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Sample GSM79655 Query DataSets for GSM79655
Status Public on Oct 22, 2005
Title "14 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 "14 hr Hela Double Thymidine, exp3"
Organism Homo sapiens
Characteristics "14 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/2001-01/13135.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 1015 1240 142 74 873 1166 1020 1260 148 83 878 1186 0 0 153 315 37 45 100 100 100 100 2039 2064 .749 1.336 1.351 1.289 1.347 1.355 52 302 1.417 .92 90 1390 8370 80 89 78 87 0 1077 64 1013 1.16 1094 1030 .862 1.173 .214 .23
2 509 537 141 72 368 465 447 467 149 91 306 395 0 0 237 399 42 136 100 71 93 56 833 701 .791 1.264 1.291 .912 1.496 4.253 32 125 2.229 .52 70 1550 8380 82 89 95 102 -100 466 63 404 1.097 406 343 .911 1.121 .134 .165
3 6821 9359 147 78 6674 9281 7185 10155 206 197 7038 10077 0 0 1468 2420 324 745 100 100 100 100 15955 17115 .719 1.391 1.432 1.361 1.39 1.299 52 233 1.411 .93 90 1660 8370 80 89 105 114 0 8128 68 8060 1.208 8819 8751 .828 1.243 .272 .314
4 1146 1399 145 75 1001 1324 967 1292 150 78 822 1217 0 0 717 861 34 21 100 100 96 100 2325 2039 .756 1.323 1.481 1.537 1.395 3.876 32 86 1.487 .62 60 1820 8390 84 90 123 129 -100 1215 65 1150 1.149 1122 1057 .871 1.286 .2 .363
5 1494 2381 150 84 1344 2297 1529 2600 150 87 1379 2516 0 0 376 829 31 45 100 97 100 96 3641 3895 .585 1.709 1.825 1.526 1.795 1.755 80 270 1.952 .93 100 1940 8370 80 90 133 143 0 2068 73 1995 1.484 2258 2185 .674 1.584 .57 .664
6 1638 2106 152 81 1486 2025 1619 1823 153 85 1467 1742 0 0 990 1462 30 50 96 100 96 96 3511 3209 .734 1.363 1.187 1.153 1.372 3.491 32 124 1.644 .69 70 2080 8380 82 89 148 155 -100 1829 70 1759 1.183 1583 1513 .845 1.031 .243 .044
7 2618 3227 154 81 2464 3146 2705 3411 240 176 2551 3330 0 0 561 807 366 406 100 100 100 98 5610 5881 .783 1.277 1.305 1.254 1.291 1.345 52 214 1.306 .93 90 2210 8370 80 89 160 169 0 2802 70 2732 1.109 2962 2892 .902 1.134 .149 .181
8 2385 3713 159 92 2226 3621 2492 3916 337 348 2333 3824 0 0 500 1124 513 784 100 98 96 92 5847 6157 .615 1.627 1.639 1.55 1.651 1.404 52 197 1.715 .89 90 2350 8370 80 89 174 183 0 3225 80 3145 1.413 3401 3321 .708 1.423 .498 .509
9 1060 1015 157 87 903 928 810 744 221 202 653 657 0 0 937 927 316 588 63 55 51 28 1831 1310 .973 1.028 1.006 1.074 1.112 2.926 80 272 1.02 .87 100 2490 8340 77 87 188 198 -100 881 76 806 .892 646 571 1.12 .874 -.164 -.195
10 859 1110 152 80 707 1030 855 1014 155 83 703 934 0 0 267 306 33 25 100 100 98 100 1737 1637 .686 1.457 1.329 1.534 1.377 1.678 80 239 1.436 .89 100 2620 8350 78 88 201 211 0 964 69 895 1.265 881 811 .79 1.154 .339 .206
11 673 862 148 86 525 776 653 857 152 94 505 771 0 0 218 256 37 43 100 100 100 100 1301 1276 .677 1.478 1.527 1.531 1.47 1.323 52 227 1.427 .91 90 2750 8350 78 87 214 223 0 749 75 674 1.284 744 670 .779 1.326 .36 .407
12 791 888 154 82 637 806 772 911 155 88 618 829 0 0 205 266 37 41 100 100 100 100 1443 1447 .79 1.265 1.341 1.26 1.31 1.357 52 260 1.301 .9 90 2890 8340 77 86 228 237 0 771 71 700 1.099 791 720 .91 1.165 .136 .22
13 719 859 154 79 565 780 725 817 153 84 571 738 0 0 200 304 34 34 100 100 100 100 1345 1309 .724 1.381 1.292 1.356 1.383 1.397 52 184 1.376 .91 80 3030 8340 78 86 243 251 0 746 69 677 1.199 710 641 .834 1.122 .262 .167
14 1008 1285 154 84 854 1201 998 1337 164 101 844 1253 0 0 240 328 58 72 100 100 100 100 2055 2097 .711 1.406 1.485 1.407 1.518 1.303 52 217 1.426 .89 90 3160 8350 78 87 255 264 0 1116 73 1043 1.221 1161 1088 .819 1.289 .288 .367
15 1102 1431 157 83 945 1348 1099 1523 167 98 942 1440 0 0 383 495 56 69 100 100 100 100 2293 2382 .701 1.426 1.529 1.467 1.409 1.386 52 236 1.398 .94 90 3300 8340 77 86 269 278 0 1243 72 1171 1.239 1323 1251 .807 1.328 .309 .409
16 1934 2588 158 89 1776 2499 1934 2558 210 149 1776 2469 0 0 395 547 246 271 100 100 100 100 4275 4245 .711 1.407 1.39 1.411 1.406 1.28 52 226 1.401 .9 90 3430 8340 77 86 282 291 0 2248 77 2170 1.222 2221 2144 .818 1.207 .289 .272
17 940 1090 166 90 774 1000 927 1062 209 140 761 972 0 0 214 298 230 253 100 100 91 97 1774 1733 .774 1.292 1.277 1.29 1.28 1.301 80 261 1.309 .87 100 3570 8340 77 87 296 306 0 947 78 868 1.122 922 844 .891 1.109 .166 .15
18 1212 1442 163 80 1049 1362 1255 1482 162 82 1092 1402 0 0 372 489 38 24 100 100 98 100 2411 2494 .77 1.298 1.284 1.287 1.297 1.353 80 254 1.313 .94 100 3700 8340 77 87 309 319 0 1252 69 1183 1.128 1287 1218 .887 1.115 .173 .157
19 908 1147 160 81 748 1066 900 1095 160 83 740 1014 0 0 258 439 37 26 100 100 100 100 1814 1754 .702 1.425 1.37 1.381 1.43 1.449 80 247 1.506 .92 100 3840 8340 77 87 323 333 0 996 70 926 1.238 951 881 .808 1.19 .308 .251
20 1971 3253 165 87 1806 3166 2039 3189 169 89 1874 3102 0 0 736 898 37 26 100 100 98 100 4972 4976 .57 1.753 1.655 1.964 1.745 1.792 80 210 1.682 .94 100 3960 8350 78 88 335 345 0 2825 76 2750 1.522 2769 2694 .657 1.438 .606 .524

Total number of rows: 44160

Table truncated, full table size 9762 Kbytes.




Supplementary data files not provided
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