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Sample GSM90742 Query DataSets for GSM90742
Status Public on Jan 06, 2006
Title 3' RNA Decay of WT (N3433) in M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log 2
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 3.0' post rif
Organism Escherichia coli
Characteristics WT (N3433) in M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log 3.0' post rif
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: RNA decay, Rifampicin
Image: http://smd.stanford.edu/MicroArray/gifs/2001-08/19616.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
1 222 204 66 61 156 143 231 199 68 64 165 138 0 0 39 52 20 24 100 100 98 97 299 303 1.091 .917 .836 .884 .895 1.61 80 631 .893 .84 110 1670 25430 121 132 97 108 0 161 48 113 .722 157 109 1.385 .659 -.47 -.603
2 214 161 66 62 148 99 223 158 67 66 157 96 0 0 38 53 12 25 100 95 100 80 247 253 1.495 .669 .611 .569 .65 2.232 80 539 .735 .74 100 1890 25430 122 132 120 130 0 127 49 78 .527 124 76 1.899 .481 -.925 -1.054
3 280 173 67 65 213 108 287 169 82 81 220 104 0 0 39 40 146 110 96 42 0 0 321 324 1.972 .507 .473 .483 .476 1.599 52 412 .323 .47 90 2110 25420 121 130 142 151 0 136 51 85 .399 133 82 2.505 .372 -1.325 -1.426
4 378 198 67 60 311 138 407 198 68 62 340 138 0 0 94 58 7 23 100 97 100 92 449 478 2.254 .444 .406 .425 .393 1.796 80 503 .416 .83 100 2330 25430 122 132 164 174 0 156 47 109 .349 156 109 2.862 .32 -1.517 -1.646
5 247 207 69 62 178 145 270 211 69 66 201 149 0 0 70 61 9 31 95 95 93 91 323 350 1.228 .815 .741 .836 .803 2.02 120 670 .799 .84 120 2520 25430 121 133 182 194 0 163 49 114 .641 166 117 1.559 .584 -.641 -.777
6 473 206 70 62 403 144 471 205 73 65 401 143 0 0 42 59 25 24 100 96 100 96 547 544 2.799 .357 .357 .34 .37 1.501 80 596 .369 .83 110 2730 25430 121 132 203 214 0 162 49 113 .281 161 113 3.554 .281 -1.83 -1.832
7 249 210 73 64 176 146 258 207 75 67 185 143 0 0 47 64 20 24 98 97 96 93 322 328 1.205 .83 .773 .788 .812 2.245 120 722 .884 .81 120 2950 25430 121 133 225 237 0 165 50 115 .653 163 113 1.531 .609 -.614 -.716
8 322 156 77 67 245 89 305 145 78 69 228 78 0 0 124 55 10 23 100 90 100 78 334 306 2.753 .363 .342 .334 .348 2.366 32 170 .305 .67 60 3160 25430 124 130 249 255 0 123 53 70 .286 114 61 3.496 .269 -1.806 -1.892
9 221 186 74 67 147 119 232 181 75 69 158 114 0 0 40 49 9 24 98 100 98 92 266 272 1.235 .81 .722 .795 .799 1.805 80 616 .867 .8 110 3360 25430 121 132 266 277 0 146 53 94 .637 143 90 1.569 .568 -.65 -.816
10 733 511 77 68 656 443 757 506 80 72 680 438 0 0 131 94 27 31 100 100 100 100 1099 1118 1.481 .675 .644 .689 .67 1.481 80 607 .638 .91 110 3560 25430 121 132 286 297 0 402 54 349 .532 398 345 1.881 .507 -.911 -.979
11 229 180 80 68 149 112 237 180 82 72 157 112 0 0 40 59 25 29 96 90 94 82 261 269 1.33 .752 .713 .678 .739 2.016 120 692 .865 .77 120 3780 25430 121 133 308 320 0 142 54 88 .592 142 88 1.69 .562 -.757 -.832
12 282 179 81 70 201 109 283 174 86 73 202 104 0 0 36 49 30 29 100 100 98 85 310 306 1.844 .542 .515 .5 .525 1.681 80 588 .593 .78 110 3980 25430 121 132 328 339 0 141 55 86 .427 137 82 2.342 .405 -1.228 -1.303
13 296 166 80 71 216 95 286 170 82 74 206 99 0 0 93 69 13 24 100 81 100 68 311 305 2.274 .44 .481 .42 .423 2.177 32 170 .477 .73 60 4210 25440 125 131 354 360 0 131 56 75 .346 134 78 2.888 .378 -1.53 -1.402
14 233 191 82 70 151 121 244 194 83 72 162 124 0 0 46 57 10 25 100 95 96 88 272 286 1.248 .801 .765 .767 .822 2.39 120 718 .85 .76 120 4420 25440 122 134 372 384 0 150 55 95 .631 153 98 1.585 .603 -.664 -.73
15 215 189 84 74 131 115 216 183 85 75 132 109 0 0 39 41 12 25 100 100 100 98 246 241 1.139 .878 .826 .865 .818 1.621 80 614 .919 .75 110 4630 25440 122 133 393 404 0 149 58 91 .691 144 86 1.447 .65 -.533 -.621
16 196 151 85 73 111 78 181 143 86 75 96 70 0 0 101 64 11 23 75 84 75 59 189 166 1.423 .703 .729 .775 .593 3.999 32 170 .605 .71 60 4830 25440 125 131 416 422 0 119 57 61 .553 113 55 1.807 .574 -.854 -.801
17 245 218 83 74 162 144 249 219 84 77 166 145 0 0 37 53 11 25 100 98 97 97 306 311 1.125 .889 .873 .858 .854 1.658 80 645 .959 .84 110 5040 25440 122 133 434 445 0 172 58 113 .7 172 114 1.429 .688 -.515 -.54
18 248 191 85 74 163 117 252 183 85 76 167 109 0 0 70 68 10 25 100 92 100 83 280 276 1.393 .718 .653 .62 .681 2.334 80 528 .757 .77 100 5270 25440 123 133 458 468 0 150 58 92 .565 144 86 1.769 .514 -.823 -.96
19 251 213 88 74 163 139 256 210 90 78 168 136 0 0 38 59 20 26 99 95 97 95 302 304 1.173 .853 .81 .78 .798 1.79 120 696 .917 .81 120 5470 25440 122 134 477 489 0 168 58 109 .671 165 107 1.489 .637 -.575 -.65
20 383 328 90 77 293 251 394 325 94 80 304 248 0 0 47 77 23 26 100 100 100 100 544 552 1.167 .857 .816 .83 .809 1.386 80 618 .832 .85 110 5680 25440 122 133 498 509 0 258 61 198 .675 256 195 1.483 .642 -.568 -.639

Total number of rows: 6144

Table truncated, full table size 1304 Kbytes.




Supplementary data files not provided
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