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Sample GSM73576 Query DataSets for GSM73576
Status Public on Sep 09, 2005
Title 8' RNA Decay of MG1655 (Repaired NCM 3416) in M9 + 0.2% Glucose Trial B
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 8' post rif
Organism Escherichia coli
Characteristics MG1655 (Repaired NCM 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/2000-08/8589.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 2620 872 163 72 2457 800 null null 177 80 null null null null null null null null 98 83 null null null null 3.071 .326 null null .326 null 80 506 .314 .99 null null null 120 130 53 63 0 733 61 672 .274 null null 3.655 null -1.87 null
2 600 332 153 68 447 264 null null 161 73 null null null null null null null null 40 45 null null null null 1.693 .591 null null .587 null 80 474 .532 .93 null null null 120 130 72 82 0 279 57 222 .496 null null 2.015 null -1.011 null
3 3471 1204 166 71 3305 1133 null null 171 74 null null null null null null null null 100 100 null null null null 2.917 .343 null null .345 null 80 474 .332 .98 null null null 120 130 90 100 0 1012 60 952 .288 null null 3.471 null -1.795 null
4 1686 688 181 79 1505 609 null null 192 83 null null null null null null null null 100 100 null null null null 2.471 .405 null null .41 null 52 322 .38 .97 null null null 121 129 109 117 0 578 66 512 .34 null null 2.941 null -1.556 null
5 713 425 171 73 542 352 null null 178 78 null null null null null null null null 35 47 null null null null 1.54 .649 null null .748 null 80 474 .604 .97 null null null 120 130 126 136 0 357 61 296 .546 null null 1.832 null -.874 null
6 2189 847 189 79 2000 768 null null 245 148 null null null null null null null null 86 73 null null null null 2.604 .384 null null .385 null 52 320 .366 .96 null null null 121 129 146 154 0 712 66 645 .323 null null 3.099 null -1.632 null
7 41483 57370 247 115 41236 57255 null null 860 799 null null null null null null null null 100 100 null null null null .72 1.388 null null 1.396 null 80 462 1.386 .99 null null null 120 130 163 173 0 48210 97 48113 1.167 null null .857 null .223 null
8 17289 21775 248 139 17041 21636 null null 875 817 null null null null null null null null 100 100 null null null null .788 1.27 null null 1.269 null 80 437 1.277 .99 null null null 121 131 180 190 0 18298 117 18182 1.067 null null .937 null .093 null
9 6672 7875 195 82 6477 7793 null null 290 197 null null null null null null null null 100 96 null null null null .831 1.203 null null 1.195 null 120 679 1.191 .99 null null null 117 130 197 210 0 6618 69 6549 1.011 null null .989 null .016 null
10 5765 6643 190 76 5575 6567 null null 228 117 null null null null null null null null 99 100 null null null null .849 1.178 null null 1.165 null 120 600 1.158 .99 null null null 118 130 216 228 0 5582 64 5518 .99 null null 1.01 null -.015 null
11 3323 3280 186 79 3137 3201 null null 219 108 null null null null null null null null 100 100 null null null null .98 1.02 null null 1.014 null 80 485 1.007 .99 null null null 118 129 234 245 0 2756 66 2690 .857 null null 1.166 null -.222 null
12 2031 1937 181 75 1850 1862 null null 207 95 null null null null null null null null 98 99 null null null null .994 1.006 null null 1.003 null 120 572 .996 .98 null null null 119 131 252 264 0 1628 63 1565 .846 null null 1.182 null -.242 null
13 208 83 184 73 24 10 null null 193 77 null null null null null null null null 15 17 null null null null 2.4 .417 null null .642 null 80 425 .263 .56 null null null 119 129 270 280 -100 70 61 8 .35 null null 2.856 null -1.514 null
14 195 80 186 73 9 7 null null 193 76 null null null null null null null null 21 17 null null null null 1.286 .778 null null .565 null 80 456 .116 .21 null null null 119 129 288 298 -100 67 61 6 .654 null null 1.53 null -.614 null
15 179 70 187 75 -8 -5 null null 202 79 null null null null null null null null 5 1 null null null null null null null null .569 null 80 456 .154 .38 null null null 119 129 306 316 -100 59 63 -4 null null null null null null null
16 195 76 195 78 null -2 null null 252 122 null null null null null null null null 0 0 null null null null null null null null .453 null 80 439 1.037 .97 null null null 119 129 324 334 -100 64 66 -2 null null null null null null null
17 199 78 189 74 10 4 null null 200 79 null null null null null null null null 6 7 null null null null 2.5 .4 null null .537 null 80 442 .185 .34 null null null 119 129 342 352 -100 66 62 3 .336 null null 2.975 null -1.573 null
18 206 82 193 73 13 9 null null 220 80 null null null null null null null null 1 8 null null null null 1.444 .692 null null .619 null 80 440 .255 .51 null null null 119 129 360 370 -100 69 61 8 .582 null null 1.719 null -.781 null
19 176 72 183 72 -7 null null null 262 82 null null null null null null null null 0 5 null null null null null null null null .625 null 80 456 .156 .62 null null null 119 129 378 388 -100 61 61 0 null null null null null null null
20 182 69 167 72 15 -3 null null 183 76 null null null null null null null null 6 5 null null null null null null null null .589 null 80 445 .138 .35 null null null 119 129 396 406 -100 58 61 -3 null null null null null null null

Total number of rows: 7040

Table truncated, full table size 1674 Kbytes.




Supplementary data files not provided
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