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Sample GSM90728 Query DataSets for GSM90728
Status Public on Jan 06, 2006
Title 3' RNA Decay N-RNaseE (BZ453) in M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log 1
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 3' post rif
Organism Escherichia coli
Characteristics N-RNaseE (BZ453) in M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log 3' post rif
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: RNA decay, Rifampicin
Image: http://smd.stanford.edu/MicroArray/gifs/2001-09/19882.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
1 287 194 198 141 89 53 289 184 202 144 91 43 0 0 70 74 37 44 75 49 59 28 142 134 1.679 .596 .473 .681 .756 3.152 208 1085 .842 .44 160 1700 25360 128 144 70 86 0 229 167 63 .704 217 51 1.421 .559 -.507 -.84
2 290 210 200 139 90 71 278 199 205 145 78 60 0 0 82 76 38 45 72 57 50 37 161 138 1.268 .789 .769 .882 .992 3.092 208 893 .911 .5 160 1900 25370 129 145 90 106 0 248 164 84 .932 235 71 1.072 .909 -.101 -.137
3 335 227 202 140 133 87 331 224 205 145 129 84 0 0 85 72 35 44 84 69 78 45 220 213 1.529 .654 .651 .641 .651 3.027 156 692 .608 .53 140 2110 25390 132 146 112 126 0 268 165 103 .773 265 99 1.293 .77 -.371 -.378
4 547 394 212 148 335 246 532 382 215 155 320 234 0 0 109 117 35 49 100 95 100 92 581 554 1.362 .734 .731 .698 .753 1.764 156 869 .752 .77 150 2330 25370 129 144 133 148 0 466 175 291 .868 452 277 1.152 .864 -.204 -.21
5 413 301 211 151 202 150 391 298 215 157 180 147 0 0 105 90 35 52 98 87 96 67 352 327 1.347 .743 .817 .754 .756 1.899 156 841 .821 .66 150 2550 25370 129 144 155 170 0 356 178 177 .878 352 174 1.139 .965 -.188 -.051
6 583 371 206 152 377 219 549 352 209 157 343 200 0 0 227 163 32 50 91 86 89 75 596 543 1.721 .581 .583 .584 .581 2.295 208 925 .588 .77 160 2770 25370 129 145 177 193 0 439 180 259 .687 416 236 1.456 .689 -.542 -.537
7 391 274 206 148 185 126 373 273 209 153 167 125 0 0 79 71 34 47 98 86 98 68 311 292 1.468 .681 .749 .66 .701 2.011 156 895 .724 .6 150 2970 25370 129 144 197 212 0 324 175 149 .805 323 148 1.242 .885 -.313 -.177
8 722 518 212 149 510 369 674 542 213 151 462 393 0 0 340 212 39 44 93 93 84 87 879 855 1.382 .724 .851 .802 .538 4.051 32 170 .591 .67 60 3160 25370 134 140 221 227 0 612 176 436 .855 641 465 1.169 1.005 -.226 .008
9 374 260 212 155 162 105 353 256 216 160 141 101 0 0 89 76 37 47 98 76 91 53 267 242 1.543 .648 .716 .65 .697 2.257 156 1001 .746 .54 150 3390 25370 129 144 239 254 0 307 183 124 .766 303 119 1.305 .847 -.384 -.24
10 863 696 212 158 651 538 818 652 215 162 606 494 0 0 240 219 35 46 100 99 100 98 1189 1100 1.21 .826 .815 .801 .805 1.746 156 868 .803 .85 150 3600 25370 129 144 260 275 0 823 187 636 .977 771 584 1.024 .964 -.034 -.054
11 389 281 214 164 175 117 380 276 216 166 166 112 0 0 81 81 32 50 96 76 94 51 292 278 1.496 .669 .675 .581 .647 2.318 156 732 .825 .65 140 3810 25370 130 144 282 296 0 332 194 138 .79 326 132 1.265 .798 -.34 -.326
12 620 452 224 166 396 286 593 444 228 170 369 278 0 0 157 134 38 49 98 96 98 92 682 647 1.385 .722 .753 .715 .755 1.72 156 889 .759 .79 150 4010 25370 129 144 301 316 0 534 196 338 .854 525 329 1.171 .891 -.228 -.167
13 607 495 208 157 399 338 611 477 211 162 403 320 0 0 252 171 29 48 90 96 84 96 737 723 1.18 .847 .794 .873 .75 2.218 32 176 .706 .79 60 4210 25370 134 140 326 332 0 585 186 400 1.001 564 378 .999 .939 .002 -.091
14 575 453 222 175 353 278 579 455 226 177 357 280 0 0 98 104 38 54 99 99 98 94 631 637 1.27 .788 .784 .778 .798 1.679 156 873 .77 .77 150 4440 25380 130 145 344 359 0 535 207 329 .931 538 331 1.074 .927 -.103 -.109
15 501 391 229 173 272 218 501 380 236 178 272 207 0 0 82 85 42 57 98 97 95 90 490 479 1.248 .801 .761 .801 .76 1.811 120 690 .777 .68 130 4630 25380 131 144 364 377 0 462 204 258 .947 449 245 1.056 .9 -.078 -.153
16 1080 695 233 178 847 517 1014 736 238 181 781 558 0 0 343 277 46 62 100 93 100 87 1364 1339 1.638 .61 .714 .567 .618 1.96 32 230 .689 .75 70 4840 25350 131 138 388 395 0 822 210 611 .722 870 660 1.386 .845 -.471 -.244
17 662 536 247 185 415 351 693 562 251 189 446 377 0 0 192 191 46 57 90 89 89 84 766 823 1.182 .846 .845 .837 .92 2.106 156 958 .898 .81 140 5050 25360 129 143 406 420 0 634 219 415 1 664 446 1 .999 0 -.001
18 932 747 244 187 688 560 928 731 249 190 684 544 0 0 241 209 47 57 100 100 100 98 1248 1228 1.229 .814 .795 .801 .871 1.671 80 572 .779 .84 110 5260 25360 130 141 428 439 0 883 221 662 .962 864 643 1.039 .94 -.056 -.089
19 605 468 248 185 357 283 590 457 288 206 342 272 0 0 121 128 499 246 10 60 0 6 640 614 1.261 .793 .795 .752 .799 1.798 156 881 .793 .74 150 5470 25370 129 144 447 462 0 553 219 335 .937 540 322 1.067 .94 -.094 -.089
20 1027 877 242 179 785 698 1039 880 278 195 797 701 0 0 172 216 477 219 96 95 16 91 1483 1498 1.125 .889 .88 .856 .915 1.665 156 963 .917 .87 150 5680 25370 129 144 468 483 0 1037 212 825 1.051 1040 829 .951 1.04 .072 .056

Total number of rows: 6144

Table truncated, full table size 1341 Kbytes.




Supplementary data files not provided
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