NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM79660 Query DataSets for GSM79660
Status Public on Oct 22, 2005
Title "18 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 "18 hr Hela Double Thymidine, exp3"
Organism Homo sapiens
Characteristics "18 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/2001-01/13138.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
1 831 957 145 64 686 893 857 987 150 69 712 923 0 0 240 280 52 43 97 100 96 100 1579 1635 .768 1.302 1.296 1.808 1.254 2.404 80 316 1.153 .91 110 1470 8300 72 83 85 96 0 865 58 807 1.177 892 834 .85 1.172 .235 .229
2 248 185 142 64 106 121 151 68 150 72 9 4 0 0 219 287 59 54 26 20 21 17 227 13 .876 1.142 .444 1.286 .83 1.831 80 271 1.022 .85 100 1580 8270 70 80 97 107 -100 167 58 109 1.032 61 4 .969 .402 .045 -1.316
3 3194 3987 141 68 3053 3919 3309 4253 165 89 3168 4185 0 0 636 1055 123 110 100 100 100 100 6972 7353 .779 1.284 1.321 1.305 1.322 .333 80 235 1.268 .95 110 1740 8300 72 83 112 123 0 3604 61 3543 1.16 3845 3783 .862 1.194 .215 .256
4 198 107 148 71 50 36 160 70 185 105 12 -1 0 0 134 146 158 151 7 5 3 5 86 11 1.389 .72 null 1.561 .735 2.667 80 259 1.01 .93 100 1850 8270 70 80 124 134 -100 97 64 33 .651 63 -1 1.536 null -.62 null
5 803 952 158 73 645 879 1004 1263 205 131 846 1190 0 0 450 705 175 216 70 63 70 62 1524 2036 .734 1.363 1.407 1.417 1.405 1.188 80 333 1.338 .94 100 2000 8270 70 80 139 149 -100 861 66 795 1.232 1142 1076 .812 1.272 .301 .347
6 713 782 164 78 549 704 695 766 161 84 531 688 0 0 149 393 31 34 100 100 100 100 1253 1219 .78 1.282 1.296 1.305 1.127 .733 12 67 .985 .74 50 2160 8290 74 79 157 162 0 707 71 636 1.159 692 622 .863 1.171 .213 .228
7 1241 1399 155 72 1086 1327 1367 1476 210 135 1212 1404 0 0 927 1251 310 381 63 57 57 53 2413 2616 .818 1.222 1.158 1.202 1.168 1.034 80 255 1.192 .95 100 2260 8270 70 80 165 175 -100 1265 65 1200 1.105 1334 1269 .905 1.047 .144 .067
8 1041 1221 160 67 881 1154 421 109 293 255 261 42 0 0 961 1394 482 703 47 42 42 38 2035 303 .763 1.31 .161 1.059 1.278 .611 80 216 1.361 .95 100 2400 8260 69 79 179 189 -100 1104 61 1043 1.184 99 38 .844 .145 .244 -2.781
9 627 476 157 76 470 400 528 290 214 167 371 214 0 0 518 492 321 519 53 27 25 16 870 585 1.175 .851 .577 1.011 .894 .899 80 274 1.167 .9 100 2530 8260 69 79 192 202 0 430 69 362 .769 262 193 1.3 .521 -.378 -.939
10 849 860 156 72 693 788 860 921 158 73 704 849 0 0 160 295 35 24 100 98 100 97 1481 1553 .879 1.137 1.206 1.137 1.158 .35 80 346 1.122 .93 110 2690 8260 68 79 207 218 0 777 65 712 1.028 833 768 .973 1.09 .04 .125
11 633 569 158 66 475 503 626 582 158 69 468 516 0 0 125 155 36 27 100 100 100 100 978 984 .944 1.059 1.103 1.109 1.068 .384 52 232 .956 .87 90 2820 8270 70 79 221 230 0 514 60 455 .957 526 466 1.045 .997 -.063 -.005
12 600 509 161 74 439 435 576 512 162 75 415 438 0 0 121 150 33 26 100 100 100 100 874 853 1.009 .991 1.055 1.033 .975 .371 52 248 .903 .87 90 2950 8260 69 78 234 243 0 460 67 393 .896 463 396 1.116 .954 -.159 -.068
13 515 424 158 66 357 358 528 429 160 70 370 363 0 0 142 200 34 22 100 96 98 92 715 733 .997 1.003 .981 1.026 1.033 .54 80 273 .939 .87 100 3100 8260 69 79 249 259 0 383 60 324 .907 388 328 1.103 .887 -.142 -.173
14 675 732 159 67 516 665 701 746 162 71 542 679 0 0 160 207 34 24 100 100 100 98 1181 1221 .776 1.289 1.253 1.384 1.303 .601 80 271 1.156 .91 110 3230 8270 69 80 261 272 0 662 61 601 1.165 674 614 .858 1.133 .22 .18
15 908 933 163 75 745 858 864 846 164 79 701 771 0 0 294 392 35 27 100 100 100 100 1603 1472 .868 1.152 1.1 1.185 1.175 .395 52 228 1.105 .93 90 3370 8260 69 78 276 285 0 843 68 776 1.041 765 697 .96 .994 .058 -.008
16 1346 1503 162 70 1184 1433 1351 1524 163 73 1189 1454 0 0 284 361 36 24 100 100 100 100 2617 2643 .826 1.21 1.223 1.25 1.225 .316 80 297 1.125 .92 100 3510 8250 68 78 290 300 0 1359 63 1295 1.094 1378 1314 .914 1.106 .13 .145
17 719 724 165 68 554 656 751 767 166 70 586 699 0 0 203 253 34 22 100 100 100 100 1210 1285 .845 1.184 1.193 1.263 1.182 .512 80 250 1.084 .92 100 3650 8260 69 79 304 314 0 655 61 593 1.07 693 632 .934 1.078 .098 .109
18 1045 1205 168 69 877 1136 1075 1242 171 73 907 1173 0 0 188 275 36 22 100 100 100 100 2013 2080 .772 1.295 1.293 1.341 1.263 .401 80 245 1.203 .92 100 3780 8260 69 79 317 327 0 1089 62 1027 1.171 1123 1060 .854 1.169 .228 .225
19 916 959 167 67 749 892 949 982 171 69 782 915 0 0 168 287 36 22 100 100 100 98 1641 1697 .84 1.191 1.17 1.204 1.227 .39 80 292 1.153 .92 110 3920 8260 68 79 330 341 0 867 61 806 1.077 888 827 .929 1.058 .107 .081
20 1075 1439 167 69 908 1370 1109 1440 166 69 942 1371 0 0 286 431 33 21 100 100 100 100 2278 2313 .663 1.509 1.455 1.587 1.544 .487 80 222 1.399 .93 100 4050 8270 70 80 344 354 0 1301 62 1239 1.364 1302 1239 .733 1.316 .448 .396

Total number of rows: 44160

Table truncated, full table size 9659 Kbytes.




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