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Sample GSM79652 Query DataSets for GSM79652
Status Public on Oct 22, 2005
Title "10 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 "10 hr Hela Double Thymidine, exp3"
Organism Homo sapiens
Characteristics "10 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/2001-01/13132.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 1082 1252 169 135 913 1117 1151 1376 177 145 982 1241 0 0 351 550 55 57 97 90 96 88 2030 2223 .817 1.223 1.264 1.09 1.285 2.001 80 365 1.316 .91 100 1450 8430 86 96 84 94 0 1099 119 981 1.074 1208 1090 .931 1.109 .103 .15
2 753 805 186 148 567 657 794 813 193 166 608 665 0 0 295 361 59 93 100 100 91 100 1224 1273 .863 1.159 1.094 1.172 1.146 2.515 12 86 1.387 .61 50 1580 8430 88 93 99 104 0 707 130 577 1.017 714 584 .983 .96 .025 -.059
3 5871 6986 175 147 5696 6839 6659 8171 182 156 6484 8024 0 0 2750 3840 55 64 99 96 98 94 12535 14508 .833 1.201 1.238 .94 1.245 2.69 120 400 1.255 .93 120 1730 8440 86 98 111 123 0 6133 129 6004 1.054 7174 7045 .949 1.086 .076 .12
4 1125 1451 184 148 941 1303 994 1314 185 153 810 1166 0 0 733 1076 56 47 90 94 78 90 2244 1976 .722 1.385 1.44 1.441 1.324 3.086 52 144 1.195 .85 90 1850 8450 88 97 124 133 0 1274 130 1144 1.216 1154 1024 .823 1.264 .282 .338
5 1607 2965 211 163 1396 2802 1703 2970 362 400 1492 2807 0 0 587 966 419 726 90 96 82 90 4198 4299 .498 2.007 1.881 2.038 1.932 1.634 52 196 2.035 .93 90 1980 8450 88 97 137 146 0 2603 143 2460 1.762 2607 2464 .567 1.652 .817 .724
6 1705 2303 196 166 1509 2137 1813 2148 344 419 1617 1982 0 0 1154 1752 406 748 71 65 65 56 3646 3599 .706 1.416 1.226 1.453 1.44 3.506 32 172 1.596 .8 70 2120 8430 87 94 152 159 0 2022 146 1876 1.243 1886 1740 .804 1.076 .314 .106
7 3122 4061 181 143 2941 3918 3174 4262 186 166 2993 4119 0 0 618 1068 61 129 100 100 100 100 6859 7112 .751 1.332 1.376 1.3 1.328 1.288 80 264 1.407 .94 100 2280 8440 87 97 167 177 0 3565 126 3440 1.17 3742 3616 .855 1.208 .226 .273
8 6911 4353 181 127 6730 4226 2949 4233 189 145 2768 4106 1 0 12535 1518 83 95 100 100 100 100 10956 6874 1.593 .628 1.483 1.129 1.446 2.128 80 202 .143 .53 100 2410 8440 87 97 180 190 0 3822 111 3710 .551 3716 3605 1.814 1.302 -.859 .381
9 1277 1117 181 139 1096 978 1108 883 189 159 927 744 0 0 1003 899 73 88 85 85 77 80 2074 1671 1.121 .892 .803 1.005 .888 2.879 80 289 .873 .87 110 2540 8420 84 95 192 203 0 981 122 859 .783 775 653 1.276 .705 -.352 -.505
10 994 1245 176 152 818 1093 1023 1248 179 157 847 1096 0 0 262 249 53 58 100 100 100 100 1911 1943 .748 1.336 1.294 1.404 1.398 1.426 80 292 1.293 .89 110 2680 8420 84 95 206 217 0 1093 133 960 1.173 1096 962 .852 1.136 .23 .184
11 788 871 182 151 606 720 815 920 195 166 633 769 0 0 262 312 77 70 98 100 96 95 1326 1402 .842 1.188 1.215 1.133 1.185 1.771 80 236 1.212 .85 100 2820 8430 86 96 221 231 0 765 133 632 1.043 808 675 .959 1.067 .061 .093
12 1070 1207 181 159 889 1048 960 1087 192 170 779 928 0 0 506 672 63 64 98 95 97 91 1937 1707 .848 1.179 1.191 1.084 1.136 2.072 80 272 1.248 .89 100 2950 8410 84 94 234 244 0 1060 140 920 1.035 954 815 .966 1.046 .05 .065
13 1029 1144 190 185 839 959 998 1159 197 196 808 974 0 0 248 322 59 78 100 100 100 100 1798 1782 .875 1.143 1.205 1.112 1.167 1.44 52 225 1.267 .88 90 3090 8410 84 93 248 257 0 1004 162 842 1.003 1018 855 .997 1.058 .005 .082
14 1411 1975 189 189 1222 1786 1393 1784 195 198 1204 1595 0 0 449 658 58 76 100 100 100 100 3008 2799 .684 1.462 1.325 1.483 1.419 1.491 80 255 1.488 .92 110 3230 8430 85 96 261 272 0 1734 166 1568 1.283 1566 1400 .779 1.163 .36 .218
15 1125 1500 183 168 942 1332 1091 1402 187 178 908 1234 0 0 426 531 55 64 98 100 97 98 2274 2142 .707 1.414 1.359 1.473 1.374 1.572 80 205 1.419 .9 100 3360 8420 85 95 275 285 0 1317 147 1169 1.241 1231 1083 .806 1.193 .312 .255
16 1832 2338 183 156 1649 2182 2192 2934 282 270 2009 2778 0 0 1042 1373 423 470 75 76 72 73 3831 4787 .756 1.323 1.383 1.246 1.315 2.508 80 260 1.32 .92 100 3470 8410 84 94 286 296 0 2053 137 1916 1.162 2576 2439 .861 1.214 .216 .28
17 1009 1111 185 159 824 952 1016 1151 283 271 831 992 0 0 332 366 426 472 85 81 47 53 1776 1823 .866 1.155 1.194 1.157 1.136 1.569 80 257 1.052 .86 100 3630 8420 85 95 302 312 0 975 140 836 1.014 1010 871 .986 1.048 .02 .068
18 1424 1981 183 160 1241 1821 1334 2036 184 172 1151 1876 0 0 533 666 50 63 100 100 100 100 3062 3027 .681 1.467 1.63 1.522 1.488 1.483 80 267 1.439 .92 110 3760 8420 84 95 314 325 0 1739 140 1599 1.288 1787 1647 .776 1.431 .365 .517
19 1041 1308 181 162 860 1146 1034 1341 184 176 853 1179 0 0 282 460 51 64 100 100 100 100 2006 2032 .75 1.333 1.382 1.287 1.389 1.5 80 250 1.415 .9 100 3900 8410 84 94 329 339 0 1148 142 1006 1.17 1177 1035 .855 1.213 .226 .279
20 2176 3035 178 171 1998 2864 2257 3015 186 181 2079 2844 0 0 718 814 59 63 100 100 100 100 4862 4923 .698 1.433 1.368 1.482 1.423 1.463 80 257 1.382 .89 110 4020 8420 84 95 340 351 0 2665 150 2514 1.258 2647 2497 .795 1.201 .332 .264

Total number of rows: 44160

Table truncated, full table size 9855 Kbytes.




Supplementary data files not provided
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