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Sample GSM79621 Query DataSets for GSM79621
Status Public on Oct 22, 2005
Title "28h 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 "28h Thy-Noc, Exp4"
Organism Homo sapiens
Characteristics "28h Thy-Noc, Exp4"
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Cell-cycle, thymidine-nocodazole
Image: http://smd.stanford.edu/MicroArray/gifs/2001-03/14352.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 2103 2829 186 64 1917 2765 2143 2947 200 95 1957 2883 0 0 382 538 114 185 100 100 100 100 4682 4840 .693 1.442 1.473 1.445 1.47 1.162 52 230 1.472 .97 90 1360 8250 112 121 71 80 0 2427 55 2372 1.237 2528 2473 .808 1.264 .307 .338
2 320 295 182 65 138 230 198 71 227 135 16 6 0 0 396 715 207 333 10 11 8 10 368 22 .6 1.667 .375 .577 .526 4.577 80 327 1.667 .95 110 1480 8230 109 120 82 93 0 253 56 197 1.43 61 5 .699 .322 .516 -1.636
3 4521 7107 190 63 4331 7044 4514 7336 255 161 4324 7273 0 0 809 1040 250 401 100 100 100 100 11375 11597 .615 1.626 1.682 1.639 1.643 1.11 52 199 1.603 .98 90 1640 8250 112 121 99 108 0 6097 54 6043 1.395 6293 6239 .717 1.443 .48 .529
4 2054 2899 205 66 1849 2833 2292 3110 225 93 2087 3044 0 0 639 914 141 202 100 100 100 100 4682 5131 .653 1.532 1.459 1.567 1.585 1.287 32 92 1.514 .97 60 1750 8270 116 122 112 118 0 2487 57 2430 1.314 2668 2611 .761 1.251 .394 .323
5 2220 3458 201 68 2019 3390 2323 3619 215 90 2122 3551 0 0 446 622 106 151 98 100 98 100 5409 5673 .596 1.679 1.673 1.74 1.673 1.299 52 213 1.693 .98 90 1910 8250 112 121 126 135 0 2966 58 2908 1.44 3105 3046 .694 1.436 .526 .522
6 692 905 191 62 501 843 255 195 202 79 64 133 0 0 903 1467 96 128 45 51 33 40 1344 197 .594 1.683 2.078 1.347 1.583 2.643 80 333 1.649 .97 110 2030 8230 109 120 137 148 0 776 53 723 1.443 167 114 .693 1.783 .53 .834
7 2849 4376 189 62 2660 4314 2930 4579 257 158 2741 4517 0 0 690 799 349 523 98 100 96 98 6974 7258 .617 1.622 1.648 1.702 1.602 1.368 52 217 1.608 .97 90 2180 8250 112 121 153 162 0 3754 53 3701 1.391 3928 3875 .719 1.414 .476 .499
8 2604 3861 195 65 2409 3796 2780 4101 312 221 2585 4036 0 0 612 773 451 669 96 100 96 98 6205 6621 .635 1.576 1.561 1.643 1.566 1.352 52 228 1.575 .98 90 2320 8250 112 121 167 176 0 3312 56 3256 1.352 3518 3462 .74 1.339 .435 .422
9 1872 1941 191 62 1681 1879 1847 1734 208 73 1656 1672 0 0 888 1051 98 62 100 100 100 100 3560 3328 .895 1.118 1.01 1.095 1.169 1.435 32 169 1.179 .92 70 2460 8230 111 118 182 189 0 1665 53 1612 .959 1488 1434 1.043 .866 -.061 -.207
10 1101 1553 178 60 923 1493 1106 1592 182 62 928 1532 0 0 332 477 35 17 100 100 98 100 2416 2460 .618 1.618 1.651 1.651 1.624 1.309 80 264 1.608 .96 100 2590 8240 111 121 194 204 0 1332 51 1281 1.388 1366 1314 .721 1.416 .473 .502
11 928 1179 175 54 753 1125 896 1123 176 56 721 1069 0 0 389 582 36 14 97 100 96 100 1878 1790 .669 1.494 1.483 1.503 1.474 1.404 80 224 1.49 .96 100 2730 8250 112 122 208 218 0 1011 46 965 1.282 963 917 .78 1.272 .358 .347
12 1397 1867 184 56 1213 1811 1484 2044 186 58 1300 1988 0 0 432 677 37 14 100 100 100 100 3024 3288 .67 1.493 1.529 1.473 1.472 1.198 80 275 1.518 .98 110 2870 8240 110 121 221 232 0 1602 48 1554 1.281 1753 1705 .781 1.312 .357 .392
13 1090 1477 193 57 897 1420 1062 1534 195 59 869 1477 0 0 329 467 40 15 98 100 98 100 2317 2346 .632 1.583 1.7 1.62 1.569 1.296 80 223 1.563 .96 100 3000 8240 111 121 235 245 0 1267 49 1218 1.358 1316 1267 .736 1.458 .442 .544
14 1333 1934 197 57 1136 1877 1354 2053 203 61 1157 1996 0 0 492 658 47 22 95 98 93 98 3013 3153 .605 1.652 1.725 1.737 1.68 1.431 80 237 1.598 .96 100 3140 8240 111 121 249 259 0 1659 49 1610 1.417 1761 1712 .706 1.48 .503 .566
15 1758 2571 206 65 1552 2506 1724 2609 212 69 1518 2544 0 0 542 995 48 24 100 100 100 100 4058 4062 .619 1.615 1.676 1.582 1.641 1.25 52 187 1.664 .97 90 3280 8240 111 120 263 272 0 2206 56 2150 1.385 2238 2182 .722 1.438 .47 .524
16 2075 3161 180 61 1895 3100 2154 3316 182 64 1974 3255 0 0 601 871 38 18 100 100 100 100 4995 5229 .611 1.636 1.649 1.646 1.641 1.26 80 292 1.632 .97 110 3410 8230 109 120 275 286 0 2712 52 2659 1.403 2845 2792 .713 1.415 .489 .5
17 1410 1949 170 58 1240 1891 1407 1954 175 60 1237 1896 0 0 352 571 34 18 100 100 100 100 3131 3133 .656 1.525 1.533 1.52 1.555 1.231 52 218 1.535 .97 90 3530 8220 109 118 288 297 0 1672 50 1622 1.308 1676 1626 .764 1.315 .388 .395
18 1199 1758 175 57 1024 1701 1167 1560 179 59 992 1503 0 0 364 604 36 13 100 100 100 100 2725 2495 .602 1.661 1.515 1.679 1.705 1.263 80 321 1.678 .97 110 3670 8230 109 120 301 312 0 1508 49 1459 1.425 1338 1289 .702 1.3 .511 .378
19 950 1347 168 57 782 1290 935 1361 169 58 767 1304 0 0 289 457 35 13 100 100 100 100 2072 2071 .606 1.65 1.7 1.659 1.61 1.221 80 245 1.633 .97 100 3820 8240 111 121 317 327 0 1156 49 1107 1.415 1168 1119 .707 1.458 .501 .544
20 1400 1845 155 52 1245 1793 1418 1952 157 52 1263 1900 0 0 288 394 31 12 100 100 100 100 3038 3163 .694 1.44 1.504 1.444 1.473 1.246 80 212 1.464 .97 100 3940 8250 112 122 329 339 0 1583 45 1538 1.235 1675 1630 .809 1.291 .305 .368

Total number of rows: 44160

Table truncated, full table size 9761 Kbytes.




Supplementary data files not provided
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