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Sample GSM73574 Query DataSets for GSM73574
Status Public on Sep 09, 2005
Title 6' 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 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/2000-08/8586.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 2738 1082 241 87 2497 995 null null 249 94 null null null null null null null null 100 100 null null null null 2.51 .398 null null .408 null 52 318 .38 .94 null null null 89 97 57 65 0 949 76 873 .35 null null 2.861 null -1.516 null
2 410 186 254 89 156 97 null null 1157 548 null null null null null null null null 0 0 null null null null 1.608 .622 null null .451 null 52 303 .338 .96 null null null 90 98 75 83 -100 163 78 85 .545 null null 1.833 null -.875 null
3 2893 1226 259 87 2634 1139 null null 267 95 null null null null null null null null 100 100 null null null null 2.313 .432 null null .427 null 80 485 .405 .96 null null null 87 97 92 102 0 1075 76 999 .379 null null 2.636 null -1.399 null
4 2746 1176 268 89 2478 1087 null null 290 101 null null null null null null null null 100 100 null null null null 2.28 .439 null null .457 null 52 315 .379 .93 null null null 88 96 111 119 0 1032 78 954 .385 null null 2.599 null -1.378 null
5 379 148 262 87 117 61 null null 274 95 null null null null null null null null 26 35 null null null null 1.918 .521 null null .636 null 80 482 .323 .75 null null null 87 97 128 138 0 130 76 54 .457 null null 2.187 null -1.129 null
6 2672 1046 267 92 2405 954 null null 432 256 null null null null null null null null 78 56 null null null null 2.521 .397 null null .392 null 80 518 .47 .84 null null null 84 95 147 158 0 918 81 837 .348 null null 2.874 null -1.523 null
7 39630 49975 313 116 39317 49859 null null 716 554 null null null null null null null null 100 100 null null null null .789 1.268 null null 1.29 null 120 549 1.222 .97 null null null 86 98 164 176 0 43838 102 43736 1.112 null null .899 null .154 null
8 17102 19908 316 121 16786 19787 null null 647 433 null null null null null null null null 99 99 null null null null .848 1.179 null null 1.187 null 120 552 1.131 .96 null null null 85 98 180 193 0 17463 106 17357 1.034 null null .967 null .048 null
9 7785 8546 309 119 7476 8427 null null 459 229 null null null null null null null null 95 99 null null null null .887 1.127 null null 1.148 null 120 568 1.038 .94 null null null 84 97 197 210 0 7496 104 7392 .989 null null 1.011 null -.016 null
10 6124 6537 281 91 5843 6446 null null 327 133 null null null null null null null null 100 100 null null null null .906 1.103 null null 1.107 null 120 593 1.03 .95 null null null 85 97 216 228 0 5734 80 5654 .968 null null 1.033 null -.047 null
11 3404 3246 273 90 3131 3156 null null 307 130 null null null null null null null null 100 100 null null null null .992 1.008 null null .99 null 80 471 .844 .92 null null null 85 96 233 244 0 2847 79 2768 .884 null null 1.131 null -.178 null
12 2506 2182 266 90 2240 2092 null null 294 113 null null null null null null null null 99 98 null null null null 1.071 .934 null null .925 null 120 607 .912 .96 null null null 86 98 251 263 0 1914 79 1835 .819 null null 1.221 null -.288 null
13 507 192 272 88 235 104 null null 279 90 null null null null null null null null 86 88 null null null null 2.26 .443 null null .385 null 52 317 .277 .57 null null null 81 90 270 279 0 168 77 91 .388 null null 2.576 null -1.365 null
14 289 87 286 88 3 -1 null null 291 91 null null null null null null null null 12 11 null null null null null null null null .6 null 80 471 .023 .04 null null null 86 96 287 297 -100 76 77 -1 null null null null null null null
15 285 92 283 88 2 4 null null 301 96 null null null null null null null null 2 10 null null null null .5 2 null null .554 null 80 464 0 0 null null null 86 96 305 315 -100 81 77 4 1.754 null null .57 null .811 null
16 285 87 273 85 12 2 null null 292 95 null null null null null null null null 7 5 null null null null 6 .167 null null .588 null 80 446 .151 .43 null null null 86 96 323 333 -100 76 75 2 .146 null null 6.84 null -2.774 null
17 280 89 270 86 10 3 null null 289 97 null null null null null null null null 3 8 null null null null 3.333 .3 null null .408 null 80 447 .197 .59 null null null 86 96 341 351 -100 78 75 3 .263 null null 3.8 null -1.926 null
18 256 86 266 86 -10 null null null 301 93 null null null null null null null null 0 7 null null null null null null null null .435 null 80 452 .044 .08 null null null 86 96 359 369 -100 75 75 0 null null null null null null null
19 297 94 281 89 16 5 null null 336 98 null null null null null null null null 5 15 null null null null 3.2 .313 null null .534 null 80 452 .091 .3 null null null 86 96 376 386 -100 82 78 4 .274 null null 3.648 null -1.867 null
20 305 94 271 87 34 7 null null 302 102 null null null null null null null null 2 5 null null null null 4.857 .206 null null .412 null 80 464 .026 .04 null null null 86 96 394 404 -100 82 76 6 .181 null null 5.537 null -2.469 null

Total number of rows: 7040

Table truncated, full table size 1680 Kbytes.




Supplementary data files not provided
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