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Sample GSM79641 Query DataSets for GSM79641
Status Public on Oct 22, 2005
Title "8 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 "8 hr Hela Double Thymidine, exp3"
Organism Homo sapiens
Characteristics "8 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/2001-01/13129.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 1048 1416 144 80 904 1336 1063 1491 145 81 919 1411 0 0 281 520 29 22 100 100 100 100 2240 2330 .677 1.478 1.535 1.421 1.507 1.327 80 414 1.578 .95 110 1560 8420 84 95 94 105 0 1323 75 1248 1.38 1393 1318 .724 1.434 .465 .52
2 678 973 159 90 519 883 788 943 157 91 629 853 0 0 284 437 29 22 100 100 100 100 1402 1482 .588 1.701 1.356 1.836 1.507 1.781 12 61 1.547 .84 50 1670 8430 88 93 108 113 0 909 84 825 1.589 881 797 .629 1.267 .668 .341
3 3486 4974 141 73 3345 4901 3561 5325 144 78 3420 5252 0 0 1028 1464 30 25 100 100 100 100 8246 8672 .683 1.465 1.536 1.478 1.495 1.226 80 295 1.474 .96 100 1820 8420 85 95 121 131 0 4646 68 4578 1.369 4974 4906 .731 1.434 .453 .52
4 991 1298 147 73 844 1225 949 1193 149 77 802 1120 0 0 445 693 31 27 100 100 100 100 2069 1922 .689 1.451 1.397 1.421 1.556 1.833 32 98 1.516 .93 60 1950 8430 88 94 136 142 0 1212 68 1144 1.356 1114 1046 .738 1.304 .439 .383
5 1016 1800 149 72 867 1728 1037 1916 148 77 888 1844 0 0 267 604 31 28 98 97 98 97 2595 2732 .502 1.993 2.077 1.831 2.087 1.729 80 296 2.069 .96 100 2090 8410 84 94 148 158 0 1681 67 1614 1.862 1790 1722 .537 1.94 .897 .956
6 838 1156 149 69 689 1087 866 1192 149 71 717 1123 0 0 370 473 32 21 93 100 90 100 1776 1840 .634 1.578 1.566 1.807 1.598 1.961 32 105 1.54 .91 60 2220 8430 88 94 163 169 0 1080 64 1015 1.474 1113 1049 .679 1.463 .559 .549
7 1477 2051 145 72 1332 1979 1502 2039 153 82 1357 1967 0 0 619 1026 68 68 95 92 92 91 3311 3324 .673 1.486 1.45 1.326 1.493 1.702 80 280 1.512 .96 100 2360 8410 84 94 175 185 0 1916 67 1849 1.388 1905 1837 .721 1.354 .473 .437
8 1274 1698 152 73 1122 1625 1270 1728 160 87 1118 1655 0 0 368 653 72 76 98 97 98 97 2747 2773 .69 1.448 1.48 1.328 1.477 1.82 80 262 1.536 .93 100 2500 8410 84 94 189 199 0 1586 68 1518 1.353 1614 1546 .739 1.383 .436 .468
9 1139 743 145 71 994 672 1064 699 148 74 919 628 0 0 550 474 34 27 100 96 100 88 1666 1547 1.479 .676 .683 .513 .634 2.255 52 222 .725 .94 90 2650 8390 82 91 204 213 0 694 66 628 .631 653 587 1.584 .638 -.663 -.648
10 579 666 145 76 434 590 581 640 146 77 436 564 0 0 142 191 30 22 100 100 100 100 1024 1000 .736 1.359 1.294 1.369 1.369 1.274 80 281 1.356 .94 110 2770 8400 82 93 215 226 0 622 71 551 1.27 598 527 .788 1.208 .345 .273
11 493 513 147 74 346 439 517 539 149 76 370 465 0 0 134 188 30 22 100 98 100 98 785 835 .788 1.269 1.257 1.186 1.252 1.763 80 270 1.329 .93 100 2900 8400 83 93 229 239 0 479 69 410 1.185 503 434 .844 1.174 .245 .231
12 576 537 139 72 437 465 562 544 144 73 423 472 0 0 135 192 29 19 100 100 100 100 902 895 .94 1.064 1.116 1.015 1.036 1.421 52 235 1.142 .92 90 3040 8390 82 91 243 252 0 502 67 434 .994 508 441 1.006 1.042 -.009 .06
13 484 437 147 74 337 363 490 446 147 76 343 372 0 0 118 165 29 22 98 98 98 96 700 715 .928 1.077 1.085 .997 1.084 1.618 80 270 1.157 .91 100 3180 8390 82 92 257 267 0 408 69 339 1.006 417 347 .994 1.013 .009 .019
14 642 823 154 75 488 748 644 804 155 77 490 729 0 0 132 182 29 22 100 100 100 100 1236 1219 .652 1.533 1.488 1.548 1.545 1.318 80 219 1.541 .92 100 3320 8400 83 93 271 281 0 769 70 699 1.432 751 681 .698 1.39 .518 .475
15 662 716 158 79 504 637 600 648 159 82 442 569 0 0 240 328 31 24 100 100 98 98 1141 1011 .791 1.264 1.287 1.205 1.3 1.398 80 236 1.3 .96 100 3450 8390 82 92 284 294 0 669 74 595 1.181 605 531 .847 1.202 .239 .266
16 1300 1587 159 80 1141 1507 1286 1606 160 84 1127 1526 0 0 196 331 31 24 100 100 100 100 2648 2653 .757 1.321 1.354 1.302 1.311 1.206 80 276 1.345 .97 110 3590 8390 81 92 297 308 0 1482 75 1408 1.234 1500 1425 .811 1.265 .303 .339
17 806 921 153 75 653 846 668 730 157 77 515 655 0 0 654 990 31 21 100 100 100 98 1499 1170 .772 1.296 1.272 1.14 1.251 1.757 80 237 1.458 .96 100 3720 8390 82 92 311 321 0 860 70 790 1.21 682 612 .826 1.188 .275 .249
18 830 1075 157 79 673 996 882 1059 159 81 725 980 0 0 244 308 31 23 100 100 100 100 1669 1705 .676 1.48 1.352 1.554 1.481 1.399 80 270 1.474 .95 110 3850 8400 82 93 323 334 0 1004 74 930 1.382 989 915 .723 1.263 .467 .336
19 657 780 156 84 501 696 637 744 159 86 481 660 0 0 170 277 32 23 100 100 98 100 1197 1141 .72 1.389 1.372 1.355 1.354 1.335 80 248 1.456 .94 100 4000 8390 82 92 339 349 0 729 78 650 1.298 695 616 .771 1.282 .376 .358
20 1111 1315 149 82 962 1233 1095 1324 152 84 946 1242 0 0 258 461 30 22 100 100 100 100 2195 2188 .78 1.282 1.313 1.202 1.309 1.503 80 257 1.36 .95 110 4120 8390 81 92 350 361 0 1228 77 1152 1.197 1237 1160 .835 1.226 .26 .294

Total number of rows: 44160

Table truncated, full table size 9627 Kbytes.




Supplementary data files not provided
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