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Sample GSM73567 Query DataSets for GSM73567
Status Public on Sep 09, 2005
Title 2' 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 2' post rif
Organism Escherichia coli
Characteristics MG1655 (Repaired NCM 3416) in M9 + 0.2% Glucose 2' post rif
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: RNA decay, Rifampicin
Image: http://smd.stanford.edu/MicroArray/gifs/2000-08/8536.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 3655 2141 260 96 3395 2045 null null 270 103 null null null null null null null null 100 100 null null null null 1.66 .602 null null .604 null 80 545 .566 .95 null null null 33 44 51 62 0 2933 132 2801 .825 null null 1.212 null -.277 null
2 507 248 264 98 243 150 null null 284 108 null null null null null null null null 26 35 null null null null 1.62 .617 null null .478 null 80 476 .366 .68 null null null 33 43 71 81 -100 340 134 205 .846 null null 1.183 null -.242 null
3 3886 2329 273 96 3613 2233 null null 289 105 null null null null null null null null 100 100 null null null null 1.618 .618 null null .608 null 80 548 .612 .94 null null null 33 44 89 100 0 3190 132 3059 .847 null null 1.181 null -.24 null
4 2033 1332 278 100 1755 1232 null null 293 117 null null null null null null null null 96 95 null null null null 1.425 .702 null null .677 null 80 490 .587 .82 null null null 34 44 109 119 0 1825 137 1688 .962 null null 1.04 null -.056 null
5 2031 995 259 100 1772 895 null null 284 130 null null null null null null null null 91 83 null null null null 1.98 .505 null null .46 null 12 104 .452 .86 null null null 36 41 129 134 0 1363 137 1226 .692 null null 1.445 null -.531 null
6 2926 1945 282 105 2644 1840 null null 299 128 null null null null null null null null 98 100 null null null null 1.437 .696 null null .822 null 52 332 .535 .84 null null null 33 42 145 154 0 2664 144 2521 .953 null null 1.049 null -.069 null
7 33042 28003 283 100 32759 27903 null null 296 117 null null null null null null null null 100 100 null null null null 1.174 .852 null null .865 null 208 847 .852 .97 null null null 30 46 159 175 0 38360 137 38223 1.167 null null .857 null .223 null
8 17069 12530 277 97 16792 12433 null null 286 110 null null null null null null null null 100 100 null null null null 1.351 .74 null null .754 null 156 601 .722 .97 null null null 31 46 177 192 0 17164 133 17032 1.014 null null .986 null .02 null
9 8076 5434 269 97 7807 5337 null null 288 110 null null null null null null null null 100 100 null null null null 1.463 .684 null null .681 null 156 738 .638 .95 null null null 30 45 193 208 0 7444 133 7311 .936 null null 1.068 null -.095 null
10 5354 3560 260 94 5094 3466 null null 275 107 null null null null null null null null 100 100 null null null null 1.47 .68 null null .689 null 120 609 .627 .94 null null null 31 44 213 226 0 4877 129 4748 .932 null null 1.073 null -.101 null
11 2357 1398 261 89 2096 1309 null null 267 94 null null null null null null null null 100 100 null null null null 1.601 .625 null null .629 null 156 761 .592 .95 null null null 30 45 230 245 0 1915 122 1793 .856 null null 1.169 null -.225 null
12 1998 1279 269 90 1729 1189 null null 278 96 null null null null null null null null 100 100 null null null null 1.454 .688 null null .666 null 120 554 .472 .59 null null null 33 45 250 262 0 1752 123 1629 .942 null null 1.062 null -.086 null
13 283 95 290 100 -7 -5 null null 309 110 null null null null null null null null 5 11 null null null null null null null null .813 null 80 415 .184 .29 null null null 34 44 269 279 -100 130 137 -7 null null null null null null null
14 410 134 279 97 131 37 null null 291 108 null null null null null null null null 38 18 null null null null 3.541 .282 null null .407 null 80 432 .24 .47 null null null 34 44 287 297 -100 184 133 51 .387 null null 2.585 null -1.37 null
15 285 90 273 91 12 -1 null null 285 103 null null null null null null null null 13 1 null null null null null null null null .438 null 80 432 .122 .24 null null null 34 44 305 315 -100 123 125 -1 null null null null null null null
16 276 91 269 94 7 -3 null null 284 108 null null null null null null null null 7 1 null null null null null null null null .306 null 80 417 .078 .08 null null null 34 44 323 333 -100 125 129 -4 null null null null null null null
17 280 96 266 91 14 5 null null 280 102 null null null null null null null null 11 6 null null null null 2.8 .357 null null .5 null 80 432 .073 .15 null null null 34 44 341 351 -100 132 125 7 .489 null null 2.044 null -1.031 null
18 258 102 262 91 -4 11 null null 271 100 null null null null null null null null 1 13 null null null null null null null null .714 null 80 432 .074 .22 null null null 34 44 359 369 -100 140 125 15 null null null null null null null
19 298 113 258 91 40 22 null null 274 99 null null null null null null null null 18 16 null null null null 1.818 .55 null null .495 null 80 412 .06 .1 null null null 34 44 377 387 -100 155 125 30 .753 null null 1.327 null -.408 null
20 231 98 238 89 -7 9 null null 279 115 null null null null null null null null 0 0 null null null null null null null null .387 null 80 460 .068 .11 null null null 34 44 395 405 -100 134 122 12 null null null null null null null

Total number of rows: 7040

Table truncated, full table size 1693 Kbytes.




Supplementary data files not provided
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