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Sample GSM90738 Query DataSets for GSM90738
Status Public on Jan 06, 2006
Title 6' RNA Decay of RhlB- (SU02) in M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log Replicate A1
Sample type RNA
 
Channel 1
Source name RhlB- (SU02) in M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log
Organism Escherichia coli
Characteristics RhlB- (SU02) in M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name RhlB- (SU02) in M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log 6' post rif
Organism Escherichia coli
Characteristics RhlB- (SU02) 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/2001-08/19341.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
1 374 274 114 96 260 178 395 266 120 100 281 170 0 0 91 78 89 35 90 96 87 90 438 451 1.461 .685 .605 .676 .63 2.255 120 718 .576 .72 120 1700 25390 35 47 57 69 0 242 85 157 .604 235 150 1.656 .533 -.728 -.906
2 432 251 113 98 319 153 441 247 120 104 328 149 0 0 75 70 84 48 100 91 93 82 472 477 2.085 .48 .454 .429 .473 2.041 80 532 .467 .74 100 1910 25390 36 46 79 89 0 221 86 135 .423 218 131 2.364 .401 -1.241 -1.32
3 497 279 115 102 382 177 551 287 135 109 436 185 0 0 151 84 175 52 82 92 68 76 559 621 2.158 .463 .424 .445 .446 1.796 80 546 .453 .84 100 2130 25390 36 46 101 111 0 246 90 156 .409 253 163 2.447 .374 -1.291 -1.418
4 870 297 119 105 751 192 909 295 135 110 790 190 0 0 170 89 164 41 100 95 97 88 943 980 3.911 .256 .241 .236 .262 1.812 80 522 .238 .79 100 2350 25390 36 46 123 133 0 262 93 169 .225 260 168 4.436 .212 -2.149 -2.237
5 449 313 127 108 322 205 476 334 138 112 349 226 0 0 95 88 134 37 93 95 80 90 527 575 1.571 .637 .648 .602 .645 2.072 120 684 .345 .62 120 2550 25390 35 47 142 154 0 276 95 181 .561 295 199 1.781 .571 -.833 -.808
6 873 303 135 111 738 192 886 299 148 116 751 188 0 0 89 62 65 43 100 100 100 96 930 939 3.844 .26 .25 .248 .258 1.444 80 574 .235 .82 110 2750 25390 35 46 162 173 0 267 98 169 .229 264 166 4.359 .221 -2.124 -2.18
7 515 351 134 112 381 239 537 351 142 118 403 239 0 0 90 79 54 41 98 99 97 97 620 642 1.594 .627 .593 .63 .64 1.965 120 714 .611 .83 120 2970 25390 35 47 184 196 0 310 99 211 .553 310 211 1.808 .523 -.854 -.935
8 343 178 136 110 207 68 170 144 138 115 34 34 0 0 325 99 25 35 53 47 38 36 275 68 3.044 .329 1 .523 .508 3.845 80 572 .254 .68 110 3180 25400 36 47 205 216 -50 157 97 60 .29 127 30 3.452 .882 -1.787 -.181
9 385 273 141 113 244 160 432 280 149 117 291 167 0 0 126 89 43 39 88 90 82 79 404 458 1.525 .656 .574 .691 .624 2.497 120 683 .617 .77 120 3390 25400 36 48 226 238 0 241 100 141 .578 247 147 1.729 .506 -.79 -.983
10 1186 433 169 124 1017 309 1263 435 173 127 1094 311 0 0 289 113 49 41 99 99 98 97 1326 1405 3.291 .304 .284 .311 .292 1.862 120 696 .284 .87 120 3600 25390 35 47 247 259 0 382 109 272 .268 384 274 3.732 .251 -1.9 -1.996
11 469 310 167 126 302 184 476 295 170 128 309 169 0 0 56 79 35 38 100 100 98 94 486 478 1.641 .609 .547 .568 .577 1.639 120 672 .663 .8 120 3810 25390 35 47 268 280 0 273 111 162 .537 260 149 1.861 .482 -.896 -1.052
12 585 315 145 118 440 197 600 312 149 121 455 194 0 0 80 69 29 35 100 99 99 95 637 649 2.234 .448 .426 .425 .44 1.631 120 700 .435 .83 120 4020 25390 35 47 289 301 0 278 104 174 .395 275 171 2.533 .376 -1.341 -1.411
13 687 280 139 115 548 165 628 261 142 115 489 146 0 0 329 119 24 36 100 87 96 78 713 635 3.321 .301 .299 .331 .372 2.19 32 160 .289 .79 60 4220 25380 37 43 312 318 0 247 101 146 .266 230 129 3.766 .263 -1.913 -1.925
14 470 378 158 131 312 247 477 376 176 139 319 245 0 0 52 84 114 54 100 98 93 95 559 564 1.263 .792 .768 .746 .774 1.609 80 614 .532 .6 110 4440 25380 34 45 331 342 0 333 116 218 .698 332 216 1.432 .677 -.518 -.562
15 483 396 173 141 310 255 474 404 186 144 301 263 0 0 67 110 111 47 100 97 92 92 565 564 1.216 .823 .874 .743 .78 1.776 80 602 .783 .7 110 4650 25380 34 45 352 363 0 349 124 225 .725 356 232 1.379 .771 -.463 -.376
16 367 245 150 129 217 116 186 159 155 132 36 30 0 0 372 199 39 39 45 45 36 30 333 66 1.871 .535 .833 .795 .655 4.488 80 607 .495 .8 110 4860 25400 36 47 373 384 -50 216 114 102 .471 140 26 2.121 .735 -1.085 -.444
17 701 509 154 133 547 376 702 512 159 137 548 379 0 0 77 90 34 41 100 100 100 100 923 927 1.455 .687 .692 .674 .683 1.301 80 621 .668 .89 110 5070 25390 35 46 394 405 0 449 117 332 .606 451 334 1.65 .61 -.722 -.713
18 686 423 165 138 521 285 627 366 168 142 462 228 0 0 336 171 32 42 97 97 95 95 806 690 1.828 .547 .494 .591 .537 2.046 80 532 .487 .83 100 5280 25390 36 46 416 426 0 373 122 251 .482 323 201 2.073 .435 -1.052 -1.2
19 500 400 169 138 331 262 509 406 176 143 340 268 0 0 59 87 83 43 99 100 97 97 593 608 1.263 .792 .788 .76 .783 1.549 120 804 .84 .83 130 5490 25390 34 47 435 448 0 353 122 231 .698 358 236 1.433 .695 -.519 -.525
20 963 493 171 139 792 354 984 491 187 145 813 352 0 0 128 83 203 51 100 100 97 100 1146 1165 2.237 .447 .433 .439 .43 1.409 80 610 .431 .87 110 5700 25390 35 46 457 468 0 435 123 312 .394 433 310 2.537 .382 -1.343 -1.389

Total number of rows: 6144

Table truncated, full table size 1333 Kbytes.




Supplementary data files not provided
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