NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM79698 Query DataSets for GSM79698
Status Public on Oct 22, 2005
Title "10h 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 "10h Thy-Noc, Exp4"
Organism Homo sapiens
Characteristics "10h Thy-Noc, Exp4"
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Cell-cycle, thymidine-nocodazole
Image: http://smd.stanford.edu/MicroArray/gifs/2001-03/14345.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 3292 3024 153 74 3139 2950 3573 3062 181 88 3420 2988 0 0 829 672 218 144 100 100 100 100 6089 6408 1.064 .94 .874 .958 .944 1.207 52 266 .902 .97 90 1330 8370 84 93 44 53 0 3398 83 3315 1.056 3440 3357 .947 .982 .079 -.027
2 2109 2320 168 74 1941 2246 2440 2257 185 76 2272 2183 0 0 1263 1284 105 35 90 96 84 96 4187 4455 .864 1.157 .961 1.467 1.146 1.935 32 80 .975 .93 60 1480 8390 88 94 61 67 0 2607 83 2524 1.3 2536 2453 .769 1.08 .379 .11
3 7449 8011 156 74 7293 7937 8290 8889 227 108 8134 8815 0 0 4257 4384 555 291 91 93 90 93 15230 16949 .919 1.088 1.084 1.195 1.095 1.567 80 328 1.051 .97 110 1600 8360 82 93 70 81 0 9001 83 8918 1.223 9988 9904 .818 1.218 .29 .284
4 3487 3809 159 81 3328 3728 3733 4055 338 156 3574 3974 0 0 891 692 874 460 96 100 90 100 7056 7548 .893 1.12 1.112 1.169 1.112 1.443 32 129 1.022 .93 70 1730 8380 86 93 85 92 0 4280 91 4189 1.259 4556 4465 .795 1.249 .332 .321
5 3662 4089 150 71 3512 4018 4015 4428 158 76 3865 4357 0 0 1147 1143 66 36 98 100 98 100 7530 8222 .874 1.144 1.127 1.182 1.123 1.414 80 224 1.116 .97 100 1880 8360 83 93 99 109 0 4594 80 4515 1.285 4975 4895 .778 1.267 .362 .341
6 352 396 145 73 207 323 166 80 258 172 21 7 0 0 761 1030 645 588 5 11 3 7 530 28 .641 1.56 .333 1.017 1 3.992 80 302 1.021 .94 110 1990 8330 79 90 109 120 -100 445 82 363 1.753 90 8 .57 .375 .81 -1.417
7 4622 4437 152 76 4470 4361 5220 4945 301 208 5068 4869 0 0 1852 1466 754 691 90 93 87 91 8831 9937 1.025 .976 .961 1.091 .953 1.788 80 217 .924 .97 100 2150 8360 83 93 126 136 0 4985 85 4900 1.096 5556 5471 .912 1.079 .132 .11
8 4205 4127 152 75 4053 4052 4732 4576 172 82 4580 4501 0 0 1552 1341 149 41 97 100 97 98 8105 9081 1 1 .983 1.062 .975 1.55 80 221 .948 .97 100 2280 8360 83 93 139 149 0 4637 84 4553 1.123 5142 5057 .89 1.104 .168 .143
9 2499 1530 151 80 2348 1450 2068 962 175 87 1917 882 0 0 1635 1239 155 40 96 100 94 100 3798 2799 1.619 .618 .46 .589 .557 2.14 52 200 .658 .92 80 2430 8330 81 89 155 163 0 1719 90 1629 .694 1081 991 1.441 .517 -.527 -.952
10 2079 1979 146 74 1933 1905 2005 1995 149 76 1859 1921 0 0 673 546 31 25 100 100 100 100 3838 3780 1.015 .986 1.033 1.024 .957 1.426 80 282 .957 .96 100 2560 8330 80 90 167 177 0 2224 83 2140 1.107 2242 2158 .903 1.161 .147 .215
11 2061 2069 144 68 1917 2001 2045 2116 147 73 1901 2048 0 0 676 689 33 26 100 100 100 100 3918 3949 .958 1.044 1.077 1.044 1.049 1.247 52 181 1.049 .96 90 2690 8350 82 91 180 189 0 2325 76 2248 1.173 2377 2301 .853 1.21 .23 .276
12 3075 3201 139 69 2936 3132 3042 3171 143 71 2903 3102 0 0 1231 1221 33 24 100 100 100 100 6068 6005 .937 1.067 1.069 1.076 1.049 1.269 80 244 1.054 .97 100 2810 8340 81 91 192 202 0 3597 78 3519 1.199 3563 3485 .834 1.201 .261 .264
13 1591 1492 150 71 1441 1421 1301 1219 151 73 1151 1148 0 0 904 876 34 23 97 100 96 100 2862 2299 1.014 .986 .997 1.092 .949 2.05 80 276 .982 .96 100 2940 8330 80 90 205 215 0 1676 80 1597 1.108 1370 1290 .903 1.121 .148 .164
14 2255 2415 138 67 2117 2348 2232 2446 143 70 2094 2379 0 0 894 825 35 22 100 100 100 100 4465 4473 .902 1.109 1.136 1.157 1.081 1.419 80 340 1.077 .96 110 3100 8330 79 90 220 231 0 2713 75 2638 1.246 2748 2673 .802 1.277 .318 .352
15 3064 2685 130 68 2934 2617 3108 2766 132 73 2978 2698 0 0 1277 1099 29 23 100 100 100 100 5551 5676 1.121 .892 .906 .917 .903 1.386 52 153 .878 .96 80 3230 8340 82 90 235 243 0 3017 76 2940 1.002 3108 3031 .998 1.018 .003 .026
16 2925 2864 128 72 2797 2792 2864 2893 131 74 2736 2821 0 0 767 905 32 24 100 100 100 100 5589 5557 1.002 .998 1.031 .984 .99 1.283 80 234 1.011 .95 100 3350 8340 81 91 246 256 0 3218 81 3137 1.122 3251 3170 .892 1.158 .166 .212
17 1754 1464 128 67 1626 1397 1645 1278 131 68 1517 1211 0 0 853 808 29 23 100 100 100 100 3023 2728 1.164 .859 .798 .823 .833 1.274 80 238 .886 .97 100 3470 8340 81 91 258 268 0 1645 75 1570 .965 1436 1361 1.036 .897 -.051 -.157
18 1707 1620 125 71 1582 1549 1749 1569 128 72 1624 1498 0 0 495 592 29 24 100 100 100 100 3131 3122 1.021 .979 .922 .949 .954 1.456 80 249 1.006 .93 100 3610 8340 81 91 272 282 0 1820 80 1740 1.1 1763 1683 .909 1.036 .138 .052
19 1595 1611 121 71 1474 1540 1582 1611 126 74 1461 1540 0 0 558 544 35 28 98 100 98 100 3014 3001 .957 1.045 1.054 1.055 1.031 1.346 80 218 1.045 .95 100 3750 8360 83 93 286 296 0 1810 80 1730 1.174 1810 1730 .852 1.184 .231 .244
20 2345 2490 124 66 2221 2424 2514 2625 126 69 2390 2559 0 0 731 691 29 25 100 100 98 100 4645 4949 .916 1.091 1.071 1.146 1.094 1.492 80 305 1.062 .95 110 3880 8330 79 90 298 309 0 2798 74 2724 1.226 2949 2875 .815 1.203 .294 .267

Total number of rows: 44160

Table truncated, full table size 9828 Kbytes.




Supplementary data files not provided
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap