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Sample GSM73575 Query DataSets for GSM73575
Status Public on Sep 09, 2005
Title 6' RNA Decay of MG1655 (Repaired NCM 3416) in M9 + 0.2% Glucose Trial A
Sample type RNA
 
Channel 1
Source name MG1655 (Repaired NCM 3416) in M9 + 0.2% Glucose
Organism Escherichia coli
Characteristics MG1655 (Repaired NCM 3416) in M9 + 0.2% Glucose
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name MG1655 (Repaired NCM 3416) in M9 + 0.2% Glucose 6' post rif
Organism Escherichia coli
Characteristics MG1655 (Repaired NCM 3416) in M9 + 0.2% Glucose 6' post rif
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: RNA decay, Rifampicin
Image: http://smd.stanford.edu/MicroArray/gifs/2000-08/8540.gif
Data processing VALUE is Log (base 2) of the ratio of the mean of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)
 
Submission date Sep 08, 2005
Last update date Sep 22, 2006
Organization Stanford Microarray Database (SMD)
E-mail(s) array@genome.stanford.edu
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 GPL2820
Series (2)
GSE3267 mRNA decay in E. coli
GSE4344 Global analysis of mRNA decay and abundance in Escherichia coli

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 LOG_RAT2N_MEDIANs 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 LOG_RAT2N_MEDIAN of mean Channel 2 (usually 635 nm) intensity (CH2I_MEAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH2BN_MEDIAN Normalized LOG_RAT2N_MEDIAN of median Channel 2 (usually 635 nm) background (CH2B_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
CH2DN_MEAN Normalized LOG_RAT2N_MEDIAN 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 LOG_RAT2N_MEDIAN of median Channel 2 (usually 635 nm) intensity (CH2I_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale
CH2DN_MEDIAN Normalized LOG_RAT2N_MEDIAN 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
VALUE 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
LOG_RAT2N_MEDIAN 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 VALUE LOG_RAT2N_MEDIAN
1 2701 903 287 102 2414 801 null null 313 113 null null null null null null null null 100 93 null null null null 3.014 .332 null null .343 null 80 587 .288 .89 null null null 51 62 54 65 0 1038 117 921 .381 null null 2.622 null -1.391 null
2 587 184 288 103 299 81 null null 320 113 null null null null null null null null 37 53 null null null null 3.691 .271 null null .318 null 32 236 .084 .34 null null null 52 59 76 83 0 211 118 93 .311 null null 3.211 null -1.683 null
3 3401 1124 302 107 3099 1017 null null 319 123 null null null null null null null null 100 100 null null null null 3.047 .328 null null .332 null 80 540 .305 .92 null null null 50 61 91 102 0 1292 123 1169 .377 null null 2.651 null -1.407 null
4 2100 801 322 120 1778 681 null null 365 140 null null null null null null null null 100 100 null null null null 2.611 .383 null null .373 null 52 385 .307 .8 null null null 51 60 109 118 0 921 138 783 .44 null null 2.271 null -1.184 null
5 2836 1615 330 140 2506 1475 null null 383 166 null null null null null null null null 62 68 null null null null 1.699 .589 null null .648 null 32 236 .326 .53 null null null 52 59 129 136 0 1856 161 1695 .677 null null 1.478 null -.564 null
6 3697 1629 390 167 3307 1462 null null 877 420 null null null null null null null null 34 34 null null null null 2.262 .442 null null .385 null 52 278 .375 .77 null null null 52 60 148 156 0 1872 192 1680 .508 null null 1.968 null -.977 null
7 38488 31554 379 140 38109 31414 null null 950 429 null null null null null null null null 98 100 null null null null 1.213 .824 null null .809 null 208 867 .821 .95 null null null 46 62 161 177 0 36269 161 36108 .947 null null 1.055 null -.078 null
8 15330 11499 355 122 14975 11377 null null 425 153 null null null null null null null null 98 100 null null null null 1.316 .76 null null .758 null 208 675 .725 .94 null null null 48 64 179 195 0 13217 140 13077 .873 null null 1.145 null -.196 null
9 8918 6315 320 108 8598 6207 null null 332 115 null null null null null null null null 100 100 null null null null 1.385 .722 null null .73 null 208 823 .692 .92 null null null 47 63 197 213 0 7259 124 7134 .83 null null 1.205 null -.269 null
10 7304 5417 313 111 6991 5306 null null 348 133 null null null null null null null null 100 100 null null null null 1.318 .759 null null .76 null 120 589 .717 .94 null null null 48 61 215 228 0 6226 128 6099 .872 null null 1.146 null -.197 null
11 3355 2208 323 109 3032 2099 null null 358 137 null null null null null null null null 100 100 null null null null 1.444 .692 null null .696 null 120 604 .642 .93 null null null 48 61 234 247 0 2538 125 2413 .796 null null 1.257 null -.33 null
12 2571 1712 339 113 2232 1599 null null 353 121 null null null null null null null null 98 100 null null null null 1.396 .716 null null .731 null 120 542 .644 .92 null null null 49 61 251 263 0 1968 130 1838 .823 null null 1.214 null -.28 null
13 356 113 352 114 4 -1 null null 361 120 null null null null null null null null 10 12 null null null null null null null null .756 null 80 415 .015 .03 null null null 50 60 270 280 -100 130 131 -1 null null null null null null null
14 366 127 362 111 4 16 null null 368 115 null null null null null null null null 10 28 null null null null .25 4 null null .65 null 80 433 .057 .09 null null null 50 60 288 298 -100 146 128 18 4.598 null null .218 null 2.201 null
15 399 126 370 118 29 8 null null 410 129 null null null null null null null null 6 7 null null null null 3.625 .276 null null .32 null 80 466 .045 .1 null null null 49 59 306 316 -100 145 136 9 .317 null null 3.154 null -1.657 null
16 367 124 367 118 null 6 null null 379 125 null null null null null null null null 0 5 null null null null null null null null .474 null 80 396 .037 .05 null null null 49 59 324 334 -100 143 136 7 null null null null null null null
17 379 112 359 118 20 -6 null null 393 127 null null null null null null null null 3 1 null null null null null null null null .793 null 80 412 .063 .14 null null null 49 59 341 351 -100 129 136 -7 null null null null null null null
18 394 120 362 117 32 3 null null 372 122 null null null null null null null null 15 17 null null null null 10.667 .094 null null .634 null 80 424 .045 .11 null null null 49 59 359 369 -100 138 134 3 .108 null null 9.28 null -3.214 null
19 379 123 364 119 15 4 null null 377 122 null null null null null null null null 11 18 null null null null 3.75 .267 null null .595 null 80 421 .025 .07 null null null 49 59 377 387 -100 141 137 5 .307 null null 3.263 null -1.706 null
20 371 138 370 123 1 15 null null 383 127 null null null null null null null null 10 23 null null null null .067 15 null null .632 null 80 409 .011 0 null null null 49 59 395 405 -100 159 141 17 17.241 null null .058 null 4.108 null

Total number of rows: 7040

Table truncated, full table size 1701 Kbytes.




Supplementary data files not provided
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