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Sample GSM79677 Query DataSets for GSM79677
Status Public on Oct 22, 2005
Title 6h mitotic selection
Sample type RNA
 
Channel 1
Source name "Hela Reference 3, total RNA amplified by Whitfield's modified protocol"
Organism Homo sapiens
Characteristics "Hela Reference 3, total RNA amplified by Whitfield's modified protocol"
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name 6h mitotic selection
Organism Homo sapiens
Characteristics 6h mitotic selection
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Cell-cycle, Mitotic selection
Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16447.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 GPL2937
Series (1)
GSE3497 Cell division cycle in a human cancer cell line (HeLa)

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
1 756 910 86 99 670 811 892 1045 109 126 806 946 0 0 370 509 119 133 83 77 80 77 1481 1752 .826 1.21 1.174 1.194 1.238 2.232 80 474 1.249 .93 110 1520 9220 88 99 58 69 0 890 97 793 1.184 1022 925 .845 1.148 .243 .199
2 573 476 85 103 488 373 588 489 112 109 503 386 0 0 280 203 66 52 100 100 83 91 861 889 1.308 .764 .767 .819 .868 1.984 12 79 .743 .78 50 1620 9250 94 99 71 76 0 466 101 365 .747 478 377 1.338 .75 -.42 -.414
3 952 755 86 110 866 645 1023 708 116 134 937 598 0 0 646 560 161 147 78 71 71 61 1511 1535 1.343 .745 .638 .692 .726 1.935 80 460 .782 .93 110 1790 9220 88 99 85 96 0 738 108 631 .728 692 585 1.373 .624 -.457 -.68
4 593 572 100 100 493 472 520 381 101 107 420 281 0 0 346 418 38 50 91 91 91 83 965 701 1.044 .957 .669 .84 .64 2 12 68 1.143 .83 40 1920 9240 94 98 102 106 0 559 98 462 .936 373 275 1.068 .654 -.095 -.612
5 974 1357 85 94 889 1263 998 1436 91 100 913 1342 0 0 352 529 36 52 100 98 97 97 2152 2255 .704 1.421 1.47 1.411 1.437 1.677 120 394 1.482 .91 120 2060 9240 90 102 112 124 0 1327 92 1235 1.389 1404 1312 .72 1.437 .474 .524
6 89 102 84 96 5 6 86 98 91 105 2 2 0 0 38 42 40 51 8 11 3 1 11 4 .833 1.2 1 1.323 1.409 4.852 80 329 6.063 .1 110 2200 9220 88 99 126 137 0 100 94 6 1.174 96 2 .852 .978 .231 -.032
7 1239 1421 86 90 1153 1331 1159 1340 94 102 1073 1250 0 0 674 825 43 62 100 100 100 100 2484 2323 .866 1.154 1.165 1.127 1.118 1.541 80 269 1.191 .93 100 2330 9240 91 101 140 150 0 1390 88 1302 1.129 1310 1222 .886 1.139 .175 .188
8 1035 1516 88 88 947 1428 1073 1499 98 102 985 1411 0 0 300 573 43 62 98 100 98 100 2375 2396 .663 1.508 1.432 1.481 1.496 1.733 80 257 1.56 .93 110 2470 9240 90 101 153 164 0 1483 86 1397 1.475 1466 1380 .678 1.401 .56 .486
9 111 118 89 100 22 18 108 105 97 116 19 5 0 0 41 46 43 86 27 11 6 0 40 24 1.222 .818 .263 1.24 1.2 5.592 80 287 5.403 .24 110 2610 9220 88 99 167 178 0 115 98 18 .8 103 5 1.25 .257 -.322 -1.958
10 1444 1801 95 109 1349 1692 1395 1694 116 134 1300 1585 0 0 488 740 94 118 100 100 100 100 3041 2885 .797 1.254 1.219 1.211 1.186 1.301 80 342 1.323 .96 110 2740 9230 89 100 180 191 0 1761 107 1655 1.227 1657 1550 .815 1.192 .295 .254
11 575 669 99 131 476 538 605 642 132 151 506 511 0 0 292 297 109 112 81 93 78 84 1014 1017 .885 1.13 1.01 1.339 .913 2.672 32 162 1.128 .84 70 2890 9230 91 98 197 204 0 654 128 526 1.105 628 500 .905 .988 .144 -.018
12 1242 1600 107 169 1135 1431 1275 1594 134 196 1168 1425 0 0 477 622 105 117 100 100 97 100 2566 2593 .793 1.261 1.22 1.256 1.307 1.342 80 320 1.271 .96 110 3010 9240 90 101 207 218 0 1565 165 1399 1.233 1559 1394 .811 1.193 .302 .255
13 829 1111 115 165 714 946 832 1109 140 188 717 944 0 0 268 418 103 119 100 97 96 97 1660 1661 .755 1.325 1.317 1.243 1.308 1.831 80 268 1.392 .91 100 3150 9230 90 100 222 232 0 1086 161 925 1.296 1085 923 .772 1.288 .374 .365
14 1032 1982 113 120 919 1862 1102 2058 161 177 989 1938 0 0 596 1151 145 181 96 97 81 93 2781 2927 .494 2.026 1.96 2.085 2.013 1.463 80 345 2.042 .95 110 3290 9230 89 100 235 246 0 1938 117 1821 1.981 2013 1895 .505 1.916 .987 .938
15 711 751 99 81 612 670 767 826 118 121 668 745 0 0 314 350 99 151 90 86 84 78 1282 1413 .913 1.095 1.115 1.038 1.08 1.754 52 178 1.101 .89 80 3420 9220 90 98 250 258 0 734 79 655 1.071 808 729 .934 1.091 .098 .125
16 1604 1986 95 69 1509 1917 1697 1992 108 87 1602 1923 0 0 537 711 76 102 98 98 98 98 3426 3525 .787 1.27 1.2 1.269 1.279 1.227 80 291 1.277 .97 110 3560 9220 88 99 262 273 0 1942 67 1875 1.242 1948 1881 .805 1.174 .313 .231
17 1036 1071 94 65 942 1006 1043 1009 108 84 949 944 0 0 505 558 77 89 98 99 95 97 1948 1893 .936 1.068 .995 1.066 1.037 1.446 120 367 1.075 .96 120 3690 9230 89 101 275 287 0 1047 64 984 1.044 987 923 .958 .973 .063 -.04
18 825 1097 93 68 732 1029 905 1154 99 83 812 1086 0 0 256 338 46 56 100 100 98 100 1761 1898 .711 1.406 1.337 1.461 1.395 1.415 52 230 1.38 .93 90 3830 9220 89 98 290 299 0 1073 67 1006 1.375 1129 1062 .727 1.308 .459 .387
19 654 776 87 66 567 710 692 844 93 75 605 778 0 0 264 348 35 42 98 97 95 95 1277 1383 .799 1.252 1.286 1.208 1.256 1.595 80 261 1.304 .93 100 3960 9230 90 100 303 313 0 759 65 694 1.225 825 761 .817 1.258 .292 .331
20 800 680 89 64 711 616 753 690 96 72 664 626 0 0 398 283 37 42 100 98 96 98 1327 1290 1.154 .866 .943 .948 .864 1.557 80 277 .805 .92 100 4090 9220 89 99 316 326 0 665 63 602 .847 675 612 1.18 .922 -.239 -.117

Total number of rows: 45312

Table truncated, full table size 9781 Kbytes.




Supplementary data files not provided
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