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Sample GSM79645 Query DataSets for GSM79645
Status Public on Oct 22, 2005
Title "11 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 "11 hr Hela Double Thymidine, exp3"
Organism Homo sapiens
Characteristics "11 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/2001-02/13416.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 1469 1480 238 134 1231 1346 1533 1628 279 207 1295 1494 0 0 271 429 187 261 100 100 100 87 2577 2789 .915 1.093 1.154 1.036 1.132 1.381 32 137 1.202 .93 70 1000 7640 72 79 76 83 0 1375 125 1251 1.016 1513 1388 .984 1.072 .023 .1
2 225 121 232 133 -7 -12 219 116 266 173 -13 -17 0 0 46 32 158 185 0 0 0 0 -19 -30 null null null .914 .862 3.593 80 376 .924 .74 110 1110 7600 66 77 85 96 -100 112 124 -11 null 108 -16 null null null null
3 10035 10165 237 131 9798 10034 10523 10895 296 222 10286 10764 0 0 4568 5315 306 491 96 90 92 88 19832 21050 .976 1.024 1.046 .844 .998 2.157 80 239 1.081 .92 110 1270 7640 70 81 101 112 0 9446 122 9325 .952 10125 10003 1.051 .972 -.071 -.04
4 376 239 231 132 145 107 233 132 260 191 2 0 0 0 379 371 248 423 15 7 11 5 252 2 1.355 .738 null .528 .55 3.164 80 325 1.536 .77 110 1380 7610 67 78 112 123 -100 222 123 99 .686 123 0 1.458 null -.544 null
5 1969 3161 232 127 1737 3034 1983 3257 253 162 1751 3130 0 0 284 514 121 199 100 100 100 100 4771 4881 .573 1.747 1.788 1.74 1.72 1.255 52 242 1.83 .95 90 1540 7630 70 79 129 138 0 2938 118 2820 1.623 3027 2909 .616 1.661 .699 .732
6 957 900 228 129 729 771 1069 934 231 129 841 805 0 0 335 327 44 34 100 100 91 100 1500 1646 .946 1.058 .957 1.15 .969 2.689 12 50 1.341 .65 40 1670 7650 75 79 145 149 0 836 120 716 .983 868 748 1.017 .89 -.025 -.169
7 3265 3517 222 128 3043 3389 3396 3828 283 216 3174 3700 0 0 925 1394 337 453 100 88 98 88 6432 6874 .898 1.114 1.166 .934 1.143 2.022 52 250 1.161 .93 90 1810 7620 69 78 156 165 0 3268 119 3149 1.035 3557 3438 .966 1.083 .05 .115
8 3514 3784 245 136 3269 3648 3711 4433 558 500 3466 4297 0 0 1279 1610 976 1165 90 86 84 82 6917 7763 .896 1.116 1.24 .996 1.14 1.625 52 200 1.139 .93 90 1950 7620 69 78 170 179 0 3516 126 3390 1.037 4120 3993 .964 1.152 .052 .204
9 1990 1145 244 133 1746 1012 1789 1009 494 416 1545 876 0 0 1146 654 942 1101 76 32 38 9 2758 2421 1.725 .58 .567 .645 .671 3.339 52 192 .799 .8 80 2080 7620 70 78 184 192 0 1064 124 940 .539 938 814 1.857 .527 -.893 -.924
10 1279 1337 234 138 1045 1199 1253 1390 238 144 1019 1252 0 0 473 458 46 42 100 100 100 100 2244 2271 .872 1.147 1.229 1.15 1.242 1.544 52 234 1.088 .9 90 2220 7610 68 77 197 206 0 1242 128 1114 1.066 1292 1163 .938 1.142 .093 .191
11 1021 1078 232 135 789 943 1046 1113 236 147 814 978 0 0 262 287 51 53 100 100 100 100 1732 1792 .837 1.195 1.201 1.201 1.23 1.313 52 213 1.161 .9 90 2350 7610 68 77 210 219 0 1002 125 876 1.111 1034 909 .9 1.117 .151 .159
12 774 679 224 129 550 550 773 700 226 136 549 571 0 0 162 193 52 46 100 100 100 98 1100 1120 1 1 1.04 .963 .984 1.498 52 231 1.018 .88 90 2470 7610 68 77 222 231 0 631 120 511 .929 651 531 1.076 .967 -.106 -.049
13 985 936 220 131 765 805 1015 975 222 136 795 844 0 0 241 250 48 39 100 100 100 100 1570 1639 .95 1.052 1.062 1.044 1.059 1.398 52 210 1.007 .91 90 2610 7620 69 78 236 245 0 870 122 748 .978 906 784 1.023 .987 -.032 -.019
14 1097 1211 218 119 879 1092 1116 1264 220 124 898 1145 0 0 274 368 46 39 100 100 100 98 1971 2043 .805 1.242 1.275 1.195 1.273 1.668 80 248 1.282 .91 100 2740 7620 69 79 249 259 0 1125 111 1015 1.154 1175 1064 .866 1.185 .207 .245
15 1391 1411 230 118 1161 1293 1359 1454 231 128 1129 1336 0 0 386 537 48 63 100 100 100 100 2454 2465 .898 1.114 1.183 1.063 1.033 1.438 52 224 1.228 .89 90 2870 7610 68 77 262 271 0 1311 110 1202 1.035 1351 1242 .966 1.1 .05 .137
16 2697 2453 234 136 2463 2317 2971 2929 238 146 2737 2793 0 0 929 1139 51 58 96 92 95 90 4780 5530 1.063 .941 1.02 .787 .939 1.96 80 326 1.04 .92 110 3010 7600 66 77 275 286 0 2280 126 2153 .874 2722 2596 1.144 .948 -.194 -.077
17 1333 1244 224 133 1109 1111 1372 1269 229 139 1148 1136 0 0 463 446 48 43 100 100 100 100 2220 2284 .998 1.002 .99 1.011 .987 1.507 80 248 1.001 .92 100 3130 7610 68 78 288 298 0 1156 124 1032 .931 1179 1056 1.074 .92 -.103 -.121
18 1556 1760 229 136 1327 1624 1656 1841 234 139 1427 1705 0 0 535 625 46 42 100 100 100 100 2951 3132 .817 1.224 1.195 1.236 1.23 1.382 80 265 1.224 .93 100 3270 7620 69 79 302 312 0 1636 126 1509 1.137 1711 1584 .879 1.11 .186 .151
19 1541 1688 235 138 1306 1550 1573 1819 237 144 1338 1681 0 0 354 492 43 44 100 100 100 100 2856 3019 .843 1.187 1.256 1.142 1.217 1.562 52 234 1.23 .91 90 3410 7610 68 77 316 325 0 1569 128 1440 1.103 1690 1562 .907 1.168 .141 .223
20 2466 2919 230 145 2236 2774 2692 3051 236 151 2462 2906 0 0 1006 1035 49 43 100 100 100 100 5010 5368 .806 1.241 1.18 1.296 1.245 1.57 80 239 1.194 .93 100 3540 7620 69 79 329 339 0 2713 135 2578 1.153 2835 2701 .867 1.097 .205 .133

Total number of rows: 44160

Table truncated, full table size 9837 Kbytes.




Supplementary data files not provided
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