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Sample GSM90736 Query DataSets for GSM90736
Status Public on Jan 06, 2006
Title 4.5' RNA Decay N-RNaseE (BZ453) in M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log
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 4.5' post rif
Organism Escherichia coli
Characteristics N-RNaseE (BZ453) in M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log 4.5' post rif
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: RNA decay, Rifampicin
Image: http://smd.stanford.edu/MicroArray/gifs/2001-09/19799.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
1 334 237 141 107 193 130 252 190 146 110 111 83 0 0 396 225 48 35 98 84 63 58 323 194 1.485 .674 .748 .687 .69 2.266 156 998 .486 .66 150 1730 25640 132 147 81 96 0 237 107 130 .674 190 83 1.483 .748 -.569 -.418
2 249 192 136 107 113 85 247 190 146 111 111 83 0 0 54 47 39 37 90 87 80 57 198 194 1.329 .752 .748 .717 .667 2.379 120 747 .816 .59 130 1940 25660 135 148 103 116 0 192 107 85 .753 190 83 1.328 .748 -.409 -.418
3 344 222 143 108 201 114 340 224 155 115 197 116 0 0 65 51 47 41 98 92 96 73 315 313 1.763 .567 .589 .533 .568 1.724 80 539 .507 .65 110 2150 25660 136 147 125 136 0 222 108 114 .568 224 116 1.761 .589 -.817 -.763
4 523 298 142 106 381 192 502 291 151 111 360 185 0 0 112 76 91 35 98 97 97 94 573 545 1.984 .504 .514 .488 .511 1.77 156 859 .462 .8 150 2380 25640 132 147 146 161 0 298 106 192 .504 291 185 1.982 .514 -.987 -.959
5 277 237 138 103 139 134 281 230 143 108 143 127 0 0 65 62 88 32 83 96 25 87 273 270 1.037 .964 .888 .918 .908 1.936 208 871 .902 .73 160 2580 25640 132 148 166 182 0 237 103 134 .965 230 127 1.036 .889 -.051 -.17
6 368 211 138 108 230 103 367 208 144 113 229 100 0 0 67 55 34 36 98 89 97 71 333 329 2.233 .448 .437 .423 .451 2.161 208 819 .434 .7 160 2790 25640 132 148 187 203 0 211 108 103 .448 208 100 2.231 .437 -1.158 -1.194
7 232 175 143 110 89 65 234 169 148 113 91 59 0 0 76 63 33 33 77 68 66 44 154 150 1.369 .73 .648 .736 .747 2.545 256 1135 .721 .58 180 2990 25640 131 149 206 224 0 175 110 65 .731 169 59 1.368 .649 -.452 -.624
8 187 126 141 106 46 20 159 121 144 116 18 15 0 0 77 41 22 119 42 5 30 0 66 33 2.3 .435 .833 .675 .687 3.714 80 549 .55 .51 110 3220 25620 132 143 232 243 -50 126 106 20 .435 121 15 2.298 .834 -1.2 -.262
9 324 266 140 107 184 159 316 269 144 115 176 162 0 0 63 59 39 96 96 85 95 27 343 338 1.157 .864 .92 .839 .86 1.729 156 897 .941 .69 150 3430 25640 132 147 251 266 0 266 107 159 .865 269 162 1.156 .921 -.209 -.118
10 991 638 148 115 843 523 964 648 158 117 816 533 0 0 184 155 44 34 100 98 100 97 1366 1349 1.612 .62 .653 .6 .644 1.571 156 969 .614 .87 150 3630 25630 131 146 271 286 0 639 115 524 .621 649 534 1.61 .654 -.687 -.613
11 308 223 148 114 160 109 308 224 157 115 160 110 0 0 41 50 38 31 99 92 96 86 269 270 1.468 .681 .688 .686 .713 1.683 156 879 .757 .72 150 3840 25630 131 146 292 307 0 223 114 109 .682 224 110 1.466 .688 -.552 -.539
12 495 293 154 112 341 181 502 302 161 113 348 190 0 0 106 71 35 31 99 96 98 93 522 538 1.884 .531 .546 .532 .554 1.733 156 866 .494 .81 140 4050 25630 132 146 314 328 0 293 112 181 .531 302 190 1.882 .547 -.912 -.872
13 319 197 153 110 166 87 247 158 153 112 94 48 0 0 215 119 22 31 96 73 84 40 253 142 1.908 .524 .511 .462 .471 2.781 52 340 .433 .61 80 4260 25630 135 143 338 346 0 197 110 87 .525 158 48 1.906 .511 -.931 -.968
14 260 209 150 113 110 96 265 205 152 116 115 92 0 0 46 58 25 32 95 87 92 72 206 207 1.146 .873 .8 .771 .852 2.165 208 1015 1.003 .64 160 4480 25640 132 148 356 372 0 209 113 96 .874 205 92 1.145 .801 -.195 -.32
15 244 189 148 113 96 76 242 187 152 115 94 74 0 0 43 47 25 30 98 83 89 62 172 168 1.263 .792 .787 .703 .879 2.501 156 847 .927 .58 150 4690 25640 132 147 377 392 0 189 113 76 .792 187 74 1.262 .788 -.336 -.344
16 765 405 157 112 608 293 457 244 159 115 300 132 0 0 598 329 26 30 100 84 98 67 901 432 2.075 .482 .44 .418 .431 2.943 52 389 .465 .78 90 4880 25620 133 142 399 408 0 405 112 293 .482 244 132 2.073 .44 -1.052 -1.183
17 409 359 152 116 257 243 427 351 155 119 275 235 0 0 121 117 25 31 92 94 92 91 500 510 1.058 .946 .855 .958 .931 1.965 156 929 .951 .82 140 5100 25630 132 146 419 433 0 359 116 243 .946 351 235 1.057 .855 -.079 -.225
18 357 262 152 117 205 145 344 252 155 120 192 135 0 0 99 80 26 31 99 95 96 84 350 327 1.414 .707 .703 .674 .701 2.14 120 721 .707 .75 130 5310 25650 134 147 440 453 0 262 117 145 .708 252 135 1.412 .704 -.498 -.507
19 344 310 151 118 193 192 351 306 154 121 200 188 0 0 57 62 25 31 99 99 96 98 385 388 1.005 .995 .94 1.01 .964 1.785 156 860 1.012 .81 150 5530 25640 132 147 461 476 0 310 118 192 .996 306 188 1.004 .941 -.006 -.088
20 574 451 148 120 426 331 603 462 151 122 455 342 0 0 125 88 25 33 99 100 97 99 757 797 1.287 .777 .752 .811 .757 1.855 156 960 .721 .86 150 5730 25640 132 147 481 496 0 451 120 331 .778 462 342 1.286 .752 -.363 -.41

Total number of rows: 6144

Table truncated, full table size 1319 Kbytes.




Supplementary data files not provided
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