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Sample GSM79639 Query DataSets for GSM79639
Status Public on Oct 22, 2005
Title "6 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 "6 hr Hela Double Thymidine, exp3"
Organism Homo sapiens
Characteristics "6 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/2001-01/13128.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
1 715 788 131 70 584 718 873 968 154 100 742 898 0 0 456 642 129 163 70 61 65 57 1302 1640 .813 1.229 1.21 1.208 1.239 .702 80 389 1.236 .94 100 1410 8800 87 97 80 90 0 686 61 625 1.07 842 781 .935 1.053 .098 .075
2 602 622 141 70 461 552 493 561 201 148 352 491 0 0 328 408 199 259 75 65 43 46 1013 843 .835 1.197 1.395 2.964 1.127 7.318 32 146 .928 .79 70 1550 8840 92 99 95 102 0 541 61 480 1.042 488 427 .96 1.214 .059 .28
3 4489 6074 130 71 4359 6003 4385 5465 133 76 4255 5394 0 0 1747 2382 31 24 100 100 100 100 10362 9649 .726 1.377 1.268 1.447 1.409 .495 80 242 1.2 .92 100 1700 8830 90 100 109 119 0 5286 62 5224 1.198 4756 4694 .834 1.103 .261 .142
4 354 306 126 72 228 234 152 94 130 77 26 22 0 0 482 547 38 44 43 27 30 21 462 48 .974 1.026 .846 1.049 .672 1.146 80 244 1.048 .85 100 1820 8800 87 97 121 131 -100 266 63 204 .893 82 19 1.12 .736 -.163 -.441
5 986 1549 135 72 851 1477 1247 2024 190 163 1112 1952 0 0 627 1144 223 379 70 66 70 65 2328 3064 .576 1.736 1.755 2.022 1.79 2.321 80 296 1.651 .94 100 1960 8800 87 97 135 145 -100 1348 63 1285 1.51 1761 1699 .662 1.528 .595 .611
6 1462 1886 138 78 1324 1808 1567 2046 200 175 1429 1968 0 0 629 951 232 387 93 90 87 84 3132 3397 .732 1.366 1.377 1.945 1.419 2.12 32 119 1.134 .82 60 2100 8830 92 98 151 157 0 1641 68 1573 1.188 1781 1713 .841 1.199 .249 .261
7 1901 2241 131 70 1770 2171 1961 2398 134 81 1830 2328 0 0 712 982 39 76 98 92 97 92 3941 4158 .815 1.227 1.272 1.216 1.265 .465 80 270 1.16 .93 100 2240 8820 89 99 163 173 0 1950 61 1889 1.067 2087 2026 .937 1.107 .094 .147
8 2531 3195 127 67 2404 3128 2627 3410 133 80 2500 3343 0 0 861 1262 40 81 100 100 100 98 5532 5843 .769 1.301 1.337 1.372 1.295 .918 80 238 1.248 .94 100 2380 8820 89 99 177 187 0 2780 58 2722 1.132 2968 2909 .883 1.164 .179 .219
9 1328 818 127 78 1201 740 1222 702 130 81 1095 624 0 0 694 516 28 23 100 100 100 98 1941 1719 1.623 .616 .57 .651 .63 .323 52 174 .577 .88 80 2520 8800 88 96 192 200 0 712 68 644 .536 611 543 1.865 .496 -.899 -1.012
10 667 707 129 70 538 637 681 733 135 72 552 663 0 0 130 212 35 22 100 100 100 97 1175 1215 .845 1.184 1.201 1.202 1.203 .398 80 306 1.099 .89 110 2650 8800 86 97 203 214 0 615 61 554 1.03 638 577 .97 1.045 .043 .064
11 628 732 137 70 491 662 648 738 150 73 511 668 0 0 156 155 48 26 100 100 98 100 1153 1179 .742 1.348 1.307 1.597 1.394 1.057 52 195 1.108 .88 90 2780 8820 89 98 217 226 0 637 61 576 1.173 642 581 .852 1.138 .231 .186
12 946 1139 137 76 809 1063 927 1183 143 80 790 1107 0 0 288 475 39 24 100 100 100 100 1872 1897 .761 1.314 1.401 1.337 1.343 .45 52 256 1.243 .91 90 2920 8790 86 95 231 240 0 991 66 925 1.143 1030 963 .875 1.219 .193 .286
13 613 644 137 70 476 574 635 665 137 72 498 595 0 0 175 272 25 21 100 100 100 100 1050 1093 .829 1.206 1.195 1.266 1.247 .544 80 255 1.121 .89 100 3060 8800 87 97 245 255 0 560 61 500 1.049 579 518 .953 1.04 .07 .056
14 927 1130 142 74 785 1056 863 1038 142 75 721 964 0 0 280 422 26 23 100 100 100 100 1841 1685 .743 1.345 1.337 1.398 1.377 .438 80 227 1.276 .93 100 3200 8800 87 97 259 269 0 983 64 919 1.171 903 839 .854 1.164 .227 .219
15 917 935 136 76 781 859 798 771 136 78 662 695 0 0 428 621 26 19 100 96 98 95 1640 1357 .909 1.1 1.05 1.076 1.065 .519 80 235 1.112 .92 100 3340 8790 86 96 273 283 0 814 66 748 .957 671 605 1.045 .914 -.063 -.13
16 1581 1936 137 68 1444 1868 1606 2004 136 71 1469 1936 0 0 388 420 27 22 100 100 100 100 3312 3405 .773 1.294 1.318 1.407 1.283 .65 80 265 1.159 .93 110 3470 8800 86 97 285 296 0 1685 59 1626 1.126 1744 1685 .888 1.147 .171 .198
17 901 1010 140 74 761 936 916 1074 143 79 776 1000 0 0 214 253 28 33 100 100 100 100 1697 1776 .813 1.23 1.289 1.272 1.238 .312 52 216 1.145 .93 90 3600 8790 86 95 299 308 0 879 64 815 1.07 935 870 .934 1.121 .098 .165
18 1143 1350 136 76 1007 1274 1180 1372 140 80 1044 1296 0 0 209 259 29 29 100 100 100 100 2281 2340 .79 1.265 1.241 1.306 1.294 .325 80 290 1.174 .93 110 3740 8800 86 97 312 323 0 1175 66 1109 1.101 1194 1128 .908 1.08 .139 .111
19 871 986 137 72 734 914 886 1001 141 74 749 929 0 0 139 267 31 20 100 100 100 100 1648 1678 .803 1.245 1.24 1.263 1.237 .38 80 257 1.191 .91 100 3880 8790 86 96 327 337 0 858 63 795 1.084 871 808 .923 1.079 .116 .11
20 1375 1690 136 80 1239 1610 1379 1728 138 80 1243 1648 0 0 317 559 29 21 100 100 100 100 2849 2891 .77 1.299 1.326 1.323 1.377 .401 80 284 1.246 .92 110 4010 8790 85 96 339 350 0 1471 70 1401 1.131 1504 1434 .884 1.154 .177 .206

Total number of rows: 44160

Table truncated, full table size 9747 Kbytes.




Supplementary data files not provided
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