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Sample GSM79702 Query DataSets for GSM79702
Status Public on Oct 22, 2005
Title "16h 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 "16h Thy-Noc, Exp4"
Organism Homo sapiens
Characteristics "16h Thy-Noc, Exp4"
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Cell-cycle, thymidine-nocodazole
Image: http://smd.stanford.edu/MicroArray/gifs/2001-03/14348.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 2777 3297 232 87 2545 3210 3133 3626 295 149 2901 3539 0 0 1049 943 342 357 90 96 86 96 5755 6440 .793 1.261 1.22 1.399 1.197 1.775 52 278 1.239 .95 90 1240 8050 52 61 67 76 0 3563 94 3469 1.363 3919 3825 .734 1.318 .447 .399
2 2043 2312 246 96 1797 2216 2110 2635 323 155 1864 2539 0 0 906 1099 376 289 90 100 87 90 4013 4403 .811 1.233 1.362 1.269 1.379 2.223 32 83 1.309 .89 60 1390 8070 56 62 84 90 0 2499 104 2395 1.333 2848 2744 .75 1.472 .414 .558
3 15399 20189 228 82 15171 20107 17511 22292 234 89 17283 22210 0 0 5439 6257 88 39 100 100 98 100 35278 39493 .755 1.325 1.285 1.449 1.298 1.605 80 227 1.303 .96 100 1520 8050 52 62 95 105 0 21818 89 21730 1.432 24091 24003 .698 1.389 .518 .474
4 2207 2883 232 84 1975 2799 2152 3463 240 92 1920 3379 0 0 1713 2086 99 43 76 90 69 86 4774 5299 .706 1.417 1.76 1.389 1.333 3.27 52 160 1.331 .95 90 1640 8050 52 61 107 116 0 3116 91 3025 1.532 3742 3652 .653 1.902 .615 .927
5 3225 5502 226 85 2999 5417 3728 6070 237 90 3502 5985 0 0 1290 1621 90 30 93 100 88 100 8416 9487 .554 1.806 1.709 2.347 1.732 2.432 80 270 1.724 .94 100 1800 8040 51 61 123 133 0 5946 92 5854 1.952 6560 6468 .512 1.847 .965 .885
6 2557 2950 239 94 2318 2856 2536 2753 249 95 2297 2659 0 0 1800 2123 110 30 90 100 80 100 5174 4956 .812 1.232 1.158 1.466 1.33 3.273 52 160 1.27 .81 90 1950 8050 52 61 138 147 0 3188 102 3087 1.332 2975 2874 .751 1.251 .413 .323
7 5771 7300 246 95 5525 7205 6329 7871 252 98 6083 7776 0 0 1966 2002 63 31 98 100 97 100 12730 13859 .767 1.304 1.278 1.485 1.294 1.826 80 205 1.273 .93 100 2070 8040 51 61 150 160 0 7889 103 7786 1.409 8506 8404 .71 1.381 .495 .466
8 4461 5287 260 94 4201 5193 5208 6047 297 106 4948 5953 0 0 2048 2157 244 58 88 98 87 98 9394 10901 .809 1.236 1.203 1.417 1.237 2.033 80 195 1.193 .94 100 2190 8040 51 61 162 172 0 5714 102 5612 1.336 6535 6433 .749 1.3 .418 .379
9 2317 1545 245 91 2072 1454 1865 840 270 102 1620 749 0 0 2205 1663 213 52 68 78 62 76 3526 2369 1.425 .702 .462 .688 .667 2.787 80 262 .714 .92 100 2330 8020 49 59 176 186 0 1670 98 1571 .758 908 809 1.319 .5 -.399 -1.001
10 1888 2231 230 97 1658 2134 1847 2188 234 101 1617 2091 0 0 635 737 52 36 100 100 100 100 3792 3708 .777 1.287 1.293 1.318 1.28 1.43 80 242 1.256 .95 100 2470 8030 50 60 190 200 0 2411 105 2306 1.391 2365 2260 .719 1.398 .476 .483
11 1832 2028 221 91 1611 1937 2000 2120 225 92 1779 2029 0 0 516 668 60 28 100 100 100 100 3548 3808 .832 1.202 1.141 1.199 1.155 1.311 52 182 1.214 .92 90 2600 8030 50 59 203 212 0 2192 98 2093 1.299 2291 2193 .77 1.233 .378 .302
12 2590 3106 218 88 2372 3018 2569 3264 221 89 2351 3176 0 0 1040 1494 50 26 100 100 100 100 5390 5527 .786 1.272 1.351 1.178 1.23 1.525 80 247 1.328 .95 100 2730 8020 49 59 216 226 0 3357 95 3262 1.375 3527 3432 .727 1.46 .459 .546
13 1524 1540 223 90 1301 1450 1464 1374 233 93 1241 1284 0 0 538 697 53 25 100 100 100 100 2751 2525 .897 1.115 1.035 1.108 1.074 1.825 80 227 1.183 .9 100 2860 8020 49 59 229 239 0 1664 97 1567 1.204 1485 1388 .83 1.118 .268 .161
14 2395 3362 243 94 2152 3268 2670 3313 254 100 2427 3219 0 0 1094 1340 79 36 95 98 93 98 5420 5646 .659 1.519 1.326 1.769 1.508 1.909 80 274 1.492 .95 110 3000 8020 48 59 242 253 0 3633 102 3532 1.641 3580 3479 .609 1.433 .715 .519
15 2738 3069 249 98 2489 2971 2594 2414 257 106 2345 2316 0 0 1473 1864 86 42 98 100 97 100 5460 4661 .838 1.194 .988 1.237 1.145 1.851 80 200 1.239 .93 100 3150 8030 50 60 258 268 0 3317 106 3211 1.29 2609 2503 .775 1.067 .367 .094
16 4383 5372 254 106 4129 5266 4358 5649 257 108 4104 5543 0 0 662 1153 58 35 100 100 100 100 9395 9647 .784 1.275 1.351 1.252 1.307 1.335 80 252 1.335 .93 110 3260 8020 48 59 268 279 0 5806 115 5691 1.378 6105 5990 .726 1.46 .463 .546
17 1902 2103 257 101 1645 2002 1933 2207 262 104 1676 2106 0 0 596 740 56 32 100 100 98 100 3647 3782 .822 1.217 1.257 1.237 1.156 1.523 80 251 1.245 .92 100 3380 8020 49 59 281 291 0 2273 109 2164 1.315 2385 2276 .76 1.358 .395 .441
18 1950 2316 245 97 1705 2219 2026 2363 252 98 1781 2266 0 0 587 666 50 29 100 100 98 100 3924 4047 .768 1.301 1.272 1.377 1.295 1.742 80 263 1.319 .91 100 3530 8020 49 59 296 306 0 2503 105 2398 1.407 2554 2449 .711 1.375 .492 .459
19 2080 2694 232 91 1848 2603 2152 2767 243 93 1920 2676 0 0 569 787 52 27 100 100 100 100 4451 4596 .71 1.409 1.394 1.406 1.444 1.415 80 179 1.436 .95 100 3660 8050 52 62 309 319 0 2911 98 2813 1.522 2990 2892 .657 1.506 .606 .591
20 4584 5899 248 92 4336 5807 4802 5911 252 95 4554 5819 0 0 1132 1069 53 30 100 100 100 100 10143 10373 .747 1.339 1.278 1.398 1.288 1.439 80 264 1.327 .95 110 3780 8030 49 60 320 331 0 6375 99 6276 1.447 6388 6289 .691 1.381 .533 .466

Total number of rows: 44160

Table truncated, full table size 9806 Kbytes.




Supplementary data files not provided
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