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Sample GSM350507 Query DataSets for GSM350507
Status Public on Jul 10, 2009
Title SHFY67|HCC3153
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 HCC3153 genomic DNA
Organism Homo sapiens
Characteristics Breast Tumor Cell Line HCC3153 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 = 1800, 5400; Software: type: feature extraction; Performer: Melanie,,Bocanegra
Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-12-02; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 540; Parameter Laser on time = 68959; Parameter Laser Power = 3.64; Parameter Scan Time = 13:55:18; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 29.96; Performer: Melanie,,Bocanegra
Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-12-02; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 540; Parameter Scan Power = 100; Parameter Laser on time = 69004; Parameter Laser Power = 3.45; Parameter Scan Time = 13:55:18; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 29.96; Performer: Melanie,,Bocanegra
Description Simple annotation: Breast, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/66007.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) [email protected]
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 GPL7779
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 2052 1653 416 323 1636 1330 2102 1683 460 348 1686 1360 0 0 626 588 232 200 100 99 98 94 2966 3046 1.23 .813 .807 .84 .81 .34 80 361 .81 .99 100 2410 5840 39 49 56 66 0 1378 269 1109 .678 1403 1134 1.475 .673 -.561 -.572
2 2375 1691 403 335 1972 1356 2230 1499 432 355 1827 1164 0 0 854 749 203 189 100 100 100 97 3328 2991 1.454 .688 .637 .69 .72 .27 70 343 .71 .99 90 2560 5830 38 47 71 80 0 1410 279 1131 .573 1250 970 1.744 .531 -.803 -.913
3 2249 1517 381 324 1868 1193 2252 1425 415 341 1871 1101 0 0 800 636 183 165 100 98 100 95 3061 2972 1.566 .639 .588 .66 .65 .3 60 352 .67 .98 80 2700 5840 40 48 86 94 0 1265 270 995 .532 1188 918 1.878 .491 -.909 -1.027
4 2043 1522 378 313 1665 1209 2073 1348 410 322 1695 1035 0 0 706 693 179 161 100 100 98 95 2874 2730 1.377 .726 .611 .73 .71 .3 60 367 .73 .98 80 2850 5840 40 48 101 109 0 1269 261 1008 .605 1124 863 1.652 .509 -.724 -.974
5 1858 1123 399 306 1459 817 1920 1052 432 326 1521 746 0 0 719 446 212 181 95 95 93 86 2276 2267 1.786 .56 .49 .66 .62 .39 44 366 .61 .96 70 2990 5840 40 47 115 122 0 936 255 681 .467 877 622 2.142 .409 -1.099 -1.29
6 2681 2525 395 314 2286 2211 2625 2302 432 350 2230 1988 0 0 1106 1291 219 202 98 100 98 100 4497 4218 1.034 .967 .891 1.02 .93 .44 51 391 .93 .98 80 3130 5840 40 48 129 137 0 2105 262 1843 .806 1919 1657 1.24 .743 -.31 -.428
7 2020 1107 384 325 1636 782 1923 1058 424 352 1539 733 0 0 837 546 201 199 100 87 94 77 2418 2272 2.092 .478 .476 .5 .48 .27 70 377 .55 .96 90 3290 5840 39 48 144 153 0 923 271 652 .399 882 611 2.509 .397 -1.327 -1.332
8 2286 2032 410 324 1876 1708 2341 1997 447 344 1931 1673 0 0 866 912 261 191 97 97 94 96 3584 3604 1.098 .91 .866 .97 .93 .52 70 321 .89 .99 90 3440 5840 39 48 159 168 0 1694 270 1424 .759 1665 1395 1.317 .722 -.398 -.469
9 2299 2311 524 393 1775 1918 2389 2339 1514 885 1865 1946 0 0 618 747 2583 1276 8 81 0 19 3693 3811 .925 1.081 1.043 1.19 1.08 .65 80 322 1.01 .98 100 3580 5840 39 49 173 183 0 1927 328 1599 .901 1950 1622 1.11 .87 -.151 -.201
10 4282 4388 518 434 3764 3954 4215 4109 1430 872 3697 3675 0 0 1198 1373 2388 1200 86 100 16 84 7718 7372 .952 1.05 .994 1.06 1.08 .26 51 390 1.02 .99 80 3730 5830 39 47 189 197 0 3658 362 3297 .876 3426 3064 1.142 .829 -.191 -.271
11 1654 1718 416 328 1238 1390 1616 1647 512 387 1200 1319 0 0 567 683 419 332 92 98 74 86 2628 2519 .891 1.123 1.099 1.23 1.12 .7 86 330 1.04 .98 100 3880 5840 39 49 203 213 0 1432 273 1159 .936 1373 1100 1.068 .916 -.095 -.126
12 2218 1624 402 334 1816 1290 2108 1439 466 361 1706 1105 0 0 954 1052 333 203 98 95 95 90 3106 2811 1.408 .71 .648 .71 .63 .44 80 307 .72 .97 100 4030 5840 39 49 218 228 0 1354 278 1076 .592 1200 921 1.688 .54 -.756 -.889
13 2277 2114 428 351 1849 1763 2136 2029 537 385 1708 1678 0 0 761 831 401 205 100 100 93 98 3612 3386 1.049 .953 .982 .99 .96 .39 86 289 .92 .98 100 4170 5840 39 49 232 242 0 1763 293 1470 .795 1692 1399 1.258 .819 -.331 -.288
14 3277 3582 409 313 2868 3269 3163 3231 443 348 2754 2918 0 0 1268 1471 194 177 100 100 100 100 6137 5672 .877 1.14 1.06 1.18 1.12 .38 97 333 1.08 .99 110 4310 5840 38 49 245 256 0 2986 261 2725 .95 2694 2433 1.052 .883 -.074 -.179
15 1854 2292 392 300 1462 1992 1849 2379 426 328 1457 2079 0 0 558 804 195 168 100 100 99 99 3454 3536 .734 1.363 1.427 1.43 1.39 .53 97 319 1.23 .99 110 4460 5840 38 49 260 271 0 1911 250 1661 1.136 1983 1733 .88 1.19 .184 .251
16 4021 5017 387 286 3634 4731 3839 4799 416 324 3452 4513 0 0 2002 2543 170 179 99 100 97 100 8365 7965 .768 1.302 1.307 1.53 1.32 1.12 70 330 1.24 .99 90 4610 5840 39 48 276 285 0 4183 238 3944 1.085 4001 3763 .921 1.09 .118 .124
17 2582 3647 391 305 2191 3342 2648 3637 411 324 2257 3332 0 0 955 1196 186 164 100 100 100 100 5533 5589 .656 1.525 1.476 1.67 1.59 .63 97 308 1.4 .99 110 4750 5840 38 49 289 300 0 3041 254 2786 1.272 3032 2778 .786 1.231 .347 .3
18 2996 3526 387 308 2609 3218 2952 3622 413 329 2565 3314 0 0 727 990 172 162 100 100 100 100 5827 5879 .811 1.233 1.292 1.25 1.25 .31 104 283 1.18 .99 110 4900 5840 38 49 304 315 0 2940 257 2683 1.028 3020 2763 .972 1.077 .04 .107
19 4856 6974 387 290 4469 6684 4448 6670 420 325 4061 6380 0 0 2280 2928 188 170 100 100 100 100 11153 10441 .669 1.496 1.571 1.62 1.47 .56 97 299 1.45 .99 110 5040 5840 38 49 318 329 0 5814 242 5573 1.247 5561 5319 .802 1.31 .318 .389
20 2057 2025 396 271 1661 1754 2013 1940 420 310 1617 1669 0 0 632 688 185 171 100 100 100 99 3415 3286 .947 1.056 1.032 1.12 1 .47 104 288 .98 .99 110 5190 5850 39 50 333 344 0 1688 226 1462 .88 1617 1391 1.136 .861 -.184 -.217

Total number of rows: 41472

Table truncated, full table size 9564 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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