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Sample GSM79661 Query DataSets for GSM79661
Status Public on Oct 22, 2005
Title "25 hr Hela Double Thymidine, exp3"
Sample type RNA
 
Channel 1
Source name Hela Reference 3 primed with oligo dT
Organism Homo sapiens
Characteristics Hela Reference 3 primed with oligo dT
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name "25 hr Hela Double Thymidine, exp3"
Organism Homo sapiens
Characteristics "25 hr Hela Double Thymidine, exp3"
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Cell-cycle, Dbl thymidine
Image: http://smd.stanford.edu/MicroArray/gifs/2001-02/13423.gif
Data processing VALUE is Log (base 2) of the ratio of the mean of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)
 
Submission date Oct 21, 2005
Last update date Sep 22, 2006
Organization Stanford Microarray Database (SMD)
E-mail(s) array@genome.stanford.edu
Phone 650-498-6012
URL http://genome-www5.stanford.edu/
Department Stanford University, School of Medicine
Street address 300 Pasteur Drive
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
 
Platform ID GPL3001
Series (2)
GSE3497 Cell division cycle in a human cancer cell line (HeLa)
GSE4301 Diverse and specific gene expression responses to stresses in cultured human cells.

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
VALUE 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
LOG_RAT2N_MEDIAN 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 VALUE LOG_RAT2N_MEDIAN
1 1024 1144 189 91 835 1053 1036 1135 195 105 847 1044 0 0 314 507 53 77 100 96 94 94 1888 1891 .793 1.261 1.233 1.158 1.249 1.573 52 234 1.366 .93 80 1050 8490 109 117 81 89 0 984 78 906 1.085 976 898 .922 1.06 .118 .085
2 651 731 184 93 467 638 566 545 199 108 382 452 0 0 362 501 66 83 90 93 84 87 1105 834 .732 1.366 1.183 1.341 1.567 3.131 32 113 1.568 .68 60 1180 8510 112 118 95 101 0 629 80 549 1.175 469 389 .851 1.018 .233 .026
3 8094 11911 192 103 7902 11808 8526 11903 277 311 8334 11800 0 0 1845 3070 609 1295 100 100 100 100 19710 20134 .669 1.494 1.416 1.479 1.494 1.163 52 184 1.531 .96 90 1320 8490 108 117 107 116 0 10248 89 10159 1.286 10241 10152 .778 1.218 .362 .285
4 439 258 194 107 245 151 229 134 248 228 35 27 0 0 675 451 464 986 13 6 7 1 396 62 1.623 .616 .771 .588 .654 3.453 80 320 1.525 .83 110 1430 8470 105 116 117 128 -100 222 92 130 .53 115 23 1.886 .664 -.915 -.591
5 1646 2859 204 105 1442 2754 1624 2875 216 134 1420 2770 0 0 312 448 70 185 100 100 100 100 4196 4190 .524 1.91 1.951 1.929 1.951 1.185 52 171 1.867 .94 90 1590 8490 108 117 134 143 0 2460 90 2369 1.643 2473 2383 .609 1.678 .716 .747
6 408 330 208 110 200 220 215 124 218 135 7 14 0 0 446 566 82 197 28 20 25 16 420 21 .909 1.1 2 .857 .763 3.774 80 332 1.59 .78 110 1700 8470 105 116 144 155 -100 284 95 189 .946 107 12 1.057 1.721 -.08 .783
7 3012 4144 220 120 2792 4024 3034 4240 324 218 2814 4120 0 0 796 1069 403 402 100 100 100 100 6816 6934 .694 1.441 1.464 1.457 1.465 1.206 52 217 1.385 .94 90 1860 8490 108 117 161 170 0 3565 103 3462 1.24 3648 3545 .806 1.26 .31 .333
8 2802 3175 230 120 2572 3055 2972 3470 438 309 2742 3350 0 0 639 993 612 605 98 92 94 90 5627 6092 .842 1.188 1.222 1.088 1.212 1.727 52 199 1.2 .89 90 2000 8480 107 116 175 184 0 2732 103 2628 1.022 2985 2882 .979 1.051 .031 .072
9 2532 1070 211 104 2321 966 2424 898 309 194 2213 794 0 0 1277 658 450 463 92 76 84 46 3287 3007 2.403 .416 .359 .352 .454 2.694 52 229 .422 .82 90 2130 8460 105 114 188 197 0 921 89 831 .358 773 683 2.793 .309 -1.482 -1.696
10 805 896 210 101 595 795 826 925 211 103 616 824 0 0 257 371 40 31 100 98 100 98 1390 1440 .748 1.336 1.338 1.324 1.416 1.642 80 248 1.377 .91 100 2270 8480 107 117 202 212 0 771 87 684 1.15 796 709 .87 1.151 .201 .203
11 798 971 199 88 599 883 825 991 199 95 626 903 0 0 186 296 40 43 100 100 100 100 1482 1529 .678 1.474 1.442 1.442 1.518 1.471 52 228 1.505 .86 90 2400 8460 105 114 215 224 0 835 76 760 1.268 853 777 .788 1.241 .343 .312
12 720 756 197 87 523 669 536 589 198 93 339 502 0 0 369 510 37 41 98 96 97 92 1192 841 .782 1.279 1.481 1.141 1.349 2.375 80 275 1.375 .89 100 2540 8460 105 115 229 239 0 650 75 576 1.101 507 432 .909 1.274 .138 .349
13 780 726 202 102 578 624 693 567 203 105 491 465 0 0 369 491 34 32 100 98 100 96 1202 956 .926 1.08 .947 .939 1.129 2.121 80 235 1.237 .87 100 2670 8470 106 116 242 252 0 625 88 537 .929 488 400 1.077 .815 -.107 -.296
14 1137 1562 216 103 921 1459 1056 1525 213 105 840 1422 0 0 396 693 39 31 100 100 100 97 2380 2262 .631 1.584 1.693 1.423 1.722 2.014 80 217 1.687 .92 100 2810 8470 106 116 256 266 0 1344 89 1255 1.363 1312 1223 .734 1.456 .447 .542
15 1086 1199 219 115 867 1084 988 1099 220 118 769 984 0 0 452 644 38 38 100 97 100 95 1951 1753 .8 1.25 1.28 1.119 1.337 1.99 80 233 1.334 .91 100 2940 8450 104 114 269 279 0 1032 99 933 1.076 946 847 .93 1.101 .105 .139
16 2241 2405 217 128 2024 2277 2254 2583 220 132 2037 2455 0 0 280 605 40 42 100 100 100 100 4301 4492 .889 1.125 1.205 1.066 1.179 1.438 80 276 1.203 .93 110 3070 8450 103 114 281 292 0 2069 110 1959 .968 2222 2112 1.033 1.037 -.047 .052
17 1059 1247 235 141 824 1106 1126 1253 237 145 891 1112 0 0 401 478 41 42 97 100 97 100 1930 2003 .745 1.342 1.248 1.477 1.372 1.73 80 242 1.319 .91 100 3190 8460 105 115 294 304 0 1073 121 952 1.155 1078 957 .866 1.074 .208 .103
18 1625 2037 238 138 1387 1899 1676 2272 242 142 1438 2134 0 0 527 838 41 42 100 100 100 97 3286 3572 .73 1.369 1.484 1.238 1.375 1.841 80 263 1.451 .93 100 3330 8470 106 116 308 318 0 1753 119 1634 1.178 1955 1836 .849 1.277 .236 .352
19 1496 1892 238 135 1258 1757 1498 2076 242 140 1260 1941 0 0 290 521 44 43 100 100 100 100 3015 3201 .716 1.397 1.54 1.343 1.463 1.433 52 225 1.509 .92 90 3470 8470 106 115 322 331 0 1628 116 1512 1.202 1786 1670 .832 1.325 .265 .406
20 1779 2386 246 137 1533 2249 1823 2517 247 143 1577 2380 0 0 483 665 45 39 100 100 100 100 3782 3957 .682 1.467 1.509 1.474 1.554 1.405 80 255 1.482 .93 100 3610 8470 106 116 336 346 0 2053 118 1935 1.262 2165 2048 .792 1.298 .336 .377

Total number of rows: 44160

Table truncated, full table size 9986 Kbytes.




Supplementary data files not provided
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