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Sample GSM27526 Query DataSets for GSM27526
Status Public on Aug 06, 2004
Title Regulation of an overlapping set of genes - Slide 6
Sample type RNA
 
Channel 1
Source name control
Organism Arabidopsis thaliana
Extracted molecule total RNA
 
Channel 2
Source name Aza + TSA
Organism Arabidopsis thaliana
Extracted molecule total RNA
 
 
Description Category: DNA metabolism
Subcategory: treated
Slide 6 - Testing the hypothesis that cytosine methylation and histone deacetylation regulate an overlapping set of genes
Experimenter: Craig Pikaard
Contact email: [email protected]
Scanning Software: GenePix
Software version: Pro
Scanning parameters: PMTVolts=00LaserPower=00
Lot batch = K157
 
Submission date Jul 27, 2004
Last update date Nov 22, 2005
Contact name Shuang Chang
E-mail(s) [email protected]
Phone 1-314-935-8529
Organization name Washington University
Department Biology
Lab Dr. Craig Pikaard's Lab
Street address
City St.Louis
State/province MO
ZIP/Postal code 63130
Country USA
 
Platform ID GPL1382
Series (1)
GSE1612 Overlapping gene regulation by cytosine methylation and histone deacetylation

Data table header descriptions
ID_REF
CH1I_MEAN Mean spot pixel intensity at Channel 1
CH1D_MEDIAN Median spot pixel intensity at Channel 1 with the median-background subtracted (CH1I_MEDIAN - CH1B_MEDIAN)
CH1I_MEDIAN Median spot pixel intensity at Channel 1
CH1_PER_SAT Percentage of spot pixels at Channel 1 that are saturated
CH1I_SD Standard deviation of the spot intensity at Channel 1
CH1B_MEAN Mean spot background in Channel 1
CH1B_MEDIAN Median spot background intensity in Channel 1
CH1B_SD Standard deviation of the spot background intensity in Channel 1
CH1D_MEAN Mean Channel 1 intensity with the median-background subtracted (CH1I_MEAN - CH1B_MEDIAN)
CH2I_MEAN Mean spot pixel intensity at Channel 2
CH2D_MEAN Mean spot pixel intensity at Channel 2 with the median-background subtracted (CH2I_MEAN - CH2B_MEDIAN)
CH2D_MEDIAN Median spot pixel intensity at Channel 2 with the median-background subtracted (CH2I_MEDIAN - CH2B_MEDIAN)
CH2I_MEDIAN Median spot pixel intensity at Channel 2
CH2_PER_SAT Percentage of spot pixels at Channel 2 that are saturated
CH2I_SD Standard deviation of the spot pixel intensity at at Channel 2
CH2B_MEAN Mean spot background intensity in Channel 2
CH2B_MEDIAN Median spot background intensity in Channel 2
CH2B_SD Standard deviation of the spot background intensity in Channel 2
CH2BN_MEDIAN Normalized value of median Channel 2 background (CH2B_MEDIAN/Normalization factor)
CH2DN_MEAN Normalized value of mean Channel 2 intensity with normalized background subtracted (CH2IN_MEAN - CH2BN)
CH2IN_MEAN Normalized value of mean Channel 2 intensity (CH2I_MEAN/Normalization factor)
CH2DN_MEDIAN Normalized value of median Channel 2 intensity with normalized background subtracted (CH2IN_MEDIAN - CH2BN)
CH2IN_MEDIAN Normalized value of median Channel 2 intensity (CH2_MEDIAN/Normalization factor)
CORR Coefficient of determination for the current regression value
DIAMETER Diameter in �m of the spot indicator
FLAG Type of flag associated with a spot (default=0)
VALUE same as UNF_VALUE but with flagged values removed
LOG_RAT2N_MEDIAN Log (base 2) of the ratio of the medians of Channel 2 to Channel 1 [log (base 2) (RAT2N_MEDIAN)]
PIX_RAT2_MEAN Geometric mean of the pixel-by-pixel ratios of Channel 2 to Channel 1 pixel intensities, with the median background subtracted
PIX_RAT2_MEDIAN Median of pixel by-pixel ratios of Channel 2 to Channel 1 pixel intensities, with the median background subtracted
PERGTBCH1I_1SD Percentage of spot pixels with intensities more than one standard deviation above the background pixel intensity, at Channel 1
PERGTBCH1I_2SD
PERGTBCH2I_1SD Percentage of spot pixels with intensities more than one standard deviation above the background pixel intensity, at Channel 2
PERGTBCH2I_2SD Percentage of spot pixels with intensities more than two standard deviations above the background pixel intensity, at Channel 1
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
RAT1N_MEAN Ratio of the means of Channel 1 intensity to normalized Channel 2 intensity with median background subtracted (CH1D_MEAN/CH2DN_MEAN). Channel 1/Channel 2 ratio normalized or Green/Red ratio normalized
RAT2_MEAN Ratio of the arithmetic mean intensities of each spot for each wavelength, with the median background subtracted. Channel 2/Channel 1 ratio, (CH2I_MEAN - CH2B_MEDIAN)/(CH1_MEAN - CH1B_MEDIAN) or Red/Green ratio
RAT2_MEDIAN Ratio of the median intensities of each spot for each wavelength, with the median background subtracted
RAT2_SD Standard deviation of pixel intensity ratios
RAT2N_MEAN Channel 2/Channel 1 ratio normalized, RAT2N_MEAN/Normalization factor or Red/Green mean ratio normalized
RAT2N_MEDIAN Channel 2/Channel 1 ratio normalized, RAT2N_MEDIAN/Normalization factor or Red/Green median ratio normalized
REGR Regression ratio
SUM_MEAN Sum of the arithmetic mean intensities for each wavelength, with the median background subtracted (CH1D_MEAN + CH2D_MEAN)
SUM_MEDIAN Sum of the median intensities for each wavelength, with the median-background subtracted (CH1D_MEDIAN + CH2D_MEDIAN)
TOT_BPIX Total number of background pixels
TOT_SPIX Total number of signal (spot) pixels
X_COORD X-coordinate in �m of the center of the spot-indicator associated with the spot, where (0,0) is the top left of the image
Y_COORD Y-coordinate in �m of the center of the spot-indicator associated with the spot, where (0,0) is the top left of the image
TOP Box top: int(((centerX - radius) - Xoffset) / pixelSize)
BOT Box bottom: int(((centerX + radius) - Xoffset) / pixelSize)
LEFT Box left: int(((centerY - radius) - yoffset) / pixelSize)
RIGHT Box right: int(((centerY + radius) - yoffset) / pixelSize)
UNF_VALUE aka LOG_RAT2N_MEAN, or Log (base 2) of the ratio of the mean of Channel 2 to Channel 1 [log (base 2) (RAT2N_MEAN)]

Data table
ID_REF CH1I_MEAN CH1D_MEDIAN CH1I_MEDIAN CH1_PER_SAT CH1I_SD CH1B_MEAN CH1B_MEDIAN CH1B_SD CH1D_MEAN CH2I_MEAN CH2D_MEAN CH2D_MEDIAN CH2I_MEDIAN CH2_PER_SAT CH2I_SD CH2B_MEAN CH2B_MEDIAN CH2B_SD CH2BN_MEDIAN CH2DN_MEAN CH2IN_MEAN CH2DN_MEDIAN CH2IN_MEDIAN CORR DIAMETER FLAG VALUE LOG_RAT2N_MEDIAN PIX_RAT2_MEAN PIX_RAT2_MEDIAN PERGTBCH1I_1SD PERGTBCH1I_2SD PERGTBCH2I_1SD PERGTBCH2I_2SD RAT1_MEAN RAT1N_MEAN RAT2_MEAN RAT2_MEDIAN RAT2_SD RAT2N_MEAN RAT2N_MEDIAN REGR SUM_MEAN SUM_MEDIAN TOT_BPIX TOT_SPIX X_COORD Y_COORD TOP BOT LEFT RIGHT UNF_VALUE
1 1036 911 1025 0 412 125 114 63 922 1147 1019 996 1124 0 573 184 128 179 138 1096 1233 1071 1209 .85 140 0 .249 .233 1.03 1.122 99 99 94 86 .905 .841 1.105 1.093 1.793 1.188 1.176 1.214 1941 1907 1016 156 2070 7410 274 288 200 214 .249
2 545 413 528 0 160 125 115 64 430 557 437 394 514 0 309 176 120 177 129 470 599 424 553 .45 110 0 .128 .037 .811 .974 98 98 77 57 .984 .915 1.016 .954 2.705 1.093 1.026 2.138 867 807 642 80 2300 7420 276 287 224 235 .128
3 773 591 753 0 210 178 162 110 611 322 189 123 256 0 241 198 133 204 143 203 346 132 275 .23 110 0 -1.588 -2.16 .304 .329 100 100 37 13 3.233 3.007 .309 .208 3 .333 .224 .401 800 714 642 80 2530 7410 275 286 247 258 -1.588
4 4152 4018 4221 0 759 229 203 137 3949 4627 4484 4445 4588 0 1240 197 143 192 154 4822 4975 4780 4933 .94 130 0 .288 .25 1.118 1.134 100 100 100 100 .881 .819 1.135 1.106 1.385 1.221 1.19 1.176 8433 8463 841 120 2760 7420 275 288 269 282 .288
5 1230 848 1208 0 265 403 360 567 870 980 735 683 928 0 437 325 245 443 263 790 1054 734 998 .57 120 0 -.139 -.207 .776 .789 89 13 75 34 1.184 1.101 .845 .805 2.091 .908 .866 1.237 1605 1531 695 120 2990 7420 276 288 293 305 -.139
6 6652 6593 6837 0 1877 454 244 2697 6408 5694 5491 5501 5704 0 2177 364 203 1499 218 5904 6123 5915 6133 .94 140 0 -.118 -.157 .816 .829 94 73 98 87 1.167 1.085 .857 .834 1.36 .921 .897 .706 11899 12094 896 156 3210 7430 276 290 314 328 -.118
7 1910 1699 1932 0 375 273 233 366 1677 1407 1218 1131 1320 0 499 277 189 539 203 1310 1513 1216 1419 .81 130 0 -.357 -.482 .678 .672 100 99 91 58 1.377 1.28 .726 .666 1.757 .781 .716 .736 2895 2830 812 120 3440 7420 275 288 337 350 -.357
8 1145 945 1158 0 362 264 213 390 932 1578 1411 1448 1615 0 769 263 167 559 180 1517 1697 1557 1737 .87 120 0 .703 .72 1.349 1.475 94 65 86 65 .661 .614 1.514 1.532 1.926 1.628 1.648 1.696 2343 2393 740 120 3670 7430 277 289 361 373 .703
9 2232 1897 2016 0 916 132 119 75 2113 2082 1940 1796 1938 0 1017 191 142 181 153 2086 2239 1931 2084 .89 130 0 -.019 .026 .873 .869 100 100 100 98 1.089 1.013 .918 .947 1.561 .987 1.018 .958 4053 3693 839 120 3910 7430 276 289 384 397 -.019
10 353 231 353 0 132 131 122 73 231 429 313 281 397 0 246 179 116 202 125 337 461 302 427 .18 100 0 .543 .387 1.323 1.49 88 72 60 33 .738 .686 1.355 1.216 3.892 1.457 1.308 8.861 544 512 554 80 4140 7430 278 288 409 419 .543
11 1007 899 1022 0 320 132 123 68 884 1663 1535 1526 1654 0 726 178 128 189 138 1651 1788 1641 1778 .86 120 0 .901 .868 1.664 1.727 100 100 99 97 .576 .536 1.736 1.697 1.606 1.867 1.825 2.012 2419 2425 754 120 4360 7430 277 289 430 442 .901
12 2160 1945 2102 0 633 195 157 133 2003 2229 2064 1860 2025 0 818 210 165 188 177 2219 2397 2000 2177 .91 120 0 .148 .04 1.005 1.029 100 100 100 100 .97 .903 1.03 .956 1.427 1.108 1.028 1.094 4067 3805 740 120 4600 7430 277 289 454 466 .148
13 779 418 769 0 186 376 351 195 428 644 416 418 646 0 371 276 228 227 245 447 692 449 695 .4 130 0 .064 .105 .9 .993 90 55 63 43 1.029 .957 .972 1 2.948 1.045 1.075 2.269 844 836 698 120 4820 7420 275 288 475 488 .064
14 2462 2110 2462 0 838 479 352 728 2110 1462 1200 1199 1461 0 679 425 262 870 282 1290 1572 1289 1571 .77 130 0 -.71 -.711 .493 .569 97 73 66 22 1.758 1.635 .569 .568 2.095 .612 .611 .693 3310 3309 748 120 5050 7430 276 289 498 511 -.71
15 1106 788 1094 0 257 364 306 480 800 942 718 644 868 0 452 333 224 636 241 772 1013 692 933 .65 210 0 -.051 -.186 .782 .872 92 21 50 11 1.114 1.036 .898 .817 2.222 .965 .879 1.117 1518 1432 1668 316 5280 7430 272 293 517 538 -.051
16 6192 5624 5940 0 2057 354 316 355 5876 10634 10434 10253 10453 0 3817 259 200 247 215 11219 11434 11025 11240 .98 120 0 .933 .971 1.757 1.774 100 100 100 100 .563 .524 1.776 1.823 1.238 1.909 1.96 1.802 16310 15877 694 120 5520 7430 277 289 546 558 .933
17 2983 2662 2913 0 556 309 251 384 2732 2738 2566 2411 2583 0 1043 248 172 349 185 2759 2944 2592 2777 .82 110 0 .014 -.038 .885 .864 100 100 100 100 1.065 .99 .939 .906 1.506 1.01 .974 .97 5298 5073 636 80 5740 7430 277 288 568 579 .014
18 2876 2966 3090 0 1043 142 124 94 2752 3767 3631 3669 3805 0 1668 182 136 180 146 3904 4051 3945 4091 .93 120 0 .505 .412 1.298 1.335 100 100 100 99 .758 .705 1.319 1.237 1.499 1.419 1.33 1.405 6383 6635 814 120 5980 7430 277 289 592 604 .505
19 22828 24008 24140 0 7389 140 132 70 22696 36696 36587 39196 39305 0 11187 166 109 175 117 39341 39458 42146 42263 .99 120 0 .794 .812 1.633 1.633 100 100 100 100 .62 .577 1.612 1.633 1.109 1.733 1.756 1.601 59283 63204 752 120 2060 7650 299 311 200 212 .794
20 1436 1306 1426 0 276 129 120 65 1316 1172 1043 958 1087 0 596 190 129 188 139 1122 1260 1030 1169 .75 110 0 -.231 -.342 .661 .731 100 100 98 88 1.262 1.173 .793 .734 2.06 .852 .789 .909 2359 2264 650 80 2300 7650 299 310 224 235 -.231

Total number of rows: 15360

Table truncated, full table size 3659 Kbytes.




Supplementary data files not provided
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