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Sample GSM71898 Query DataSets for GSM71898
Status Public on Aug 26, 2005
Title 1223c overexpressed 24 hr
Sample type RNA
 
Channel 1
Source name RNA pool of all tp, three strains;2ug RNA
Organism Campylobacter jejuni
Characteristics RNA pool of all tp, three strains;2ug RNA
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name 1223c mt + 1223c OE 24hr;2ug RNA
Organism Campylobacter jejuni
Characteristics 1223c mt + 1223c OE 24hr;2ug RNA
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Mutant vs Wild-type, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2003-07/43070.gif
Data processing VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)
 
Submission date Aug 25, 2005
Last update date Sep 22, 2006
Organization Stanford Microarray Database (SMD)
E-mail(s) [email protected]
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 GPL2782
Series (1)
GSE3198 Cj1223c Mutant vs. Overexpressed, Time Course

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
LOG_RAT2N_MEAN 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
VALUE 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 LOG_RAT2N_MEAN VALUE
1 974 1376 168 106 806 1270 487 369 170 110 319 263 0 0 1180 2265 45 38 100 96 100 96 2076 582 .635 1.576 .824 1.045 1.168 2 32 220 1.927 .9 70 1670 12870 59 66 55 62 0 1542 119 1423 1.765 413 295 .566 .924 .82 -.114
2 1483 606 163 104 1320 502 803 280 167 105 640 176 0 0 1754 936 38 29 98 94 98 88 1822 816 2.629 .38 .275 .281 .308 1.849 52 340 .466 .91 80 1920 12880 60 68 80 88 0 679 117 562 .426 314 197 2.347 .308 -1.231 -1.698
3 885 598 155 102 730 496 472 243 160 102 317 141 0 0 1149 1023 36 27 98 96 94 86 1226 458 1.472 .679 .445 .502 .505 1.997 52 340 .842 .97 80 2150 12870 59 67 103 111 0 670 114 556 .761 272 158 1.314 .498 -.393 -1.005
4 604 452 158 102 446 350 452 281 161 105 294 179 0 0 443 505 34 30 100 100 100 93 796 473 1.274 .785 .609 .612 .607 1.771 32 176 1.007 .89 60 2390 12880 61 67 128 134 0 506 114 392 .879 315 201 1.137 .682 -.186 -.552
5 627 711 159 103 468 608 389 337 161 107 230 234 0 0 729 1084 38 29 93 100 90 93 1076 464 .77 1.299 1.017 1.115 1.087 2.095 32 236 1.425 .93 70 2620 12880 60 67 150 157 0 797 115 681 1.456 378 262 .687 1.14 .542 .189
6 1079 585 155 99 924 486 587 265 158 100 432 166 0 0 1307 987 35 26 100 98 100 88 1410 598 1.901 .526 .384 .364 .395 1.935 52 420 .68 .93 90 2860 12880 59 68 173 182 0 655 111 545 .589 297 186 1.697 .431 -.763 -1.216
7 598 717 155 101 443 616 312 255 160 103 157 154 0 0 794 1203 33 29 96 100 90 96 1059 311 .719 1.391 .981 1.156 1.177 1.786 52 420 1.503 .98 90 3110 12870 58 67 198 207 0 803 113 690 1.558 286 173 .642 1.099 .64 .136
8 873 713 156 102 717 611 488 295 170 105 332 193 0 0 933 1004 181 28 84 100 48 98 1328 525 1.173 .852 .581 .674 .697 1.533 52 340 .942 .9 80 3350 12870 59 67 223 231 0 799 114 685 .955 331 216 1.047 .651 -.067 -.618
9 734 915 153 96 581 819 464 344 157 99 311 248 0 0 1005 1717 34 27 98 100 92 90 1400 559 .709 1.41 .797 .974 .945 1.859 52 340 1.728 .91 80 3590 12870 59 67 247 255 0 1025 108 918 1.579 385 278 .633 .893 .659 -.162
10 687 734 161 104 526 630 476 392 163 105 315 288 0 0 731 981 35 27 98 100 98 100 1156 603 .835 1.198 .914 1.012 .984 1.799 52 340 1.334 .9 80 3820 12870 59 67 270 278 0 822 117 706 1.342 439 323 .745 1.024 .424 .035
11 904 979 165 102 739 877 481 425 170 106 316 323 0 0 1044 1723 38 31 96 100 96 96 1616 639 .843 1.187 1.022 .994 1.034 1.787 32 236 1.602 .9 70 4070 12890 61 68 295 302 0 1097 114 983 1.33 476 362 .752 1.145 .411 .196
12 533 569 176 103 357 466 350 262 175 106 174 159 0 0 504 808 37 30 92 98 82 94 823 333 .766 1.305 .914 1.01 1 2.022 52 340 1.576 .92 80 4320 12870 59 67 320 328 0 638 115 522 1.463 294 178 .684 1.024 .549 .034
13 651 722 176 106 475 616 478 413 179 107 302 307 0 0 506 870 37 29 100 100 96 100 1091 609 .771 1.297 1.017 1.033 1.112 1.743 52 340 1.595 .96 80 4550 12870 59 67 343 351 0 809 119 690 1.453 463 344 .688 1.139 .539 .188
14 1180 631 179 112 1001 519 736 395 184 113 557 283 0 0 1138 711 42 30 100 100 100 96 1520 840 1.929 .518 .508 .447 .426 1.846 32 236 .567 .93 70 4790 12880 60 67 367 374 0 707 125 582 .581 443 317 1.721 .569 -.784 -.813
15 1039 1084 176 115 863 969 550 401 181 119 374 286 0 0 1197 1725 40 30 100 100 96 98 1832 660 .891 1.123 .765 .886 .879 1.812 52 340 1.38 .96 80 5030 12880 60 68 391 399 0 1215 129 1086 1.258 449 320 .795 .857 .331 -.223
16 1321 1053 180 113 1141 940 839 561 185 117 659 448 0 0 1361 1527 43 33 100 98 100 96 2081 1107 1.214 .824 .68 .652 .674 1.767 52 340 1.033 .95 80 5270 12880 60 68 415 423 0 1180 127 1053 .923 629 502 1.083 .762 -.115 -.393
17 479 596 158 95 321 501 334 293 160 100 176 198 0 0 440 812 34 30 92 90 90 84 822 374 .641 1.561 1.125 1.08 1.203 2.725 52 320 1.883 .88 80 1680 13110 83 91 56 64 0 668 106 561 1.749 328 222 .572 1.261 .806 .334
18 746 517 159 100 587 417 462 241 163 104 303 141 0 0 795 680 37 27 100 96 98 84 1004 444 1.408 .71 .465 .552 .557 1.915 52 340 .785 .84 80 1910 13110 83 91 79 87 0 579 112 467 .796 270 158 1.256 .521 -.329 -.94
19 532 516 155 96 377 420 432 291 157 101 277 195 0 0 331 628 34 29 100 100 100 93 797 472 .898 1.114 .704 .826 .781 2.132 32 236 1.714 .8 70 2160 13120 84 91 104 111 0 578 108 471 1.248 326 218 .801 .789 .32 -.342
20 587 620 160 103 427 517 389 332 162 106 229 229 0 0 544 834 37 31 96 96 90 94 944 458 .826 1.211 1 1.005 .95 2.442 52 340 1.532 .84 80 2400 13120 84 92 128 136 0 695 115 579 1.357 372 257 .737 1.12 .44 .164

Total number of rows: 3840

Table truncated, full table size 873 Kbytes.




Supplementary data files not provided
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