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Sample GSM90741 Query DataSets for GSM90741
Status Public on Jan 06, 2006
Title 1.5' RNA Decay of WT (N3433) in M9 0.2% Glycerol 0.2% Tryptone at 30 C Mid Log Rep. B2
Sample type RNA
 
Channel 1
Source name WT (N3433) M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log
Organism Escherichia coli
Characteristics WT (N3433) M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name WT (N3433) in M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log 1.5' post rif
Organism Escherichia coli
Characteristics WT (N3433) in M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log 1.5' post rif
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: RNA decay, Rifampicin
Image: http://smd.stanford.edu/MicroArray/gifs/2001-08/19615.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 Jan 05, 2006
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 GPL2821
Series (2)
GSE3978 mRNA Decay in E. Coli Degradosome Mutants and their Parental Strains
GSE4394 Global analysis of Escherichia coli RNA degradosome function

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
1 337 338 85 80 252 258 371 338 86 83 286 258 0 0 89 113 9 29 99 98 97 95 510 544 .977 1.024 .902 1.007 1.028 1.725 120 699 1.074 .9 120 1210 24830 61 73 51 63 0 457 108 349 1.384 457 349 .723 1.219 .468 .286
2 318 243 87 80 231 163 331 243 87 82 244 163 0 0 76 73 14 27 100 98 100 97 394 407 1.417 .706 .668 .676 .685 1.648 80 602 .714 .85 110 1420 24820 60 71 72 83 0 328 108 220 .954 328 220 1.049 .903 -.069 -.148
3 365 260 87 79 278 181 387 249 88 82 300 170 0 0 91 84 14 27 100 100 100 95 459 470 1.536 .651 .567 .612 .626 1.587 80 620 .662 .85 110 1640 24820 60 71 94 105 0 351 107 245 .88 336 230 1.137 .766 -.185 -.385
4 744 447 87 78 657 369 807 447 88 82 720 369 0 0 172 100 10 28 100 100 100 100 1026 1089 1.78 .562 .513 .567 .559 1.415 80 582 .539 .92 110 1860 24820 60 71 116 127 0 604 105 499 .759 604 499 1.318 .693 -.398 -.53
5 398 348 91 83 307 265 434 349 93 86 343 266 0 0 98 100 11 27 98 100 98 97 572 609 1.158 .863 .776 .869 .827 1.719 120 672 .878 .9 120 2060 24810 59 71 136 148 0 470 112 358 1.166 472 359 .857 1.048 .222 .068
6 800 461 103 90 697 371 875 474 105 92 772 384 0 0 209 127 15 29 100 97 99 96 1068 1156 1.879 .532 .497 .518 .514 1.854 120 679 .521 .93 120 2270 24810 59 71 157 169 0 623 122 501 .719 641 519 1.39 .672 -.475 -.573
7 351 293 111 90 240 203 371 284 112 92 260 194 0 0 73 78 18 29 97 100 97 98 443 454 1.182 .846 .746 .818 .812 1.594 120 719 .87 .87 120 2490 24810 59 71 179 191 0 396 122 274 1.143 384 262 .875 1.008 .193 .012
8 625 356 115 93 510 263 582 305 115 95 467 212 0 0 326 209 12 30 100 87 96 78 773 679 1.939 .516 .454 .418 .415 2.965 32 220 .524 .84 70 2700 24790 59 66 202 209 0 481 126 355 .697 412 286 1.435 .613 -.521 -.705
9 341 243 108 92 233 151 348 238 114 95 240 146 0 0 54 72 70 31 100 97 88 91 384 386 1.543 .648 .608 .622 .631 1.529 80 624 .568 .72 110 2900 24790 57 68 220 231 0 328 124 204 .876 322 197 1.142 .822 -.191 -.283
10 1503 1177 114 97 1389 1080 1625 1238 119 101 1511 1141 0 0 456 358 67 31 98 100 97 100 2469 2652 1.286 .778 .755 .819 .799 1.683 120 701 .765 .96 120 3120 24800 58 70 242 254 0 1591 131 1459 1.051 1673 1542 .952 1.02 .071 .029
11 308 208 116 97 192 111 320 204 117 100 204 107 0 0 45 58 12 30 100 93 99 77 303 311 1.73 .578 .525 .521 .574 1.903 120 671 .644 .76 120 3330 24800 58 70 263 275 0 281 131 150 .781 276 145 1.28 .709 -.356 -.497
12 479 283 118 95 361 188 499 297 119 100 381 202 0 0 79 77 15 32 100 95 100 92 549 583 1.92 .521 .53 .486 .55 1.813 120 702 .517 .83 120 3540 24790 57 69 284 296 0 382 128 254 .704 401 273 1.421 .716 -.507 -.481
13 705 395 113 94 592 301 681 435 116 99 568 341 0 0 299 160 16 31 100 96 100 90 893 909 1.967 .508 .6 .482 .517 1.652 32 220 .484 .89 70 3740 24770 57 64 306 313 0 534 127 407 .687 588 461 1.455 .811 -.541 -.302
14 868 578 115 98 753 480 379 298 116 102 264 200 0 0 1881 836 13 36 99 96 99 92 1233 464 1.569 .637 .758 .77 .697 2.967 120 736 .313 .56 120 3960 24790 57 69 326 338 0 781 132 649 .861 403 270 1.161 1.024 -.215 .034
15 326 262 112 99 214 163 330 252 113 102 218 153 0 0 35 53 14 31 100 100 100 98 377 371 1.313 .762 .702 .733 .714 1.448 80 604 .825 .82 110 4170 24780 56 67 347 358 0 354 134 220 1.029 341 207 .972 .948 .042 -.076
16 256 197 112 98 144 99 134 125 113 100 22 27 0 0 230 153 14 32 57 46 46 38 243 49 1.455 .688 1.227 .931 .835 2.995 80 598 .665 .85 110 4380 24780 56 67 368 379 -50 266 132 134 .929 169 36 1.076 1.658 -.106 .73
17 353 265 117 104 236 161 352 263 119 106 235 159 0 0 36 62 22 35 100 97 100 92 397 394 1.466 .682 .677 .626 .701 1.615 80 618 .742 .81 110 4580 24770 55 66 388 399 0 358 141 218 .922 355 215 1.085 .914 -.117 -.129
18 472 384 121 108 351 276 463 359 124 109 342 251 0 0 136 110 21 33 100 100 100 100 627 593 1.272 .786 .734 .788 .769 1.406 52 412 .75 .88 90 4790 24770 56 65 410 419 0 519 146 373 1.063 485 339 .941 .992 .088 -.012
19 354 294 132 111 222 183 361 296 134 114 229 185 0 0 46 72 23 35 100 99 99 94 405 414 1.213 .824 .808 .782 .848 1.593 120 714 .886 .83 120 5010 24780 56 68 431 443 0 397 150 247 1.114 400 250 .898 1.092 .156 .127
20 593 546 134 111 459 435 607 545 136 114 473 434 0 0 74 107 25 36 100 100 100 100 894 907 1.055 .948 .918 .935 .946 1.323 80 598 .931 .92 110 5210 24770 55 66 451 462 0 738 150 588 1.281 736 586 .781 1.24 .357 .31

Total number of rows: 6144

Table truncated, full table size 1324 Kbytes.




Supplementary data files not provided
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