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Sample GSM72044 Query DataSets for GSM72044
Status Public on Aug 26, 2005
Title batch 02X25 5
Sample type RNA
 
Channel 1
Source name "Chemostat: D=.25, [D]=2.4"
Organism Saccharomyces cerevisiae
Characteristics "Chemostat: D=.25, [D]=2.4"
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name "batch, hour 10"
Organism Saccharomyces cerevisiae
Characteristics "batch, hour 10"
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Starvation, Diauxic shift
Image: http://smd.stanford.edu/MicroArray/gifs/2002-10/34362.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 Aug 25, 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 GPL2638
Series (2)
GSE3206 Homeostatic Adjustment and Metabolic Remodeling in Glucose-limited Yeast Cultures Time Course 2
GSE4398 Homeostatic adjustment and metabolic remodeling in glucose-limited yeast cultures

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 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
1 1990 2113 119 106 1871 2007 2137 2261 157 128 2018 2155 0 0 825 995 100 64 93 94 93 92 3878 4173 .932 1.073 1.068 .991 1.087 2.566 120 792 1.125 .9 130 2020 8940 23 36 39 52 0 1447 73 1375 .735 1549 1476 1.361 .731 -.445 -.451
2 1046 557 115 100 931 457 1078 566 147 119 963 466 0 0 366 206 81 59 96 95 94 91 1388 1429 2.037 .491 .484 .491 .476 1.962 120 710 .467 .85 130 2220 8940 23 36 59 72 0 382 68 313 .336 388 319 2.974 .331 -1.573 -1.593
3 262 300 119 100 143 200 263 302 143 114 144 202 0 0 121 137 69 52 77 84 55 73 343 346 .715 1.399 1.403 1.307 1.344 2.148 120 643 1.323 .56 120 2420 8940 24 36 80 92 0 205 68 137 .958 207 138 1.044 .961 -.062 -.058
4 1507 852 115 104 1392 748 1690 932 145 114 1575 828 0 0 616 355 80 47 95 95 92 92 2140 2403 1.861 .537 .526 .571 .567 2.247 120 628 .525 .84 120 2630 8930 23 35 101 113 0 584 71 512 .368 638 567 2.717 .36 -1.442 -1.474
5 255 316 113 97 142 219 245 324 142 113 132 227 0 0 120 148 82 53 73 82 36 72 361 359 .648 1.542 1.72 1.496 1.685 2.354 120 681 1.301 .49 130 2820 8950 24 37 119 132 0 216 66 150 1.056 222 155 .947 1.178 .079 .236
6 312 369 110 99 202 270 318 380 144 116 208 281 0 0 118 140 106 64 85 90 46 84 472 489 .748 1.337 1.351 1.234 1.34 2.152 120 711 1.325 .58 130 3030 8940 23 36 140 153 0 253 68 185 .916 260 192 1.092 .925 -.127 -.112
7 214 436 106 98 108 338 215 460 141 110 109 362 0 0 105 193 93 49 55 88 16 85 446 471 .32 3.13 3.321 2.799 2.934 2.791 120 711 3.024 .39 130 3230 8950 24 37 160 173 0 299 67 232 2.144 315 248 .467 2.275 1.1 1.186
8 658 477 108 97 550 380 714 489 145 110 606 392 0 0 232 175 89 46 92 93 88 90 930 998 1.447 .691 .647 .716 .681 1.832 120 696 .665 .79 130 3440 8940 23 36 181 194 0 327 66 260 .473 335 268 2.113 .443 -1.079 -1.174
9 419 980 110 94 309 886 440 1068 143 112 330 974 0 0 155 400 89 54 86 96 82 94 1195 1304 .349 2.867 2.952 2.689 2.811 2.063 120 620 3.183 .81 120 3630 8950 25 37 201 213 0 671 64 607 1.964 732 667 .509 2.022 .974 1.015
10 281 524 107 97 174 427 266 501 138 112 159 404 0 0 126 229 81 53 82 92 48 90 601 563 .407 2.454 2.541 2.481 2.559 2.136 120 695 2.675 .6 130 3830 8950 24 37 220 233 0 359 66 292 1.681 343 277 .595 1.74 .749 .799
11 251 330 111 103 140 227 248 342 147 122 137 239 0 0 115 141 108 59 64 85 19 80 367 376 .617 1.621 1.745 1.482 1.553 2.394 120 747 .794 .37 130 4030 8940 23 36 240 253 0 226 71 155 1.111 234 164 .9 1.195 .151 .257
12 215 243 121 114 94 129 206 252 158 143 85 138 0 0 111 111 96 77 46 71 12 43 223 223 .729 1.372 1.624 1.446 1.828 2.894 32 230 .418 .24 70 4220 8920 24 31 262 269 0 166 78 88 .94 173 95 1.064 1.112 -.089 .153
13 235 317 111 101 124 216 245 338 146 118 134 237 0 0 108 133 102 57 65 84 17 77 340 371 .574 1.742 1.769 1.48 1.73 2.592 120 683 1.514 .51 120 4430 8940 24 36 281 293 0 217 69 148 1.193 232 162 .838 1.211 .255 .277
14 269 438 113 100 156 338 272 462 152 117 159 362 0 0 101 159 104 52 79 91 25 90 494 521 .462 2.167 2.277 2.03 2.083 2.038 120 642 2.393 .49 120 4630 8940 24 36 301 313 0 300 68 232 1.484 316 248 .674 1.559 .57 .641
15 656 269 119 105 537 164 720 280 159 123 601 175 0 0 265 104 105 59 86 85 84 74 701 776 3.274 .305 .291 .356 .34 2.371 120 724 .253 .66 130 4830 8940 23 36 320 333 0 184 72 112 .209 192 120 4.781 .199 -2.257 -2.326
16 255 1127 116 101 139 1026 271 1231 151 117 155 1130 0 0 117 545 97 55 70 90 28 87 1165 1285 .135 7.381 7.29 5.238 6.573 2.921 156 827 9.849 .46 140 5030 8940 23 37 340 354 0 772 69 703 5.056 843 774 .198 4.993 2.338 2.32
17 241 433 113 99 128 334 244 466 152 119 131 367 0 0 112 190 101 79 65 85 23 79 462 498 .383 2.609 2.802 2.291 2.246 2.363 120 613 2.436 .52 120 5220 8950 25 37 360 372 0 297 68 229 1.787 319 251 .56 1.919 .838 .94
18 332 676 113 104 219 572 335 689 146 121 222 585 0 0 157 323 107 61 78 93 54 90 791 807 .383 2.612 2.635 2.09 2.415 2.762 120 719 3.094 .53 130 5430 8940 23 36 380 393 0 463 71 392 1.789 472 401 .559 1.805 .839 .852
19 239 310 119 107 120 203 220 301 157 130 101 194 0 0 105 126 108 62 48 88 13 73 323 295 .591 1.692 1.921 1.705 1.771 2.222 52 294 1.382 .45 80 5610 8910 23 31 401 409 0 212 73 139 1.159 206 133 .863 1.316 .212 .396
20 295 309 123 109 172 200 279 307 165 129 156 198 0 0 154 150 114 62 72 81 27 73 372 354 .86 1.163 1.269 1.322 1.293 2.367 80 598 .622 .44 110 5820 8920 22 33 420 431 0 212 75 137 .796 210 136 1.256 .869 -.328 -.202

Total number of rows: 6912

Table truncated, full table size 1482 Kbytes.




Supplementary data files not provided
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