NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM73578 Query DataSets for GSM73578
Status Public on Sep 09, 2005
Title 8' RNA Decay of MG1655 (Repaired MCM 3416) in M9 + 0.2% Glucose Trial A
Sample type RNA
 
Channel 1
Source name MG1655 (Repaired MCM 3416) in M9 + 0.2% Glucose
Organism Escherichia coli
Characteristics MG1655 (Repaired MCM 3416) in M9 + 0.2% Glucose
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name MG1655 (Repaired MCM 3416) in M9 + 0.2% Glucose 8' post rif
Organism Escherichia coli
Characteristics MG1655 (Repaired MCM 3416) in M9 + 0.2% Glucose 8' post rif
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: RNA decay, Rifampicin
Image: http://smd.stanford.edu/MicroArray/gifs/2000-08/8542.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 5916 2364 361 142 5555 2222 null null 388 157 null null null null null null null null 97 96 null null null null 2.5 .4 null null .414 null 80 516 .36 .93 null null null 31 41 72 82 0 2149 129 2020 .364 null null 2.75 null -1.459 null
2 3631 2028 352 160 3279 1868 null null 410 179 null null null null null null null null 83 100 null null null null 1.755 .57 null null .346 null 12 104 .494 .68 null null null 34 39 93 98 0 1844 145 1698 .518 null null 1.931 null -.949 null
3 6394 2372 372 157 6022 2215 null null 396 170 null null null null null null null null 100 100 null null null null 2.719 .368 null null .376 null 80 557 .369 .96 null null null 30 41 108 119 0 2156 143 2014 .334 null null 2.991 null -1.58 null
4 3808 1552 361 155 3447 1397 null null 385 161 null null null null null null null null 97 100 null null null null 2.467 .405 null null .438 null 80 437 .341 .86 null null null 31 41 128 138 0 1411 141 1270 .368 null null 2.714 null -1.441 null
5 1273 987 346 150 927 837 null null 362 169 null null null null null null null null 43 31 null null null null 1.108 .903 null null .739 null 80 437 .807 .88 null null null 30 40 144 154 -100 897 136 761 .821 null null 1.218 null -.285 null
6 5685 2146 379 168 5306 1978 null null 438 217 null null null null null null null null 100 100 null null null null 2.683 .373 null null .369 null 52 336 .345 .93 null null null 31 40 162 171 0 1951 153 1798 .339 null null 2.951 null -1.561 null
7 37314 40133 379 155 36935 39978 null null 429 191 null null null null null null null null 94 100 null null null null .924 1.082 null null 1.047 null 208 884 1.017 .96 null null null 27 43 178 194 -100 36485 141 36344 .984 null null 1.016 null -.023 null
8 19015 22878 348 143 18667 22735 null null 552 337 null null null null null null null null 98 98 null null null null .821 1.218 null null 1.197 null 156 717 1.132 .94 null null null 29 44 197 212 0 20798 130 20668 1.107 null null .903 null .147 null
9 11409 13109 319 144 11090 12965 null null 658 479 null null null null null null null null 100 100 null null null null .855 1.169 null null 1.158 null 80 423 1.037 .92 null null null 31 41 217 227 -100 11917 131 11786 1.063 null null .941 null .088 null
10 7876 8544 312 124 7564 8420 null null 339 151 null null null null null null null null 100 100 null null null null .898 1.113 null null 1.135 null 120 675 1.047 .94 null null null 29 42 234 247 0 7767 113 7655 1.012 null null .988 null .017 null
11 3672 3574 333 126 3339 3448 null null 346 131 null null null null null null null null 100 100 null null null null .968 1.033 null null 1.073 null 156 768 1.009 .96 null null null 28 43 251 266 0 3249 115 3135 .939 null null 1.065 null -.091 null
12 3047 2875 351 130 2696 2745 null null 364 136 null null null null null null null null 100 100 null null null null .982 1.018 null null 1.052 null 120 537 .972 .94 null null null 31 43 270 282 0 2614 118 2495 .926 null null 1.08 null -.112 null
13 426 140 370 137 56 3 null null 385 140 null null null null null null null null 8 8 null null null null 18.667 .054 null null .437 null 80 422 .049 .17 null null null 31 41 289 299 -100 127 125 3 .049 null null 20.533 null -4.36 null
14 396 141 373 135 23 6 null null 387 139 null null null null null null null null 5 16 null null null null 3.833 .261 null null .655 null 80 452 .068 .14 null null null 31 41 307 317 -100 128 123 5 .237 null null 4.217 null -2.076 null
15 681 244 396 144 285 100 null null 430 156 null null null null null null null null 26 36 null null null null 2.85 .351 null null .375 null 80 456 .043 .13 null null null 31 41 325 335 -100 222 131 91 .319 null null 3.135 null -1.648 null
16 397 135 387 145 10 -10 null null 410 155 null null null null null null null null 5 8 null null null null null null null null .827 null 80 419 .007 0 null null null 32 42 343 353 -100 123 132 -9 null null null null null null null
17 471 169 393 144 78 25 null null 421 154 null null null null null null null null 11 21 null null null null 3.12 .321 null null .98 null 80 472 .101 .25 null null null 32 42 361 371 -100 154 131 23 .291 null null 3.432 null -1.779 null
18 402 140 400 144 2 -4 null null 419 156 null null null null null null null null 6 3 null null null null null null null null .592 null 80 448 .083 .2 null null null 32 42 379 389 -100 127 131 -4 null null null null null null null
19 411 146 385 137 26 9 null null 397 146 null null null null null null null null 11 17 null null null null 2.889 .346 null null .638 null 80 429 .027 .07 null null null 32 42 397 407 -100 133 125 8 .315 null null 3.178 null -1.668 null
20 390 129 362 129 28 null null null 384 142 null null null null null null null null 8 7 null null null null null null null null .532 null 80 421 -.002 0 null null null 32 42 415 425 -100 117 117 0 null null null null null null null

Total number of rows: 7040

Table truncated, full table size 1699 Kbytes.




Supplementary data files not provided
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap