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Sample GSM73573 Query DataSets for GSM73573
Status Public on Sep 09, 2005
Title 4' 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 4' post rif
Organism Escherichia coli
Characteristics MG1655 (Repaired NCM 3416) in M9 + 0.2% Glucose 4' post rif
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: RNA decay, Rifampicin
Image: http://smd.stanford.edu/MicroArray/gifs/2000-08/8584.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 1813 807 217 74 1596 733 null null 228 80 null null null null null null null null 100 96 null null null null 2.177 .459 null null .493 null 80 552 .434 .96 null null null 107 118 53 64 0 740 68 672 .421 null null 2.373 null -1.247 null
2 305 136 209 74 96 62 null null 220 79 null null null null null null null null 23 35 null null null null 1.548 .646 null null .653 null 80 481 .333 .74 null null null 107 117 73 83 0 125 68 57 .593 null null 1.688 null -.755 null
3 3656 1733 194 70 3462 1663 null null 199 73 null null null null null null null null 100 100 null null null null 2.082 .48 null null .476 null 52 396 .475 .97 null null null 108 117 92 101 0 1590 64 1526 .441 null null 2.269 null -1.182 null
4 1591 824 184 73 1407 751 null null 202 78 null null null null null null null null 100 98 null null null null 1.874 .534 null null .521 null 52 314 .45 .85 null null null 109 117 111 119 0 756 67 689 .49 null null 2.042 null -1.03 null
5 729 514 210 74 519 440 null null 222 81 null null null null null null null null 36 42 null null null null 1.18 .848 null null .486 null 80 474 .712 .88 null null null 107 117 127 137 0 472 68 404 .778 null null 1.286 null -.363 null
6 3397 1744 235 81 3162 1663 null null 250 87 null null null null null null null null 100 100 null null null null 1.901 .526 null null .533 null 52 266 .498 .94 null null null 108 116 146 154 0 1600 74 1526 .483 null null 2.073 null -1.051 null
7 22762 28799 243 84 22519 28715 null null 571 393 null null null null null null null null 84 76 null null null null .784 1.275 null null 1.134 null 156 847 1.239 .98 null null null 101 116 158 173 -100 26421 77 26344 1.17 null null .855 null .226 null
8 13677 15444 211 85 13466 15359 null null 755 572 null null null null null null null null 84 88 null null null null .877 1.141 null null 1.143 null 120 569 1.077 .96 null null null 106 118 180 192 0 14169 78 14091 1.046 null null .956 null .065 null
9 6872 7163 209 79 6663 7084 null null 278 126 null null null null null null null null 100 100 null null null null .941 1.063 null null 1.059 null 120 650 1.014 .97 null null null 105 118 197 210 0 6572 72 6499 .975 null null 1.025 null -.036 null
10 5856 6100 206 75 5650 6025 null null 226 89 null null null null null null null null 100 100 null null null null .938 1.066 null null 1.067 null 80 528 1.01 .97 null null null 106 117 216 227 0 5596 69 5528 .978 null null 1.022 null -.032 null
11 3099 2723 212 75 2887 2648 null null 226 84 null null null null null null null null 100 100 null null null null 1.09 .917 null null .902 null 80 524 .892 .98 null null null 106 117 234 245 0 2498 69 2429 .841 null null 1.188 null -.249 null
12 2468 2075 225 75 2243 2000 null null 234 81 null null null null null null null null 100 100 null null null null 1.122 .892 null null .885 null 80 525 .86 .97 null null null 106 117 252 263 0 1904 69 1835 .818 null null 1.222 null -.29 null
13 196 70 210 73 -14 -3 null null 216 75 null null null null null null null null 5 8 null null null null null null null null .488 null 80 456 .051 .14 null null null 106 116 271 281 -100 64 67 -3 null null null null null null null
14 267 82 235 78 32 4 null null 258 83 null null null null null null null null 8 7 null null null null 8 .125 null null .354 null 80 466 .119 .57 null null null 106 116 289 299 -100 75 72 4 .115 null null 8.72 null -3.124 null
15 272 80 274 84 -2 -4 null null 297 98 null null null null null null null null 5 3 null null null null null null null null .537 null 80 466 .181 .27 null null null 106 116 307 317 -100 73 77 -4 null null null null null null null
16 305 89 252 77 53 12 null null 258 83 null null null null null null null null 31 5 null null null null 4.417 .226 null null .344 null 80 409 .035 .04 null null null 106 116 325 335 -100 82 71 11 .208 null null 4.814 null -2.267 null
17 215 81 224 75 -9 6 null null 231 79 null null null null null null null null 2 13 null null null null null null null null .588 null 80 439 .117 .14 null null null 106 116 343 353 -100 74 69 6 null null null null null null null
18 281 83 255 78 26 5 null null 297 88 null null null null null null null null 0 6 null null null null 5.2 .192 null null .546 null 80 452 .085 .18 null null null 106 116 361 371 -100 76 72 5 .176 null null 5.668 null -2.503 null
19 309 90 294 87 15 3 null null 352 98 null null null null null null null null 0 7 null null null null 5 .2 null null .371 null 80 466 .163 .35 null null null 106 116 379 389 -100 83 80 3 .183 null null 5.45 null -2.446 null
20 301 88 279 80 22 8 null null 287 86 null null null null null null null null 15 7 null null null null 2.75 .364 null null .5 null 80 448 .105 .25 null null null 106 116 398 408 -100 81 73 7 .334 null null 2.998 null -1.584 null

Total number of rows: 7040

Table truncated, full table size 1684 Kbytes.




Supplementary data files not provided
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