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Sample GSM79658 Query DataSets for GSM79658
Status Public on Oct 22, 2005
Title "21 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 "21 hr Hela Double Thymidine, exp3"
Organism Homo sapiens
Characteristics "21 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/2001-02/13421.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 2930 3533 372 566 2558 2967 3040 3775 441 636 2668 3209 0 0 493 753 304 398 100 100 100 96 5525 5877 .862 1.16 1.203 1.131 1.163 1.214 32 176 1.233 .95 70 1070 8570 165 172 83 90 0 2943 471 2471 .966 3145 2673 1.035 1.002 -.05 .003
2 2611 2711 344 382 2267 2329 2581 2845 353 372 2237 2463 0 0 831 1232 75 118 100 100 100 100 4596 4700 .973 1.027 1.101 .877 1.08 1.995 12 53 1.197 .84 40 1190 8570 167 171 97 101 0 2258 318 1940 .856 2370 2052 1.169 .917 -.225 -.125
3 18995 20354 338 490 18657 19864 19459 22724 346 481 19121 22234 0 0 4044 6349 129 143 100 100 100 100 38521 41355 .939 1.065 1.163 1.004 1.082 1.357 80 323 1.129 .96 110 1360 8570 163 174 110 121 0 16955 408 16547 .887 18929 18521 1.128 .969 -.173 -.046
4 989 1057 303 388 686 669 448 404 318 384 145 16 0 0 1111 1317 147 170 48 36 36 31 1355 161 1.025 .975 .11 1.598 1.779 5.101 80 253 1.18 .87 110 1490 8570 163 174 123 134 0 880 323 557 .812 337 13 1.231 .092 -.3 -3.444
5 2340 3772 267 150 2073 3622 2292 3817 288 191 2025 3667 0 0 1007 1340 87 105 98 98 97 97 5695 5692 .572 1.747 1.811 1.771 1.654 1.843 80 299 1.701 .92 110 1620 8570 163 174 136 147 0 3142 125 3017 1.455 3180 3055 .687 1.508 .541 .593
6 2387 3643 283 158 2104 3485 1775 3781 283 174 1492 3623 0 0 1141 1514 69 92 100 100 100 100 5589 5115 .604 1.656 2.428 1.691 1.588 1.501 12 81 1.369 .8 50 1760 8580 167 172 153 158 -100 3035 132 2903 1.38 3150 3018 .725 2.023 .464 1.016
7 5162 6777 304 263 4858 6514 5292 7087 482 445 4988 6824 0 0 1090 1372 751 825 100 100 98 100 11372 11812 .746 1.341 1.368 1.349 1.332 1.178 52 213 1.319 .94 80 1890 8560 164 172 165 173 0 5645 219 5426 1.117 5903 5684 .895 1.14 .16 .189
8 4906 6111 327 325 4579 5786 5709 7207 627 660 5382 6882 0 0 2004 2609 1009 1244 88 85 85 82 10365 12264 .791 1.264 1.279 1.194 1.267 1.838 80 250 1.266 .93 100 2030 8560 163 173 178 188 0 5090 271 4820 1.053 6003 5733 .95 1.065 .074 .091
9 3120 2877 303 298 2817 2579 2819 2446 471 484 2516 2148 0 0 1956 2002 798 1069 84 76 73 53 5396 4664 1.092 .916 .854 .826 .865 2.165 52 233 .946 .86 90 2160 8540 161 170 191 200 0 2397 248 2148 .763 2037 1789 1.311 .711 -.391 -.492
10 1646 2138 290 226 1356 1912 1603 2103 298 229 1313 1877 0 0 461 611 70 101 100 100 100 100 3268 3190 .709 1.41 1.43 1.418 1.44 1.232 52 201 1.339 .92 90 2290 8560 163 172 204 213 0 1781 188 1593 1.175 1752 1564 .851 1.191 .232 .252
11 1410 1724 281 182 1129 1542 1331 1739 296 216 1050 1557 0 0 483 715 84 108 100 97 100 97 2671 2607 .732 1.366 1.483 1.243 1.404 2.231 80 290 1.44 .93 100 2430 8540 161 171 218 228 0 1436 152 1284 1.138 1449 1297 .879 1.235 .186 .305
12 1536 1862 283 216 1253 1646 1333 1550 317 243 1050 1334 0 0 744 981 121 128 100 96 100 96 2899 2384 .761 1.314 1.27 1.26 1.503 1.876 32 172 1.345 .88 70 2550 8520 160 167 231 238 0 1551 180 1371 1.094 1291 1111 .914 1.058 .13 .082
13 1241 1438 301 229 940 1209 1223 1396 316 232 922 1167 0 0 389 536 99 113 100 100 100 100 2149 2089 .778 1.286 1.266 1.265 1.337 1.325 52 207 1.345 .91 80 2700 8550 163 171 246 254 0 1198 191 1007 1.071 1163 972 .933 1.054 .099 .076
14 1220 1499 293 234 927 1265 1228 1504 300 237 935 1270 0 0 318 394 63 102 100 100 100 100 2192 2205 .733 1.365 1.358 1.396 1.355 1.473 80 216 1.423 .92 100 2830 8560 163 173 258 268 0 1249 195 1054 1.137 1253 1058 .88 1.131 .185 .178
15 1638 2340 294 251 1344 2089 1339 1931 297 242 1045 1680 0 0 868 1347 62 112 100 100 100 100 3433 2725 .643 1.554 1.608 1.535 1.588 1.392 52 148 1.604 .9 80 2960 8530 161 169 272 280 0 1949 209 1740 1.295 1609 1399 .772 1.339 .373 .421
16 4151 5271 326 310 3825 4961 4542 5378 324 303 4216 5068 0 0 1126 891 60 79 100 100 100 100 8786 9284 .771 1.297 1.202 1.391 1.243 1.563 80 270 1.239 .94 110 3080 8540 160 171 282 293 0 4391 258 4132 1.08 4480 4222 .926 1.001 .112 .002
17 2307 2901 333 316 1974 2585 2291 2855 336 320 1958 2539 0 0 967 1381 57 61 100 100 100 98 4559 4497 .764 1.31 1.297 1.201 1.383 1.829 80 309 1.365 .94 110 3210 8530 159 170 295 306 0 2417 263 2153 1.091 2378 2115 .917 1.08 .125 .111
18 3412 4585 335 331 3077 4254 3535 4862 340 336 3200 4531 0 0 918 1568 58 67 100 100 100 100 7331 7731 .723 1.383 1.416 1.315 1.437 1.509 80 247 1.468 .94 100 3350 8550 162 172 310 320 0 3819 276 3544 1.152 4050 3774 .868 1.179 .204 .238
19 2289 3121 343 346 1946 2775 2353 3086 342 348 2010 2740 0 0 826 1008 57 73 100 100 98 100 4721 4750 .701 1.426 1.363 1.508 1.427 1.501 80 222 1.409 .94 100 3490 8560 163 173 324 334 0 2600 288 2312 1.188 2571 2282 .842 1.136 .248 .183
20 3772 5267 334 318 3438 4949 3853 5353 336 325 3519 5035 0 0 1188 1522 65 72 100 100 100 100 8387 8554 .695 1.439 1.431 1.446 1.444 1.358 80 235 1.424 .95 100 3620 8550 162 172 337 347 0 4387 265 4122 1.199 4459 4194 .834 1.192 .262 .253

Total number of rows: 44160

Table truncated, full table size 10182 Kbytes.




Supplementary data files not provided
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