NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM350517 Query DataSets for GSM350517
Status Public on Jul 10, 2009
Title shgu152|BT549vsXX
Sample type genomic
 
Channel 1
Source name Normal human female genomic DNA
Organism Homo sapiens
Characteristics Normal human female genomic DNA
Extracted molecule genomic DNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name Breast Tumor Cell Line BT549 genomic DNA
Organism Homo sapiens
Characteristics Breast Tumor Cell Line BT549 genomic DNA
Extracted molecule genomic DNA
Extraction protocol not provided
Label Cy5
Label protocol not provided
 
 
Hybridization protocol not provided
Scan protocol Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 2120, 5680; Software: type: feature extraction; Performer: Jessica,,Kao
Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-01-11; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 570; Parameter Laser on time = 70543; Parameter Laser Power = 3.69; Parameter Scan Time = 13:17:45; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 30.72; Performer: Jessica,,Kao
Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-01-11; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 520; Parameter Scan Power = 100; Parameter Laser on time = 70587; Parameter Laser Power = 3.44; Parameter Scan Time = 13:17:45; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 30.72; Performer: Jessica,,Kao
Description Simple annotation: Breast, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/68158.gif
Data processing VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)
 
Submission date Dec 11, 2008
Last update date Jul 10, 2009
Contact name Jonathan Pollack
E-mail(s) pollack1@stanford.edu
Phone 650-736-1987
Organization name Stanford University
Department Pathology
Lab Pollack Lab
Street address 269 Campus Drive, CCSR3245A
City Stanford
State/province CA
ZIP/Postal code 94305-5176
Country USA
 
Platform ID GPL7780
Series (2)
GSE13914 Molecular profiling of breast cancer cell lines defines relevant tumor models (aCGH)
GSE15376 Molecular profiling of breast cancer cell lines defines relevant tumor models

Data table header descriptions
ID_REF ID_REF
CH1I_MEAN Mean feature pixel intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale
CH2I_MEAN Mean feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale
CH1B_MEDIAN The median feature background intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel; Background
CH2B_MEDIAN The median feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
CH1D_MEAN The mean feature pixel intensity at wavelength 532 nm with the median background subtracted.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel
CH2D_MEAN .The mean feature pixel intensity at wavelength 635 nm with the median background subtracted.; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH1I_MEDIAN Median feature pixel intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale
CH2I_MEDIAN Median feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale
CH1B_MEAN The mean feature background intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Background
CH2B_MEAN The mean feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Background
CH1D_MEDIAN The median feature pixel intensity at wavelength 532 nm with the median background subtracted.; Type: integer; Scale: linear_scale
CH2D_MEDIAN The median feature pixel intensity at wavelength 635 nm with the median background subtracted.; Type: integer; Scale: linear_scale
CH1_PER_SAT The percentage of feature pixels at wavelength 532 nm that are saturated.; Type: integer; Scale: linear_scale
CH2_PER_SAT The percentage of feature pixels at wavelength 635 nm that are saturated.; Type: integer; Scale: linear_scale
CH1I_SD The standard deviation of the feature intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel
CH2I_SD The standard deviation of the feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH1B_SD The standard deviation of the feature background intensity at wavelength 532 nm.; Type: float; Scale: linear_scale; Channel: Cy3 Channel; Background
CH2B_SD The standard deviation of the feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
PERGTBCH1I_1SD The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale
PERGTBCH2I_1SD The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength 635 nm.; Type: integer; Scale: linear_scale
PERGTBCH1I_2SD The percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale
PERGTBCH2I_2SD The percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale
SUM_MEAN The sum of the arithmetic mean intensities for each wavelength, with the median background subtracted.; Type: integer; Scale: linear_scale
SUM_MEDIAN The sum of the median intensities for each wavelength, with the median background subtracted.; Type: integer; Scale: linear_scale
RAT1_MEAN Ratio of the arithmetic mean intensities of each spot for each wavelength, with the median background subtracted. Channel 1/Channel 2 ratio, (CH1I_MEAN - CH1B_MEDIAN)/(CH2I_MEAN - CH2B_MEDIAN) or Green/Red ratio.; Type: float; Scale: linear_scale
RAT2_MEAN The ratio of the arithmetic mean intensities of each feature for each wavelength, with the median background subtracted.; Type: float; Scale: linear_scale
RAT2_MEDIAN The ratio of the median intensities of each feature for each wavelength, with the median background subtracted.; Type: float; Scale: linear_scale
PIX_RAT2_MEAN The geometric mean of the pixel-by-pixel ratios of pixel intensities, with the median background subtracted.; Type: float; Scale: linear_scale
PIX_RAT2_MEDIAN The median of pixel-by-pixel ratios of pixel intensities, with the median background subtracted.; Type: float; Scale: linear_scale
RAT2_SD The geometric standard deviation of the pixel intensity ratios.; Type: float; Scale: linear_scale
TOT_SPIX The total number of feature pixels.; Type: integer; Scale: linear_scale
TOT_BPIX The total number of background pixels.; Type: integer; Scale: linear_scale
REGR The regression ratio of every pixel in a 2-feature-diameter circle around the center of the feature.; Type: float; Scale: linear_scale
CORR The correlation between channel1 (Cy3) & Channel 2 (Cy5) pixels within the spot, and is a useful quality control parameter. Generally, high values imply better fit & good spot quality.; Type: float; Scale: linear_scale
DIAMETER The diameter in um of the feature-indicator.; Type: integer; Scale: linear_scale
X_COORD X-coordinate of the center of the spot-indicator associated with the spot, where (0,0) is the top left of the image.; Type: integer; Scale: linear_scale
Y_COORD Y-coordinate of the center of the spot-indicator associated with the spot, where (0,0) is the top left of the image.; Type: integer; Scale: linear_scale
TOP Box top: int(((centerX - radius) - Xoffset) / pixelSize).; Type: integer; Scale: linear_scale
BOT Box bottom: int(((centerX + radius) - Xoffset) / pixelSize).; Type: integer; Scale: linear_scale
LEFT Box left: int(((centerY - radius) - yoffset) / pixelSize).; Type: integer; Scale: linear_scale
RIGHT Box right: int(((centerY + radius) - yoffset) / pixelSize); Type: integer; Scale: linear_scale
FLAG The type of flag associated with a feature: -100 = user-flagged null spot; -50 = software-flagged null spot; 0 = spot valid.; Type: integer; Scale: linear_scale
CH2IN_MEAN Normalized value of mean Channel 2 (usually 635 nm) intensity (CH2I_MEAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH2BN_MEDIAN Normalized value of median Channel 2 (usually 635 nm) background (CH2B_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
CH2DN_MEAN Normalized value of mean Channel 2 (usually 635 nm) intensity with normalized background subtracted (CH2IN_MEAN - CH2BN_MEDIAN).; Type: integer; Scale: linear_scale; Channel: Cy5 channel
RAT2N_MEAN Type: float; Scale: linear_scale
CH2IN_MEDIAN Normalized value of median Channel 2 (usually 635 nm) intensity (CH2I_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale
CH2DN_MEDIAN Normalized value of median Channel 2 (usually 635 nm) intensity with normalized background subtracted (CH2IN_MEDIAN - CH2BN_MEDIAN).; Type: integer; Scale: linear_scale
RAT1N_MEAN Ratio of the means of Channel 1 (usually 532 nm) intensity to normalized Channel 2 (usually 635 nm) intensity with median background subtracted (CH1D_MEAN/CH2DN_MEAN). Channel 1/Channel 2 ratio normalized or Green/Red ratio normalized.; Type: float; Scale: linear_scale
RAT2N_MEDIAN Channel 2/Channel 1 ratio normalized, RAT2_MEDIAN/Normalization factor or Red/Green median ratio normalized.; Type: float; Scale: linear_scale
LOG_RAT2N_MEAN Log (base 2) of the ratio of the mean of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm) [log (base 2) (RAT2N_MEAN)].; Type: float; Scale: log_base_2
VALUE Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm) [log (base 2) (RAT2N_MEDIAN)].; Type: float; Scale: log_base_2

Data table
ID_REF CH1I_MEAN CH2I_MEAN CH1B_MEDIAN CH2B_MEDIAN CH1D_MEAN CH2D_MEAN CH1I_MEDIAN CH2I_MEDIAN CH1B_MEAN CH2B_MEAN CH1D_MEDIAN CH2D_MEDIAN CH1_PER_SAT CH2_PER_SAT CH1I_SD CH2I_SD CH1B_SD CH2B_SD PERGTBCH1I_1SD PERGTBCH2I_1SD PERGTBCH1I_2SD PERGTBCH2I_2SD SUM_MEAN SUM_MEDIAN RAT1_MEAN RAT2_MEAN RAT2_MEDIAN PIX_RAT2_MEAN PIX_RAT2_MEDIAN RAT2_SD TOT_SPIX TOT_BPIX REGR CORR DIAMETER X_COORD Y_COORD TOP BOT LEFT RIGHT FLAG CH2IN_MEAN CH2BN_MEDIAN CH2DN_MEAN RAT2N_MEAN CH2IN_MEDIAN CH2DN_MEDIAN RAT1N_MEAN RAT2N_MEDIAN LOG_RAT2N_MEAN VALUE
1 8155 5464 758 1264 7397 4200 8314 5468 768 1287 7556 4204 0 0 1346 870 220 325 100 100 100 100 11597 11760 1.761 .568 .556 .59 .57 .27 97 322 .67 .99 110 2410 5950 21 32 23 34 0 4191 970 3222 .436 4195 3225 2.296 .427 -1.199 -1.228
2 8951 6929 757 1306 8194 5623 9141 6722 791 1332 8384 5416 0 0 2200 1911 279 346 100 100 100 100 13817 13800 1.457 .686 .646 .68 .7 .14 80 255 .78 .99 100 2560 5960 23 33 39 49 0 5315 1002 4313 .526 5157 4155 1.9 .496 -.926 -1.013
3 9094 7578 774 1304 8320 6274 9220 7595 786 1338 8446 6291 0 0 1365 1181 244 331 100 100 100 100 14594 14737 1.326 .754 .745 .75 .76 .15 86 284 .83 .99 100 2710 5950 22 32 54 64 0 5813 1000 4813 .578 5826 4826 1.729 .571 -.79 -.807
4 7310 5910 740 1333 6570 4577 7388 5690 772 1339 6648 4357 0 0 1621 1490 268 325 100 100 100 100 11147 11005 1.435 .697 .655 .69 .69 .17 70 292 .81 .99 90 2850 5960 23 32 68 77 0 4534 1023 3511 .534 4365 3342 1.871 .503 -.904 -.992
5 7121 5131 770 1285 6351 3846 7231 5150 804 1318 6461 3865 0 0 847 837 267 346 100 100 100 100 10197 10326 1.651 .606 .598 .6 .63 .14 80 308 .73 .99 100 3000 5960 23 33 83 93 0 3936 986 2950 .465 3951 2965 2.153 .459 -1.106 -1.124
6 7557 6318 782 1291 6775 5027 7752 6350 806 1350 6970 5059 0 0 1947 1701 273 349 100 100 100 100 11802 12029 1.348 .742 .726 .74 .75 .16 52 290 .84 .99 80 3150 5960 24 32 99 107 0 4847 990 3856 .569 4871 3881 1.757 .557 -.813 -.845
7 7081 9428 758 1282 6323 8146 7090 9376 785 1317 6332 8094 0 0 1227 1788 265 317 100 100 100 100 14469 14426 .776 1.288 1.278 1.31 1.33 .35 151 214 1.33 .99 140 3290 5950 20 34 110 124 0 7232 983 6249 .988 7192 6209 1.012 .981 -.017 -.028
8 5482 6107 715 1307 4767 4800 5503 6238 758 1314 4788 4931 0 0 802 1017 237 347 100 100 100 100 9567 9719 .993 1.007 1.03 1.01 1.04 .24 124 198 1.12 .99 120 3440 5950 21 33 126 138 0 4685 1003 3682 .772 4785 3783 1.295 .79 -.373 -.34
9 6102 6052 701 1288 5401 4764 6197 6110 741 1320 5496 4822 0 0 1077 1177 241 367 100 100 99 100 10165 10318 1.134 .882 .877 .91 .88 .3 104 204 1.01 .99 110 3580 5960 22 33 140 151 0 4643 988 3655 .677 4687 3699 1.478 .673 -.564 -.571
10 10755 12442 711 1274 10044 11168 10596 12336 735 1334 9885 11062 0 0 1939 2220 216 584 100 100 100 100 21212 20947 .899 1.112 1.119 1.11 1.1 .15 86 245 1.17 1 100 3730 5950 22 32 156 166 0 9544 977 8567 .853 9463 8486 1.172 .858 -.229 -.22
11 4593 5627 738 1329 3855 4298 4474 5689 750 1373 3736 4360 0 0 767 759 217 352 100 100 100 100 8153 8096 .897 1.115 1.167 1.15 1.11 .31 97 337 1.24 .99 110 3870 5950 21 32 169 180 0 4317 1019 3297 .855 4364 3345 1.169 .895 -.226 -.16
12 4877 4693 728 1313 4149 3380 5176 4622 742 1358 4448 3309 0 0 1113 1190 213 336 100 100 100 100 7529 7757 1.228 .815 .744 .82 .83 .23 60 300 .98 .99 80 4020 5960 24 32 186 194 0 3600 1007 2593 .625 3546 2538 1.6 .571 -.678 -.809
13 6780 8315 730 1293 6050 7022 6884 8556 741 1314 6154 7263 0 0 1148 1441 212 309 100 100 100 100 13072 13417 .862 1.161 1.18 1.16 1.16 .23 112 234 1.24 .99 120 4170 5960 22 34 199 211 0 6379 992 5387 .89 6563 5572 1.123 .905 -.168 -.143
14 9148 12598 725 1323 8423 11275 9216 12580 747 1328 8491 11257 0 0 1182 1356 224 339 100 100 100 100 19698 19748 .747 1.339 1.326 1.35 1.33 .24 97 230 1.38 1 110 4310 5960 22 33 213 224 0 9664 1015 8649 1.027 9650 8635 .974 1.017 .038 .024
15 4198 5990 743 1279 3455 4711 4102 6113 758 1324 3359 4834 0 0 673 812 241 338 100 100 100 100 8166 8193 .733 1.364 1.439 1.4 1.39 .33 137 215 1.44 .99 130 4460 5950 20 33 227 240 0 4595 981 3614 1.046 4689 3708 .956 1.104 .065 .143
16 20072 26770 747 1283 19325 25487 20236 27031 759 1335 19489 25748 0 0 3156 3416 223 348 100 100 100 100 44812 45237 .758 1.319 1.321 1.33 1.32 .16 146 190 1.34 1 130 4600 5960 21 34 241 254 0 20536 984 19551 1.012 20736 19752 .988 1.013 .017 .019
17 7129 10702 793 1338 6336 9364 7115 10788 809 1353 6322 9450 0 0 968 1430 238 334 100 100 100 100 15700 15772 .677 1.478 1.495 1.49 1.54 .25 86 226 1.51 .99 100 4750 5960 23 33 258 268 0 8210 1026 7183 1.134 8276 7249 .882 1.147 .181 .197
18 7448 11265 780 1328 6668 9937 7392 11545 794 1351 6612 10217 0 0 1303 1562 226 332 100 100 100 100 16605 16829 .671 1.49 1.545 1.51 1.54 .26 86 274 1.51 .99 100 4900 5950 22 32 273 283 0 8642 1019 7623 1.143 8856 7838 .875 1.185 .193 .245
19 14867 22804 736 1268 14131 21536 14837 22950 743 1313 14101 21682 0 0 2260 2839 221 317 100 100 100 100 35667 35783 .656 1.524 1.538 1.53 1.56 .19 86 275 1.54 1 100 5040 5960 23 33 287 297 0 17493 973 16521 1.169 17605 16633 .855 1.18 .225 .238
20 5819 10111 739 1309 5080 8802 5898 10432 772 1327 5159 9123 0 0 1106 1633 384 388 100 100 100 100 13882 14282 .577 1.733 1.768 1.78 1.72 .4 70 313 1.74 .99 90 5190 5960 23 32 302 311 0 7756 1004 6752 1.329 8003 6998 .752 1.357 .411 .44

Total number of rows: 41472

Table truncated, full table size 9941 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap