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Sample GSM90745 Query DataSets for GSM90745
Status Public on Jan 06, 2006
Title 6' RNA Decay of WT (N3433) in M9 + 0.2% Glycerol, .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 6' post rif
Organism Escherichia coli
Characteristics WT (N3433) in M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log 6' post rif
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: RNA decay, Rifampicin
Image: http://smd.stanford.edu/MicroArray/gifs/2001-08/19619.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
1 461 295 89 73 372 222 443 292 92 76 354 219 0 0 100 70 37 25 100 100 100 100 594 573 1.676 .597 .619 .585 .592 1.478 120 808 .535 .84 130 1610 25380 115 128 90 103 0 265 66 199 .536 262 197 1.867 .555 -.9 -.849
2 492 256 88 73 404 183 474 262 89 76 386 189 0 0 138 75 13 25 100 99 100 96 587 575 2.208 .453 .49 .437 .45 1.766 120 715 .424 .85 120 1830 25380 116 128 113 125 0 230 66 164 .407 235 170 2.459 .44 -1.298 -1.186
3 571 280 86 75 485 205 572 268 87 78 486 193 0 0 222 95 10 26 100 100 100 96 690 679 2.366 .423 .397 .434 .402 1.726 52 412 .383 .84 90 2040 25380 117 126 135 144 0 251 67 184 .379 241 173 2.636 .356 -1.398 -1.488
4 632 282 89 77 543 205 632 278 92 79 543 201 0 0 172 94 19 25 100 98 100 98 748 744 2.649 .378 .37 .37 .363 1.45 52 412 .347 .85 90 2250 25380 117 126 156 165 0 253 69 184 .339 250 180 2.951 .332 -1.561 -1.59
5 390 247 92 77 298 170 371 239 93 79 279 162 0 0 94 64 15 27 100 100 98 98 468 441 1.753 .57 .581 .565 .543 1.64 80 607 .545 .84 110 2460 25380 116 127 176 187 0 222 69 153 .512 215 145 1.953 .521 -.966 -.94
6 493 186 94 77 399 109 497 187 98 81 403 110 0 0 62 46 30 29 100 95 100 86 508 513 3.661 .273 .273 .255 .27 1.572 80 596 .244 .74 110 2670 25380 116 127 197 208 0 167 69 98 .245 168 99 4.078 .245 -2.028 -2.029
7 315 225 93 79 222 146 333 224 96 81 240 145 0 0 77 58 27 26 92 97 90 94 368 385 1.521 .658 .604 .721 .629 2.549 120 701 .647 .82 120 2890 25380 116 128 219 231 0 202 71 131 .59 201 130 1.694 .542 -.76 -.883
8 229 116 90 78 139 38 104 96 91 79 14 18 0 0 226 63 12 25 53 47 41 30 177 32 3.658 .273 1.286 .751 .429 5.279 80 586 .244 .66 110 3100 25380 116 127 240 251 -50 104 70 34 .245 86 16 4.075 1.154 -2.027 .207
9 255 170 88 76 167 94 262 166 89 78 174 90 0 0 45 49 11 25 100 96 98 77 261 264 1.777 .563 .517 .507 .518 2.166 80 534 .58 .72 100 3310 25380 117 127 262 272 0 153 68 84 .505 149 81 1.979 .464 -.985 -1.107
10 794 298 88 76 706 222 790 300 89 78 702 224 0 0 69 61 12 24 100 100 100 100 928 926 3.18 .314 .319 .304 .311 1.326 80 532 .302 .88 100 3520 25380 117 127 283 293 0 268 68 199 .282 269 201 3.543 .286 -1.825 -1.804
11 288 183 89 75 199 108 290 188 92 78 201 113 0 0 24 49 25 26 100 95 100 85 307 314 1.843 .543 .562 .508 .55 1.685 80 599 .582 .76 110 3720 25380 116 127 302 313 0 164 67 97 .487 169 101 2.053 .505 -1.037 -.987
12 324 191 86 74 238 117 324 188 89 77 238 114 0 0 37 55 22 26 100 93 100 90 355 352 2.034 .492 .479 .425 .492 1.955 80 621 .49 .8 110 3930 25380 116 127 323 334 0 171 66 105 .441 169 102 2.266 .43 -1.18 -1.218
13 342 132 85 76 257 56 385 135 87 75 300 59 0 0 188 51 10 23 87 65 81 59 313 359 4.589 .218 .197 .38 .313 4.888 32 148 .176 .59 60 4150 25360 117 123 348 354 0 118 68 50 .196 121 53 5.112 .177 -2.354 -2.502
14 279 209 87 71 192 138 280 201 88 75 193 130 0 0 32 47 10 24 100 100 100 98 330 323 1.391 .719 .674 .682 .714 1.483 80 620 .705 .8 110 4360 25380 116 127 366 377 0 188 64 124 .645 180 117 1.55 .605 -.632 -.726
15 252 183 85 71 167 112 260 180 86 75 175 109 0 0 49 53 10 24 98 95 98 88 279 284 1.491 .671 .623 .645 .637 2.317 80 540 .691 .79 100 4570 25380 117 127 388 398 0 164 64 101 .602 162 98 1.661 .559 -.732 -.839
16 168 103 85 73 83 30 89 87 86 75 4 14 0 0 173 57 9 23 43 43 28 28 113 18 2.767 .361 3.5 1.213 1.011 5.222 80 614 .295 .66 110 4780 25380 116 127 408 419 -50 92 66 27 .324 78 13 3.082 3.142 -1.624 1.652
17 281 183 84 73 197 110 288 177 85 75 204 104 0 0 38 60 9 24 100 95 100 87 307 308 1.791 .558 .51 .525 .527 1.715 80 628 .623 .77 110 4990 25380 116 127 429 440 0 164 66 99 .501 159 93 1.995 .458 -.996 -1.128
18 337 181 86 70 251 111 303 175 86 75 217 105 0 0 122 72 11 24 100 92 100 78 362 322 2.261 .442 .484 .396 .427 2.006 52 340 .432 .78 80 5200 25390 119 127 452 460 0 162 63 100 .397 157 94 2.519 .434 -1.333 -1.203
19 296 206 87 72 209 134 310 210 87 75 223 138 0 0 52 55 10 25 98 97 98 92 343 361 1.56 .641 .619 .611 .657 1.968 120 738 .652 .82 120 5420 25390 117 129 472 484 0 185 65 120 .576 189 124 1.738 .556 -.797 -.848
20 371 195 86 74 285 121 388 186 86 76 302 112 0 0 69 50 10 24 100 100 100 96 406 414 2.355 .425 .371 .413 .401 1.804 80 538 .403 .8 100 5630 25380 117 127 494 504 0 175 66 109 .381 167 101 2.624 .333 -1.392 -1.587

Total number of rows: 6144

Table truncated, full table size 1293 Kbytes.




Supplementary data files not provided
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