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Sample GSM90731 Query DataSets for GSM90731
Status Public on Jan 06, 2006
Title 1.5' RNA Decay N-RNaseE (BZ453) in M9 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log Rep. A
Sample type RNA
 
Channel 1
Source name N-RNaseE (BZ453) in M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log
Organism Escherichia coli
Characteristics N-RNaseE (BZ453) in M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name N-RNaseE (BZ453) in M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log 1.5' post rif
Organism Escherichia coli
Characteristics N-RNaseE (BZ453) 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/2001-09/19794.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
1 446 489 122 107 324 382 456 507 125 110 334 400 0 0 116 130 27 35 97 99 94 97 706 734 .848 1.179 1.198 1.157 1.168 1.926 156 918 1.223 .87 150 1610 25300 127 142 69 84 0 427 94 334 1.031 443 350 .97 1.047 .043 .066
2 552 539 127 103 425 436 563 551 135 108 436 448 0 0 171 185 37 39 98 99 95 97 861 884 .975 1.026 1.028 1.017 1.056 1.721 120 632 1.049 .87 130 1820 25310 129 142 91 104 0 471 90 381 .897 482 392 1.115 .898 -.157 -.155
3 790 734 127 99 663 635 855 777 136 103 728 678 0 0 244 257 38 35 99 99 99 96 1298 1406 1.044 .958 .931 .938 1.001 2.109 120 586 .967 .89 120 2030 25300 129 141 113 125 0 642 87 555 .837 679 593 1.194 .814 -.256 -.297
4 719 807 127 105 592 702 667 772 133 107 540 667 0 0 423 483 28 34 94 98 92 97 1294 1207 .843 1.186 1.235 1.241 1.143 2.693 208 921 1.187 .91 160 2240 25280 125 141 132 148 0 705 92 614 1.037 675 583 .965 1.08 .052 .111
5 583 615 129 109 454 506 630 646 132 110 501 537 0 0 169 183 25 32 98 98 95 96 960 1038 .897 1.115 1.072 1.162 1.064 2.299 208 857 1.128 .89 160 2460 25280 125 141 154 170 0 538 95 442 .974 565 469 1.026 .937 -.038 -.094
6 892 852 130 108 762 744 912 871 144 117 782 763 0 0 162 151 81 64 99 100 98 100 1506 1545 1.024 .976 .976 .996 .978 1.544 156 808 .957 .89 150 2650 25270 124 139 173 188 0 745 94 650 .853 761 667 1.172 .853 -.229 -.23
7 465 391 131 104 334 287 462 394 142 112 331 290 0 0 58 88 75 60 100 96 99 96 621 621 1.164 .859 .876 .833 .873 1.606 156 949 .867 .83 150 2870 25270 124 139 195 210 0 342 91 251 .751 344 253 1.331 .766 -.413 -.385
8 819 582 133 105 686 477 731 549 133 106 598 444 0 0 379 310 22 30 100 100 100 100 1163 1042 1.438 .695 .742 .64 .545 2.241 32 236 .713 .72 70 3070 25270 128 135 219 226 0 509 92 417 .608 480 388 1.645 .649 -.718 -.624
9 464 414 142 108 322 306 436 408 198 128 294 300 0 0 279 85 973 124 0 97 0 76 628 594 1.052 .95 1.02 .989 1.022 1.571 156 907 .012 .09 140 3300 25270 125 139 239 253 0 362 94 267 .831 357 262 1.204 .892 -.268 -.165
10 1872 1429 145 115 1727 1314 1539 1448 215 154 1394 1333 0 0 3726 394 970 182 89 98 1 96 3041 2727 1.314 .761 .956 .91 1.001 1.739 156 924 .091 .31 150 3510 25260 123 138 259 274 0 1249 101 1149 .665 1266 1165 1.504 .836 -.588 -.259
11 395 329 135 107 260 222 408 331 162 139 273 224 0 0 99 113 177 216 86 51 15 1 482 497 1.171 .854 .821 .836 .877 2.246 208 960 .901 .78 160 3730 25260 123 139 281 297 0 288 94 194 .746 289 196 1.34 .717 -.422 -.479
12 601 607 130 110 471 497 615 607 132 113 485 497 0 0 113 146 23 33 100 100 100 98 968 982 .948 1.055 1.025 1.02 1.087 1.601 156 865 1.071 .88 150 3930 25260 123 138 301 316 0 531 96 434 .922 531 434 1.084 .896 -.117 -.159
13 303 263 128 107 175 156 198 182 131 111 70 75 0 0 221 181 25 36 71 68 56 52 331 145 1.122 .891 1.071 .994 1 2.731 80 568 .812 .71 110 4150 25260 125 136 325 336 -50 230 94 136 .779 159 66 1.283 .937 -.36 -.095
14 307 295 124 101 183 194 342 316 125 102 218 215 0 0 123 115 72 47 83 85 81 81 377 433 .943 1.06 .986 .919 .992 1.821 156 815 .685 .71 140 4350 25260 124 138 344 358 0 258 88 170 .927 276 188 1.079 .862 -.11 -.214
15 301 202 128 108 173 94 266 201 139 113 138 93 0 0 338 103 69 45 68 66 49 50 267 231 1.84 .543 .674 .644 .69 2.545 156 936 .186 .39 140 4560 25260 124 138 365 379 0 177 94 82 .475 176 81 2.105 .589 -1.074 -.763
16 423 333 133 114 290 219 345 256 138 117 212 142 0 0 204 166 32 36 100 96 100 90 509 354 1.324 .755 .67 .734 .834 2.317 32 236 .709 .68 70 4760 25250 126 133 388 395 0 291 100 191 .66 224 124 1.515 .585 -.599 -.772
17 339 349 131 110 208 239 352 345 134 112 221 235 0 0 93 112 24 32 90 96 90 90 447 456 .87 1.149 1.063 1.173 1.184 2.109 156 919 1.177 .79 140 4970 25250 123 137 406 420 0 305 96 209 1.004 302 205 .996 .93 .006 -.105
18 228 205 132 108 96 97 232 193 134 110 100 85 0 0 50 57 20 31 95 90 92 70 193 185 .99 1.01 .85 .927 .969 2.136 120 769 1.127 .6 130 5190 25250 123 136 428 441 0 179 94 85 .883 169 74 1.132 .743 -.179 -.429
19 250 241 136 111 114 130 239 237 137 114 103 126 0 0 49 56 21 33 99 96 96 87 244 229 .877 1.14 1.223 1.108 1.177 2.014 156 901 1.272 .68 150 5400 25250 122 137 448 463 0 211 97 114 .997 207 110 1.003 1.069 -.005 .097
20 428 400 137 121 291 279 417 402 140 125 280 281 0 0 80 103 27 35 100 98 100 98 570 561 1.043 .959 1.004 .932 1.009 1.628 156 1011 1.083 .75 150 5620 25250 122 137 470 485 0 350 106 244 .838 351 246 1.193 .877 -.255 -.189

Total number of rows: 6144

Table truncated, full table size 1332 Kbytes.




Supplementary data files not provided
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