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Sample GSM71897 Query DataSets for GSM71897
Status Public on Aug 26, 2005
Title 1223c overexpressed 6 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 6hr;2ug RNA
Organism Campylobacter jejuni
Characteristics 1223c mt + 1223c OE 6hr;2ug RNA
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Mutant vs Wild-type, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2003-07/43068.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 4279 3846 621 362 3658 3484 3815 1799 623 372 3194 1437 0 0 2468 3568 130 67 100 100 100 100 7142 4631 1.05 .952 .45 .617 .7 2.693 12 98 1.161 .81 50 1740 13140 67 72 67 72 0 4661 439 4222 1.154 2180 1741 .866 .545 .207 -.875
2 4645 4596 646 388 3999 4208 4608 2473 654 421 3962 2085 0 0 1644 3775 127 143 100 100 100 100 8207 6047 .95 1.052 .526 .786 .742 1.987 12 104 1.419 .81 50 1980 13140 67 72 91 96 0 5570 470 5100 1.275 2997 2527 .784 .638 .351 -.649
3 3368 2661 613 372 2755 2289 3522 1394 620 378 2909 1022 0 0 929 2108 120 78 100 100 100 100 5044 3931 1.204 .831 .351 .582 .725 2.474 12 104 1.07 .76 50 2210 13140 67 72 114 119 0 3225 451 2774 1.007 1689 1239 .993 .426 .01 -1.232
4 3272 2137 593 346 2679 1791 3435 1458 595 350 2842 1112 0 0 792 1608 77 71 100 91 100 91 4470 3954 1.496 .669 .391 .554 .715 2.57 12 68 .762 .63 40 2450 13140 68 72 139 143 0 2590 419 2170 .81 1767 1348 1.234 .474 -.304 -1.077
5 3604 2201 497 309 3107 1892 3370 1273 511 340 2873 964 0 0 1574 2078 155 133 100 83 100 83 4999 3837 1.642 .609 .336 .32 .497 3.798 12 68 .809 .83 40 2690 13140 68 72 163 167 0 2667 374 2293 .738 1543 1168 1.355 .407 -.438 -1.298
6 3055 1764 424 248 2631 1516 2692 1367 436 253 2268 1119 0 0 1753 1364 84 56 100 96 96 96 4147 3387 1.735 .576 .493 .493 .524 2.307 32 176 .633 .89 60 2920 13150 68 74 185 191 0 2138 301 1837 .698 1657 1356 1.432 .598 -.518 -.742
7 1960 1160 420 240 1540 920 1987 837 426 249 1567 597 0 0 1230 1033 91 53 90 90 84 84 2460 2164 1.674 .597 .381 .561 .572 2.376 32 176 .644 .75 60 3180 13140 67 73 211 217 0 1406 291 1115 .724 1014 723 1.381 .462 -.466 -1.115
8 1753 1227 380 209 1373 1018 1221 686 384 213 841 477 0 0 1526 1516 73 53 96 94 88 92 2391 1318 1.349 .741 .567 .721 .675 2.728 52 340 .886 .82 80 3410 13150 67 75 233 241 0 1487 253 1234 .899 831 578 1.113 .687 -.154 -.541
9 3518 2303 406 218 3112 2085 3590 1331 435 241 3184 1113 0 0 1851 2450 186 137 100 91 100 83 5197 4297 1.493 .67 .35 .416 .421 2.242 12 104 .885 .88 50 3650 13140 67 72 258 263 0 2791 264 2527 .812 1613 1349 1.232 .424 -.301 -1.239
10 2130 1491 385 200 1745 1291 2060 861 388 213 1675 661 0 0 1304 1549 83 70 100 93 93 81 3036 2336 1.352 .74 .395 .52 .486 2.039 32 176 .936 .83 60 3890 13140 67 73 282 288 0 1807 242 1565 .897 1043 801 1.115 .478 -.158 -1.064
11 3273 2109 348 183 2925 1926 3166 1106 347 195 2818 923 0 0 1928 2079 63 61 100 100 100 100 4851 3741 1.519 .658 .328 .491 .434 2.141 12 104 .75 .72 50 4130 13150 68 73 306 311 0 2556 222 2334 .798 1340 1119 1.253 .397 -.326 -1.333
12 1555 926 345 184 1210 742 1306 645 351 189 961 461 0 0 943 746 67 44 100 100 96 100 1952 1422 1.631 .613 .48 .566 .588 1.725 32 176 .666 .88 60 4370 13150 68 74 330 336 0 1122 223 899 .743 782 559 1.346 .581 -.428 -.783
13 2156 1180 333 187 1823 993 1838 1020 341 191 1505 833 0 0 1073 695 71 44 100 100 100 100 2816 2338 1.836 .545 .553 .493 .586 1.833 32 236 .536 .85 70 4610 13140 66 73 353 360 0 1430 227 1203 .66 1236 1009 1.515 .671 -.599 -.576
14 2638 1816 359 185 2279 1631 2656 1467 363 189 2297 1282 0 0 1278 1401 76 45 100 100 100 100 3910 3579 1.397 .716 .558 .625 .735 2.046 32 176 .811 .83 60 4850 13150 68 74 378 384 0 2201 224 1977 .867 1778 1554 1.153 .676 -.205 -.564
15 2922 1844 343 187 2579 1657 2929 1211 346 193 2586 1024 0 0 1810 1789 66 45 100 100 100 96 4236 3610 1.556 .642 .396 .541 .563 2.06 32 236 .738 .75 70 5090 13150 67 74 401 408 0 2235 227 2008 .779 1468 1241 1.284 .48 -.361 -1.059
16 2989 2099 440 268 2549 1831 2790 1578 472 290 2350 1310 0 0 1598 1708 147 95 100 96 100 93 4380 3660 1.392 .718 .557 .581 .533 1.78 32 236 .844 .85 70 5330 13150 67 74 425 432 0 2544 325 2219 .871 1912 1588 1.149 .676 -.2 -.566
17 3225 1720 628 393 2597 1327 3133 1650 638 399 2505 1257 0 0 847 1247 114 102 100 83 100 83 3924 3762 1.957 .511 .502 .526 .494 2.129 12 90 .642 .65 50 1730 13380 91 96 66 71 0 2084 476 1608 .619 2000 1523 1.615 .608 -.691 -.718
18 2905 2348 610 376 2295 1972 2683 1496 625 380 2073 1120 0 0 1511 2034 114 83 100 96 100 96 4267 3193 1.164 .859 .54 .714 .736 2.406 32 176 1.097 .75 60 1970 13390 92 98 90 96 0 2845 456 2390 1.041 1813 1357 .96 .655 .058 -.611
19 3108 2322 644 387 2464 1935 3148 2221 646 393 2504 1834 0 0 950 1009 139 84 100 100 100 100 4399 4338 1.273 .785 .732 .758 .809 1.768 12 68 .641 .68 40 2210 13390 93 97 115 119 0 2814 469 2345 .952 2692 2223 1.051 .888 -.071 -.172
20 2742 1648 566 360 2176 1288 2951 1488 582 352 2385 1128 0 0 914 663 146 94 100 100 91 100 3464 3513 1.689 .592 .473 .606 .52 2.818 12 68 .464 .45 40 2460 13390 93 97 140 144 0 1997 436 1561 .717 1803 1367 1.394 .573 -.479 -.803

Total number of rows: 3840

Table truncated, full table size 881 Kbytes.




Supplementary data files not provided
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