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Sample GSM72041 Query DataSets for GSM72041
Status Public on Aug 26, 2005
Title batch 02X25 3
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 9"
Organism Saccharomyces cerevisiae
Characteristics "batch, hour 9"
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Starvation, Diauxic shift
Image: http://smd.stanford.edu/MicroArray/gifs/2002-10/34359.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 1924 2466 97 70 1827 2396 2126 2745 118 86 2029 2675 0 0 816 1052 57 51 95 95 94 94 4223 4704 .763 1.311 1.318 1.184 1.277 2.311 120 793 1.41 .87 130 2040 9310 40 53 37 50 0 2283 65 2219 1.214 2542 2477 .824 1.221 .28 .288
2 921 1399 99 72 822 1327 939 1414 121 88 840 1342 0 0 315 455 58 54 97 100 96 98 2149 2182 .619 1.614 1.598 1.655 1.648 1.584 120 629 1.697 .89 120 2240 9320 42 54 58 70 0 1295 67 1229 1.495 1309 1243 .669 1.479 .58 .565
3 247 272 100 73 147 199 251 273 124 88 151 200 0 0 98 110 63 42 82 91 60 85 346 351 .739 1.354 1.325 1.242 1.228 1.986 156 857 1.23 .6 140 2450 9320 41 55 78 92 0 252 68 184 1.253 253 185 .798 1.226 .326 .294
4 1305 2276 101 71 1204 2205 1446 2372 128 86 1345 2301 0 0 636 1079 76 44 93 98 90 97 3409 3646 .546 1.831 1.711 1.775 1.782 2.601 156 778 1.919 .89 140 2650 9310 40 54 98 112 0 2107 66 2042 1.696 2196 2131 .59 1.584 .762 .664
5 245 244 100 73 145 171 240 247 126 93 140 174 0 0 98 90 72 71 81 89 46 66 316 314 .848 1.179 1.243 1.118 1.138 2.078 120 653 .944 .58 120 2850 9320 42 54 119 131 0 226 68 158 1.092 229 161 .916 1.151 .127 .203
6 339 494 103 74 236 420 338 523 123 86 235 449 0 0 108 157 61 40 93 95 89 93 656 684 .562 1.78 1.911 1.804 1.814 1.767 120 726 1.923 .74 130 3060 9310 40 53 139 152 0 457 69 389 1.648 484 416 .607 1.769 .721 .823
7 242 216 100 72 142 144 236 210 121 84 136 138 0 0 76 74 60 39 88 90 60 83 286 274 .986 1.014 1.015 .959 1.045 2.226 120 621 .908 .57 120 3260 9310 41 53 160 172 0 200 67 133 .939 194 128 1.065 .94 -.091 -.09
8 785 1204 102 72 683 1132 853 1380 122 83 751 1308 0 0 281 522 56 38 96 97 94 94 1815 2059 .603 1.657 1.742 1.493 1.703 2.416 156 794 1.817 .89 140 3460 9310 40 54 179 193 0 1115 67 1048 1.535 1278 1211 .652 1.613 .618 .689
9 549 697 101 71 448 626 556 728 123 83 455 657 0 0 190 240 62 36 95 97 92 95 1074 1112 .716 1.397 1.444 1.394 1.455 2.147 120 634 1.5 .81 120 3650 9310 41 53 199 211 0 645 66 580 1.294 674 608 .773 1.337 .372 .419
10 260 253 99 73 161 180 233 240 123 85 134 167 0 0 100 91 69 35 90 95 46 92 341 301 .894 1.118 1.246 1.133 1.222 1.967 120 637 .896 .56 120 3850 9310 41 53 219 231 0 234 68 167 1.035 222 155 .966 1.154 .05 .207
11 319 394 105 76 214 318 326 412 125 85 221 336 0 0 126 143 63 35 86 93 78 92 532 557 .673 1.486 1.52 1.553 1.413 2.039 120 678 1.415 .78 120 4060 9310 41 53 240 252 0 365 70 294 1.376 381 311 .727 1.408 .46 .493
12 250 219 102 73 148 146 246 212 121 83 144 139 0 0 96 79 58 35 83 93 58 87 294 283 1.014 .986 .965 1.051 1.076 2.531 80 483 .831 .57 100 4240 9300 41 51 259 269 0 203 68 135 .913 196 129 1.095 .894 -.131 -.162
13 323 396 101 71 222 325 328 416 122 80 227 345 0 0 139 184 58 32 85 92 80 88 547 572 .683 1.464 1.52 1.365 1.435 2.143 120 731 1.52 .7 130 4450 9310 40 53 278 291 0 367 66 301 1.356 385 319 .738 1.407 .439 .493
14 337 352 102 72 235 280 337 368 127 80 235 296 0 0 110 109 67 30 94 94 85 93 515 531 .839 1.191 1.26 1.115 1.189 2.007 120 702 1.113 .69 130 4650 9310 40 53 298 311 0 326 67 259 1.103 341 274 .906 1.166 .142 .222
15 830 531 111 72 719 459 833 518 137 80 722 446 0 0 290 198 82 32 95 95 95 95 1178 1168 1.566 .638 .618 .637 .661 1.687 120 702 .582 .83 130 4850 9310 40 53 318 331 0 492 67 425 .591 480 413 1.692 .572 -.759 -.806
16 468 714 111 74 357 640 494 767 139 82 383 693 0 0 153 244 82 29 91 95 88 95 997 1076 .558 1.793 1.809 1.689 1.766 2.092 120 707 1.925 .76 130 5050 9310 40 53 338 351 0 661 69 593 1.66 710 642 .602 1.675 .731 .744
17 400 508 105 73 295 435 405 494 127 80 300 421 0 0 153 177 61 28 91 96 88 96 730 721 .678 1.475 1.403 1.472 1.387 1.849 120 592 1.417 .77 120 5250 9320 42 54 359 371 0 470 68 403 1.365 457 390 .732 1.299 .449 .378
18 489 571 108 72 381 499 505 576 129 79 397 504 0 0 163 205 62 30 95 96 93 95 880 901 .764 1.31 1.27 1.257 1.295 1.912 120 631 1.363 .84 120 5460 9310 41 53 380 392 0 529 67 462 1.213 533 467 .825 1.175 .278 .233
19 252 228 107 72 145 156 252 220 130 79 145 148 0 0 89 76 67 27 80 94 58 89 301 293 .929 1.076 1.021 1.095 1.127 2.618 120 678 .891 .63 130 5650 9310 40 53 398 411 0 211 67 144 .996 204 137 1.004 .945 -.006 -.081
20 314 287 104 71 210 216 303 281 130 79 199 210 0 0 135 121 79 28 83 94 67 89 426 409 .972 1.029 1.055 1.024 1.115 2.245 120 674 .894 .67 120 5850 9310 41 53 419 431 0 266 66 200 .952 260 194 1.05 .977 -.07 -.033

Total number of rows: 6912

Table truncated, full table size 1488 Kbytes.




Supplementary data files not provided
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