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Sample GSM79691 Query DataSets for GSM79691
Status Public on Oct 22, 2005
Title "0h Thy-Noc, Exp4"
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 "0h Thy-Noc, Exp4"
Organism Homo sapiens
Characteristics "0h Thy-Noc, Exp4"
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Cell-cycle, thymidine-nocodazole
Image: http://smd.stanford.edu/MicroArray/gifs/2001-03/14340.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 2479 3261 85 172 2394 3089 2619 3482 114 217 2534 3310 0 0 1144 1109 165 275 100 100 96 100 5483 5844 .775 1.29 1.306 1.415 1.297 1.491 52 213 1.182 .95 80 1240 8060 86 94 68 76 0 3315 175 3140 1.312 3540 3365 .762 1.328 .392 .409
2 262 408 81 159 181 249 112 221 103 193 31 62 0 0 304 476 141 238 36 28 20 16 430 93 .727 1.376 2 2.167 1.548 3.396 80 296 1.568 .92 110 1410 8050 83 94 83 94 0 415 162 253 1.399 225 63 .715 2.033 .484 1.024
3 5485 5289 75 152 5410 5137 5858 5500 222 254 5783 5348 0 0 1749 1228 712 585 96 100 94 100 10547 11131 1.053 .95 .925 1.007 .961 1.393 52 177 .885 .96 90 1520 8050 84 93 95 104 0 5377 155 5223 .965 5592 5437 1.036 .94 -.051 -.089
4 679 910 81 152 598 758 787 974 261 257 706 822 0 0 282 332 702 501 50 81 0 15 1356 1528 .789 1.268 1.164 1.449 1.25 1.692 32 95 1.103 .91 60 1660 8070 88 94 111 117 0 925 155 771 1.289 990 836 .776 1.184 .366 .243
5 1583 2979 82 157 1501 2822 1690 3198 127 223 1608 3041 0 0 784 1096 176 255 92 100 86 96 4323 4649 .532 1.88 1.891 2.168 1.942 1.658 52 217 1.733 .93 90 1790 8050 84 93 122 131 0 3029 160 2869 1.911 3251 3092 .523 1.923 .935 .943
6 349 605 79 145 270 460 110 245 113 194 31 100 0 0 415 666 154 227 36 36 30 31 730 131 .587 1.704 3.226 2.073 2.131 3.126 80 287 1.695 .86 110 1950 8050 83 94 137 148 -100 615 147 468 1.732 249 102 .577 3.279 .792 1.713
7 1921 2677 79 142 1842 2535 1726 2582 80 149 1647 2440 0 0 955 1258 14 62 100 100 100 98 4377 4087 .727 1.376 1.481 1.411 1.427 1.568 80 236 1.371 .94 110 2080 8050 83 94 150 161 0 2722 144 2577 1.399 2625 2481 .715 1.506 .485 .591
8 1265 1493 78 159 1187 1334 1265 1286 79 163 1187 1127 0 0 624 944 16 66 97 97 95 93 2521 2314 .89 1.124 .949 1.106 1.13 1.818 80 228 1.323 .92 100 2200 8050 84 94 163 173 0 1518 162 1356 1.143 1307 1146 .875 .965 .192 -.051
9 824 624 80 168 744 456 802 501 82 191 722 333 0 0 486 423 27 154 96 71 90 59 1200 1055 1.632 .613 .461 .429 .59 3.418 32 123 .67 .77 60 2350 8010 82 88 180 186 0 634 171 464 .623 509 339 1.605 .469 -.682 -1.093
10 592 1109 75 157 517 952 449 931 78 169 374 774 0 0 392 682 21 112 98 93 97 91 1469 1148 .543 1.841 2.07 1.79 1.823 1.633 80 288 1.862 .93 100 2470 8010 80 90 190 200 0 1127 160 968 1.872 946 787 .534 2.104 .905 1.073
11 302 504 75 148 227 356 303 459 82 156 228 311 0 0 138 282 38 63 87 81 81 72 583 539 .638 1.568 1.364 1.403 1.537 2.123 80 252 1.886 .89 100 2610 8030 82 92 204 214 0 512 150 362 1.594 467 316 .627 1.387 .673 .472
12 589 813 73 140 516 673 610 776 75 143 537 636 0 0 242 424 18 60 100 97 98 92 1189 1173 .767 1.304 1.184 1.172 1.23 1.724 80 272 1.484 .91 100 2740 8010 80 90 217 227 0 827 142 684 1.326 789 647 .754 1.204 .407 .268
13 392 576 77 141 315 435 398 565 79 146 321 424 0 0 122 207 22 58 100 96 100 94 750 745 .724 1.381 1.321 1.299 1.395 1.69 52 213 1.507 .85 90 2870 8030 82 91 230 239 0 586 143 442 1.404 574 431 .712 1.343 .489 .425
14 578 1013 75 157 503 856 520 878 76 162 445 721 0 0 208 475 14 63 100 100 100 100 1359 1166 .588 1.702 1.62 1.591 1.643 1.444 80 286 1.929 .93 100 3010 8010 80 90 244 254 0 1030 160 870 1.73 893 733 .578 1.647 .791 .72
15 604 667 76 154 528 513 498 538 77 157 422 384 0 0 442 478 15 63 88 81 87 73 1041 806 1.029 .972 .91 .948 .989 1.878 80 291 1.041 .91 110 3160 8010 79 90 258 269 0 678 157 522 .988 547 390 1.012 .925 -.018 -.112
16 1060 1169 74 147 986 1022 1136 1156 75 150 1062 1009 0 0 255 361 15 62 100 100 100 97 2008 2071 .965 1.037 .95 1.016 1.022 1.35 80 277 1.071 .93 110 3280 8010 79 90 270 281 0 1188 149 1039 1.054 1175 1026 .949 .966 .076 -.05
17 428 482 73 152 355 330 437 465 76 160 364 313 0 0 125 163 24 64 100 98 100 90 685 677 1.076 .93 .86 .871 .893 1.615 52 233 1.06 .8 90 3400 8000 79 88 283 292 0 490 155 335 .945 473 318 1.058 .874 -.082 -.194
18 418 419 71 160 347 259 427 397 74 163 356 237 0 0 100 150 23 68 100 95 98 78 606 593 1.34 .746 .666 .662 .703 1.948 80 266 .898 .73 100 3540 8020 81 91 297 307 0 426 163 263 .759 404 241 1.318 .677 -.398 -.563
19 492 702 71 163 421 539 492 659 73 162 421 496 0 0 158 281 21 75 100 100 100 96 960 917 .781 1.28 1.178 1.191 1.161 1.767 52 188 1.488 .82 90 3680 8020 81 90 311 320 0 714 166 548 1.302 670 504 .768 1.198 .38 .26
20 632 685 70 148 562 537 640 668 73 156 570 520 0 0 285 290 21 68 98 96 97 92 1099 1090 1.047 .956 .912 .946 .958 1.575 80 268 .99 .92 100 3790 8020 81 91 322 332 0 696 150 546 .971 679 529 1.029 .927 -.042 -.109

Total number of rows: 44160

Table truncated, full table size 9502 Kbytes.




Supplementary data files not provided
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