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Sample GSM79703 Query DataSets for GSM79703
Status Public on Oct 22, 2005
Title "18h 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 "18h Thy-Noc, Exp4"
Organism Homo sapiens
Characteristics "18h Thy-Noc, Exp4"
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Cell-cycle, thymidine-nocodazole
Image: http://smd.stanford.edu/MicroArray/gifs/2001-03/14349.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 2269 2285 158 74 2111 2211 2287 2309 174 91 2129 2235 0 0 298 261 123 109 100 100 100 100 4322 4364 .955 1.047 1.05 1.05 1.055 1.149 52 223 1.024 .96 80 1240 7800 68 76 68 76 0 2057 67 1991 .943 2079 2012 1.06 .945 -.085 -.081
2 1226 1320 145 73 1081 1247 1230 1327 148 77 1085 1254 0 0 630 646 28 19 100 100 100 100 2328 2339 .867 1.154 1.156 1.18 1.226 1.303 32 99 1.083 .96 60 1390 7800 69 75 84 90 0 1188 66 1123 1.039 1195 1129 .963 1.041 .055 .057
3 12541 17677 154 74 12387 17603 13018 19046 276 173 12864 18972 0 0 2339 3407 894 772 100 100 100 100 29990 31836 .704 1.421 1.475 1.422 1.399 1.17 52 185 1.392 .98 90 1510 7790 66 75 94 103 0 15915 67 15848 1.279 17147 17081 .782 1.328 .355 .409
4 1369 1805 161 87 1208 1718 1297 1780 289 190 1136 1693 0 0 1143 1552 903 779 51 57 34 51 2926 2829 .703 1.422 1.49 1.587 1.41 2.079 52 181 1.16 .94 90 1630 7800 67 76 106 115 0 1625 78 1547 1.28 1603 1524 .781 1.342 .357 .424
5 2743 4809 176 100 2567 4709 2871 5120 232 172 2695 5020 0 0 580 920 309 406 100 100 98 100 7276 7715 .545 1.834 1.863 1.849 1.872 1.237 52 235 1.765 .98 90 1790 7790 66 75 122 131 0 4330 90 4240 1.652 4610 4520 .605 1.677 .724 .746
6 2421 3121 183 100 2238 3021 2771 3294 249 192 2588 3194 0 0 1194 1478 269 347 100 100 93 96 5259 5782 .741 1.35 1.234 1.412 1.293 1.403 32 94 1.239 .97 60 1940 7810 70 76 139 145 0 2810 90 2720 1.215 2966 2876 .823 1.111 .281 .152
7 4556 5398 177 103 4379 5295 4706 5591 180 109 4529 5488 0 0 807 978 35 55 100 100 100 100 9674 10017 .827 1.209 1.212 1.21 1.207 1.189 80 242 1.206 .98 100 2070 7790 66 76 150 160 0 4860 93 4767 1.089 5034 4941 .919 1.091 .123 .126
8 3874 4346 176 111 3698 4235 4185 4664 180 115 4009 4553 0 0 1069 1112 40 31 100 100 100 98 7933 8562 .873 1.145 1.136 1.166 1.141 1.397 80 204 1.117 .98 100 2200 7790 66 76 163 173 0 3913 100 3813 1.031 4199 4099 .97 1.022 .044 .032
9 1960 1389 176 116 1784 1273 1563 784 181 129 1387 668 0 0 1874 1507 38 94 92 72 87 63 3057 2055 1.401 .714 .482 .576 .638 2.139 80 251 2.383 .54 100 2340 7770 64 74 177 187 0 1251 104 1146 .642 706 601 1.557 .434 -.638 -1.206
10 2042 2142 179 114 1863 2028 2053 2239 183 127 1874 2125 0 0 774 710 37 111 100 100 98 98 3891 3999 .919 1.089 1.134 1.153 1.106 1.308 80 270 1.043 .97 110 2470 7780 64 75 189 200 0 1928 103 1826 .98 2016 1913 1.02 1.021 -.029 .03
11 2152 2394 179 111 1973 2283 2082 2596 187 118 1903 2485 0 0 863 813 46 44 100 100 100 100 4256 4388 .864 1.157 1.306 1.19 1.196 1.214 52 209 1.11 .97 90 2610 7770 64 73 204 213 0 2155 100 2055 1.042 2337 2237 .96 1.176 .059 .233
12 2884 3191 186 120 2698 3071 3133 3541 190 126 2947 3421 0 0 939 1108 44 42 100 100 100 100 5769 6368 .879 1.138 1.161 1.113 1.157 1.296 80 246 1.15 .98 100 2750 7760 63 73 218 228 0 2873 108 2765 1.025 3188 3080 .976 1.045 .035 .064
13 2122 2315 180 114 1942 2201 2179 2344 184 118 1999 2230 0 0 730 857 33 37 100 100 100 100 4143 4229 .882 1.133 1.116 1.11 1.146 1.344 80 246 1.142 .97 110 2880 7770 63 74 230 241 0 2084 103 1982 1.02 2110 2008 .98 1.004 .029 .006
14 2808 3531 192 112 2616 3419 2781 3689 191 116 2589 3577 0 0 818 786 34 30 100 100 100 100 6035 6166 .765 1.307 1.382 1.336 1.301 1.186 80 252 1.267 .97 100 3020 7770 64 74 245 255 0 3179 101 3078 1.177 3321 3220 .85 1.244 .235 .315
15 3981 4728 202 122 3779 4606 4362 5074 199 129 4160 4952 0 0 1174 1454 40 69 100 100 100 100 8385 9112 .82 1.219 1.19 1.219 1.247 1.14 52 187 1.217 .99 90 3160 7770 64 73 259 268 0 4257 110 4147 1.097 4568 4458 .911 1.072 .134 .1
16 3879 5210 201 135 3678 5075 3924 5473 205 154 3723 5338 0 0 672 867 40 154 100 100 100 100 8753 9061 .725 1.38 1.434 1.382 1.383 1.134 80 230 1.376 .98 100 3280 7760 63 73 271 281 0 4691 122 4569 1.242 4927 4806 .805 1.291 .313 .368
17 2603 2802 193 131 2410 2671 2601 2953 198 148 2408 2822 0 0 1028 1055 38 145 100 100 100 100 5081 5230 .902 1.108 1.172 1.127 1.125 1.249 80 232 1.15 .94 100 3400 7760 63 73 283 293 0 2523 118 2405 .998 2659 2541 1.002 1.055 -.003 .077
18 2445 3115 186 126 2259 2989 2500 3149 190 130 2314 3023 0 0 618 735 42 39 100 100 100 100 5248 5337 .756 1.323 1.306 1.338 1.337 1.152 80 273 1.319 .98 110 3540 7770 63 74 296 307 0 2804 113 2691 1.191 2835 2722 .839 1.176 .252 .234
19 2492 3153 183 120 2309 3033 2529 3251 188 120 2346 3131 0 0 586 565 37 37 100 100 100 100 5342 5477 .761 1.314 1.335 1.333 1.333 1.226 80 194 1.249 .97 100 3680 7790 66 76 311 321 0 2839 108 2731 1.183 2927 2819 .846 1.202 .242 .265
20 3878 5059 173 99 3705 4960 3935 5192 175 102 3762 5093 0 0 713 892 34 27 100 100 100 100 8665 8855 .747 1.339 1.354 1.342 1.352 1.131 80 255 1.335 .99 110 3800 7780 64 75 322 333 0 4555 89 4466 1.205 4674 4585 .83 1.219 .269 .286

Total number of rows: 44160

Table truncated, full table size 9844 Kbytes.




Supplementary data files not provided
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