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Sample GSM79634 Query DataSets for GSM79634
Status Public on Oct 22, 2005
Title "0 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 "0 hr Hela Double Thymidine, exp3"
Organism Homo sapiens
Characteristics "0 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/2001-01/13121.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 1224 1549 224 97 1000 1452 1282 1619 228 99 1058 1522 0 0 219 341 42 23 100 100 100 100 2452 2580 .689 1.452 1.439 1.442 1.473 1.246 80 402 1.471 .97 110 1390 8090 131 142 77 88 0 1260 79 1181 1.181 1316 1238 .847 1.17 .24 .226
2 901 980 223 98 678 882 885 1029 227 100 662 931 0 0 365 460 39 23 100 100 96 100 1560 1593 .769 1.301 1.406 1.297 1.246 1.678 32 101 1.313 .95 60 1510 8100 135 141 92 98 0 797 80 717 1.058 837 757 .945 1.144 .081 .194
3 6976 9648 211 90 6765 9558 7236 10253 218 99 7025 10163 0 0 2343 3370 50 56 100 100 100 100 16323 17188 .708 1.413 1.447 1.379 1.428 1.316 80 253 1.428 .98 100 1660 8080 131 141 105 115 0 7845 73 7772 1.149 8337 8264 .87 1.176 .2 .234
4 506 469 205 90 301 379 245 120 214 101 40 30 0 0 546 776 68 77 37 26 25 22 680 70 .794 1.259 .75 .714 .887 3.551 80 276 1.424 .96 100 1780 8060 129 139 117 127 -100 381 73 308 1.024 98 24 .977 .61 .034 -.713
5 1415 2726 204 85 1211 2641 1470 2966 207 93 1266 2881 0 0 283 851 60 65 100 100 100 98 3852 4147 .459 2.181 2.276 2.001 2.23 1.513 80 279 2.353 .96 100 1940 8080 131 141 133 143 0 2217 69 2148 1.773 2412 2343 .564 1.85 .826 .888
6 1566 2202 212 84 1354 2118 1739 2420 210 86 1527 2336 0 0 681 1048 38 25 93 100 93 100 3472 3863 .639 1.564 1.53 1.542 1.545 1.573 32 128 1.59 .95 70 2060 8100 134 141 146 153 0 1791 68 1722 1.272 1968 1900 .786 1.244 .347 .315
7 2507 3424 209 82 2298 3342 2622 3744 211 89 2413 3662 0 0 741 1154 51 51 98 100 98 97 5640 6075 .688 1.454 1.518 1.435 1.455 1.295 80 287 1.489 .98 100 2210 8080 131 141 160 170 0 2784 67 2718 1.183 3044 2978 .846 1.234 .242 .303
8 2130 2698 219 91 1911 2607 2235 2943 226 104 2016 2852 0 0 679 1007 69 78 100 100 97 98 4518 4868 .733 1.364 1.415 1.33 1.377 1.263 80 231 1.402 .98 100 2350 8080 131 141 174 184 0 2194 74 2120 1.109 2393 2319 .901 1.15 .15 .202
9 1497 1150 218 90 1279 1060 1323 1068 228 100 1105 978 0 0 610 515 64 68 100 100 100 100 2339 2083 1.207 .829 .885 .816 .818 1.535 52 174 .821 .94 80 2490 8070 131 139 189 197 0 935 73 862 .674 868 795 1.484 .72 -.569 -.475
10 928 997 229 94 699 903 923 982 232 97 694 888 0 0 183 199 40 24 100 100 100 100 1602 1582 .774 1.292 1.28 1.305 1.326 1.246 52 225 1.29 .95 90 2620 8060 129 138 201 210 0 811 76 734 1.05 799 722 .952 1.04 .071 .057
11 825 946 225 87 600 859 827 961 228 89 602 874 0 0 132 158 43 23 100 100 100 100 1459 1476 .698 1.432 1.452 1.442 1.398 1.24 52 229 1.413 .94 90 2750 8060 129 138 214 223 0 769 71 698 1.164 781 711 .859 1.181 .219 .239
12 1013 1207 217 83 796 1124 1057 1235 223 85 840 1152 0 0 310 443 44 24 100 100 100 100 1920 1992 .708 1.412 1.371 1.419 1.417 1.281 80 264 1.424 .97 100 2880 8060 129 139 227 237 0 981 67 914 1.148 1004 937 .871 1.115 .199 .157
13 818 785 219 85 599 700 838 810 221 88 619 725 0 0 208 260 45 24 98 100 98 100 1299 1344 .856 1.169 1.171 1.175 1.198 1.414 80 248 1.191 .94 100 3020 8060 129 139 241 251 0 638 69 569 .95 659 590 1.052 .952 -.074 -.07
14 1043 1242 225 85 818 1157 1081 1227 226 88 856 1142 0 0 228 271 42 23 100 100 100 100 1975 1998 .707 1.414 1.334 1.444 1.406 1.224 80 266 1.39 .96 110 3160 8070 129 140 254 265 0 1010 69 941 1.15 998 929 .869 1.085 .202 .117
15 1104 1163 225 87 879 1076 1136 1168 226 91 911 1081 0 0 265 296 40 24 100 100 100 100 1955 1992 .817 1.224 1.187 1.244 1.261 1.228 52 224 1.195 .96 90 3300 8050 128 137 269 278 0 946 71 875 .995 950 879 1.005 .965 -.007 -.052
16 2061 2683 227 88 1834 2595 2168 2820 227 92 1941 2732 0 0 380 538 38 22 100 100 100 100 4429 4673 .707 1.415 1.408 1.417 1.411 1.229 80 288 1.437 .97 110 3440 8060 128 139 282 293 0 2182 72 2110 1.151 2293 2222 .869 1.145 .202 .195
17 959 945 218 87 741 858 1010 1015 223 89 792 928 0 0 261 302 39 21 100 100 100 100 1599 1720 .864 1.158 1.172 1.146 1.148 1.324 80 246 1.157 .96 100 3570 8050 128 138 296 306 0 768 71 698 .942 825 755 1.062 .953 -.087 -.07
18 985 1153 230 89 755 1064 995 1176 232 92 765 1087 0 0 169 220 42 22 100 100 100 100 1819 1852 .71 1.409 1.421 1.418 1.398 1.271 80 264 1.418 .95 110 3710 8060 128 139 309 320 0 938 72 865 1.146 956 884 .873 1.155 .197 .208
19 801 814 231 88 570 726 791 844 235 91 560 756 0 0 171 214 43 23 100 100 100 100 1296 1316 .785 1.274 1.35 1.267 1.269 1.398 80 248 1.289 .94 100 3850 8050 128 138 324 334 0 662 72 590 1.036 686 615 .966 1.098 .051 .135
20 1981 3571 219 92 1762 3479 2038 3740 221 93 1819 3648 0 0 475 838 38 23 100 100 100 100 5241 5467 .506 1.974 2.005 1.992 1.944 1.165 80 243 1.965 .98 100 3970 8060 129 139 336 346 0 2904 75 2829 1.606 3041 2966 .623 1.631 .683 .706

Total number of rows: 44160

Table truncated, full table size 9880 Kbytes.




Supplementary data files not provided
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