.716086525320739 0.95179125645378 0.98024389886414
RP11-260B11 13077967 140 4000 3875 1156 201 250.5 363 100 99 0 3730.5 3608.5 1221.5 289 322.5 279 99 98.5 0 0.909 0.9055 0.89 0.873 1.3755 0.946 0.94 156 667.5 7240.5 6993.5 -0.14 3799 3441.5 3674 3319.5 0.804 4280.47263681592 1.13060707804379 11.8188206526382 0.661485393263259 0.701929888381102 0.964561607923099 0.967783733837559
RP11-367E10 13077967 150 3460.5 3644 1262 196.5 211 112.5 100 100 0 2816 3189 1480.5 283 298 142.5 100 100 0 0.776 0.8445 0.8175 0.8135 1.2775 0.965 0.9015 156 692 5797 6353.5 -0.367 3264 2533 3447.5 2906 0.845 2997.63313609468 0.918564918660229 11.4889591382218 0.537841581262232 0.658677763302301 0.872283802087257 0.948815487636204
CTD-2341I10 13077967 140 7243.5 7273 1573.5 208 220.5 112 100 100 0 6415.5 6539 1583 277.5 288.5 113.5 100 100 0 0.8715 0.885 0.8835 0.876 1.167 0.908 0.964 156 668 13173.5 13326.5 -0.1985 7035.5 6138 7065 6261.5 0.8335 7364.12717456509 1.04558046331047 12.676022762378 0.758401637644991 0.783331990630497 0.979632730881873 0.980845740814035
RP11-490K2 13077967 140 6412.5 6257 2431 213 248 273.5 100 100 0 4965 4840 2053 314 352 371.5 100 100 0 0.7505 0.749 0.7515 0.7315 1.203 0.788 0.9635 156 668 10850.5 10570 -0.414 6199.5 4651 6044 4526 0.7985 5824.67125860989 0.940192875603448 12.3899383057766 0.575466886055122 0.611468211594648 0.947356004374908 0.962378494960958
RP11-491P10 13077967 130 6349 6069 1746.5 188.5 214.5 187 100 100 0 5224.5 5272.5 1798.5 284 316.5 254.5 100 100 0 0.8055 0.849 0.841 0.828 1.245 0.8915 0.938 120 605.5 11101 10869 -0.3135 6160.5 4940.5 5880.5 4988.5 0.845 5846.74556213017 0.953472536447211 12.4252984155636 0.659964729651064 0.712756071970191 0.990269370575856 0.958308776038535
RP11-43H17 13077967 140 6401.5 6519 1905.5 212.5 277.5 506.5 100 99.5 0 5855 5996 1958 286 346 541 99.5 99 0 0.8985 0.904 0.893 0.8885 1.1825 0.94 0.9565 156 678 11758 12016.5 -0.1545 6189 5569 6306.5 5710 0.8335 6681.46370725855 1.07807838038954 12.5160736160316 0.674131538058836 0.708302108361597 0.974972300162152 0.979792041760332
RP11-492D3 13077967 155 4438 4577 2067 195 239 302 99.5 99.5 0 3748.5 3874 1957.5 272.5 321 367.5 98 97 0 0.8195 0.8235 0.8075 0.782 1.386 0.869 0.907 182 688.5 7719 7983.5 -0.2875 4243 3476 4382 3601.5 0.845 4113.60946745562 0.969760693430961 11.9048338970199 0.492851689253674 0.544843000828812 0.964737128456378 0.969044494398955
RP11-97J12 13077967 140 5945 6276.5 1903.5 196 250.5 396 99.5 99 0 5139 5485.5 1801 284.5 358 795.5 99 98 0 0.844 0.855 0.839 0.842 1.3265 0.893 0.858 156 682.5 10603.5 11281.5 -0.247 5749 4854.5 6080.5 5201 0.845 5744.97041420119 0.99889842707153 12.3655763660856 0.670224519563652 0.696714758051721 0.932420890311307 0.945470017352042
RP11-541N19 13077967 145 4785 4792.5 1041.5 207.5 277 447.5 100 100 0 4056 4111.5 1060.5 282.5 339 460 100 100 0 0.8255 0.836 0.813 0.828 1.2445 0.88 0.9235 156 684.5 8351 8414 -0.276 4577.5 3773.5 4585 3829 0.845 4465.68047337278 0.977242605471875 12.011008308352 0.738044439435187 0.777501679092066 0.986954392113067 0.993466338976021
RP11-25L9 13077967 145 6470.5 6206.5 2390.5 202 232 211.5 100 100 0 5162 5102 2217 276.5 320.5 434 100 100 0 0.782 0.806 0.7935 0.782 1.2055 0.8615 0.937 156 666.5 11154 10830 -0.3555 6268.5 4885.5 6004.5 4825.5 0.845 5781.65680473373 0.925316835472534 12.4272859503845 0.567882426040403 0.619350711279668 0.987184261190925 0.957472732837454
RP11-347O8 13077967 140 4976.5 4852 1212 216.5 329.5 608 100 99.5 0 4196 4172.5 1222.5 310 421 694 99 96.5 0 0.818 0.8355 0.816 0.82 1.24 0.8865 0.9325 156 694.5 8646 8498 -0.291 4760 3886 4635.5 3862.5 0.804 4833.33333333333 1.01735092663706 12.0693416496003 0.706261862287286 0.748297821394754 0.984632821034961 0.973186164548071
RP11-518H12 13077967 145 6553.5 6522 1710 220.5 284 384.5 100 100 0 5227.5 5356.5 1704.5 330.5 380.5 357 100 99.5 0 0.7735 0.7975 0.7875 0.7785 1.206 0.8355 0.953 156 687.5 11230 11327.5 -0.371 6333 4897 6301.5 5026 0.793 6175.28373266078 0.975105924846596 12.4431653295638 0.682555336531363 0.738623373092897 0.97463470804659 0.977055311936184

Total number of rows: 3861

Table truncated, full table size 1275 Kbytes.




Supplementary file Size Download File type/resource
GSM185432.gpr.gz 833.1 Kb (ftp)(http) GPR

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