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Sample GSM95002 Query DataSets for GSM95002
Status Public on Feb 03, 2006
Title glucose pulse (0.2g/l) on galactose chemostat (t=45min)
Sample type RNA
 
Channel 1
Source name ref- t=0
Organism Saccharomyces cerevisiae
Characteristics ref- t=0
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name t=45min
Organism Saccharomyces cerevisiae
Characteristics t=45min
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Chemostat, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58960.gif
Data processing VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)
 
Submission date Feb 02, 2006
Last update date Jan 19, 2007
Organization Stanford Microarray Database (SMD)
E-mail(s) [email protected]
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 GPL3415
Series (1)
GSE4158 Transcriptional response of steady-state yeast cultures to transient perturbations in carbon source

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 values 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 value of mean Channel 2 (usually 635 nm) intensity (CH2I_MEAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH2BN_MEDIAN Normalized value of median Channel 2 (usually 635 nm) background (CH2B_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
CH2DN_MEAN Normalized value 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 value of median Channel 2 (usually 635 nm) intensity (CH2I_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale
CH2DN_MEDIAN Normalized value 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
LOG_RAT2N_MEAN 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
VALUE same as UNF_VALUE but with flagged values removed
UNF_VALUE 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 LOG_RAT2N_MEAN VALUE UNF_VALUE
1 268 149 96 94 172 55 268 148 97 97 172 54 0 0 59 35 15 26 100 75 100 50 227 226 3.127 .32 .314 .308 .324 1.964 52 372 .297 .327 90 1750 20440 67 76 34 43 0 171 108 63 .368 170 62 2.72 .361 -1.444 -1.47 -1.47
2 529 458 97 98 432 360 530 459 99 100 433 361 0 0 90 98 15 25 100 100 100 100 792 794 1.2 .833 .834 .82 .825 1.208 52 414 .867 .916 90 1930 20430 66 75 52 61 0 527 113 414 .958 528 415 1.044 .958 -.062 -.061 -.061
3 2514 2961 91 88 2423 2873 2219 2525 91 90 2128 2437 0 0 1295 1702 13 21 100 100 100 100 5296 4565 .843 1.186 1.145 1.148 1.157 1.198 52 405 1.223 .974 90 2120 20430 66 75 71 80 0 3404 101 3303 1.363 2903 2802 .734 1.317 .447 .397 .397
4 212 143 88 91 124 52 191 129 89 92 103 38 0 0 93 57 14 24 100 69 98 32 176 141 2.385 .419 .369 .395 .437 1.989 52 332 .493 .625 80 2300 20420 66 74 90 98 0 164 105 60 .482 148 44 2.074 .424 -1.053 -1.237 -1.237
5 263 122 83 87 180 35 251 121 84 91 168 34 0 0 55 28 12 23 100 63 100 32 215 202 5.143 .194 .202 .197 .219 2.096 52 402 .171 .177 90 2480 20420 65 74 107 116 0 140 100 40 .224 139 39 4.474 .233 -2.161 -2.104 -2.104
6 917 748 82 87 835 661 870 677 82 87 788 590 0 0 252 266 12 21 100 100 100 100 1496 1378 1.263 .792 .749 .759 .792 1.248 52 332 .877 .945 80 2670 20410 65 73 127 135 0 860 100 760 .91 778 678 1.099 .861 -.136 -.216 -.216
7 370 153 79 82 291 71 370 151 79 84 291 69 0 0 49 35 12 21 100 90 100 78 362 360 4.099 .244 .237 .228 .249 1.682 52 320 .244 .587 80 2860 20420 66 74 146 154 0 176 94 82 .28 174 79 3.565 .273 -1.834 -1.875 -1.875
8 110 92 80 80 30 12 92 81 81 82 12 1 0 0 59 60 12 22 47 21 28 7 42 13 2.5 .4 .083 .804 1.231 3.778 80 476 1.182 .21 100 3040 20410 64 74 163 173 -50 106 92 14 .46 93 1 2.175 .096 -1.121 -3.384
9 231 133 78 79 153 54 157 98 79 80 79 19 0 0 214 102 10 20 98 47 92 26 207 98 2.833 .353 .241 .302 .351 2.362 80 484 .435 .845 100 3230 20420 65 75 182 192 0 153 91 62 .406 113 22 2.465 .276 -1.301 -1.855 -1.855
10 104 79 79 79 25 0 90 76 80 80 11 -3 0 0 58 23 11 20 47 21 21 6 25 8 null null null 1.025 1.077 3.893 80 498 .201 .029 100 3410 20400 63 73 200 210 -50 91 91 0 null 87 -3 null null null null
11 245 109 81 80 164 29 236 107 81 81 155 27 0 0 54 27 12 19 100 57 100 40 193 182 5.655 .177 .174 .16 .179 2.673 52 394 .164 .194 90 3590 20400 63 72 218 227 0 125 92 33 .203 123 31 4.919 .2 -2.298 -2.32 -2.32
12 260 146 81 79 179 67 242 148 82 81 161 69 0 0 66 44 12 22 100 84 100 62 246 230 2.672 .374 .429 .331 .341 1.998 32 236 .419 .538 70 3790 20410 65 72 239 246 0 168 91 77 .43 170 79 2.324 .493 -1.217 -1.021 -1.021
13 217 137 79 76 138 61 195 134 80 77 116 58 0 0 82 57 11 19 100 75 96 68 199 174 2.262 .442 .5 .434 .457 1.818 32 236 .484 .562 70 3970 20400 64 71 257 264 0 157 87 70 .508 154 67 1.968 .575 -.977 -.799 -.799
14 231 226 80 80 151 146 100 95 81 82 20 15 0 0 358 366 12 21 60 41 43 26 297 35 1.034 .967 .75 1.011 .894 3.085 80 519 1.015 .94 100 4140 20390 62 72 273 283 -50 260 92 168 1.112 109 17 .9 .862 .153 -.214
15 173 95 80 81 93 14 133 87 82 81 53 6 0 0 82 28 14 18 84 40 78 18 107 59 6.643 .151 .113 .224 .226 3.353 32 226 .185 .182 70 4330 20380 62 69 293 300 0 109 93 16 .173 100 7 5.778 .13 -2.531 -2.942 -2.942
16 174 93 82 81 92 12 160 83 83 83 78 2 0 0 62 26 13 21 96 31 84 15 104 80 7.667 .13 .026 .229 .248 3.952 32 170 .089 .028 60 4530 20390 64 70 314 320 0 107 93 14 .15 95 2 6.669 .029 -2.737 -5.084 -5.084
17 112 78 80 79 32 -1 92 73 80 82 12 -6 0 0 58 21 11 21 50 15 35 2 31 6 null null null .552 .418 3.977 80 510 .218 .057 100 4690 20380 61 71 328 338 -50 90 91 -1 null 84 -7 null null null null
18 352 204 81 80 271 124 375 201 81 81 294 121 0 0 129 78 11 21 100 90 100 87 395 415 2.185 .458 .412 .435 .435 1.545 32 231 .456 .753 70 4890 20390 63 70 349 356 0 235 92 143 .526 231 139 1.901 .473 -.927 -1.08 -1.08
19 116 86 81 80 35 6 94 80 81 82 13 0 0 0 76 32 12 20 50 20 30 10 41 13 5.833 .171 null .691 .638 4.362 80 490 .347 .241 100 5050 20380 61 71 364 374 -50 99 92 7 .197 92 0 5.074 null -2.343 null
20 108 78 80 84 28 -6 94 77 81 86 14 -7 0 0 48 20 12 21 52 6 26 2 22 7 null null null .417 .643 4.131 80 494 -1 0 100 5240 20380 61 71 383 393 -50 90 97 -7 null 89 -8 null null null null

Total number of rows: 10752

Table truncated, full table size 2347 Kbytes.




Supplementary data files not provided
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