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Sample GSM72025 Query DataSets for GSM72025
Status Public on Aug 26, 2005
Title Low-D chemostat vs. High-D chemostat
Sample type RNA
 
Channel 1
Source name Reference: D=0.25
Organism Saccharomyces cerevisiae
Characteristics Reference: D=0.25
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name D=0.05
Organism Saccharomyces cerevisiae
Characteristics D=0.05
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Chemostat, Dilution Rate
Image: http://smd.stanford.edu/MicroArray/gifs/2003-09/45181.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)
GSE3205 Homeostatic Adjustment and Metabolic Remodeling in Glucose-limited Yeast Cultures Time Course 1
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 4784 5263 83 72 4701 5191 4570 4736 107 75 4487 4664 0 0 2272 2403 83 22 100 100 100 100 9892 9151 .906 1.104 1.039 1.13 1.145 1.469 120 499 1.096 .89 130 2610 10040 77 90 58 71 0 7940 109 7832 1.666 7145 7037 .6 1.568 .736 .649
2 4862 5442 81 73 4781 5369 4912 5399 107 77 4831 5326 0 0 1664 1746 79 23 100 100 100 100 10150 10157 .89 1.123 1.102 1.146 1.126 1.478 120 578 1.103 .94 130 2810 10040 77 90 78 91 0 8210 110 8100 1.694 8145 8035 .59 1.663 .761 .734
3 498 445 85 76 413 369 460 452 110 80 375 376 0 0 239 143 80 24 98 100 87 98 782 751 1.119 .893 1.003 .947 1.009 1.861 120 570 .763 .77 130 3010 10030 76 89 98 111 0 671 115 557 1.348 682 567 .742 1.513 .431 .597
4 5058 3709 81 78 4977 3631 5699 4137 105 81 5618 4059 0 0 2294 1422 78 23 98 100 98 100 8608 9677 1.371 .73 .722 .796 .711 2.086 156 599 .681 .92 140 3220 10040 77 91 119 133 0 5596 118 5478 1.101 6241 6124 .909 1.09 .138 .124
5 441 278 83 87 358 191 417 283 107 92 334 196 0 0 255 89 75 43 95 94 85 86 549 530 1.874 .534 .587 .569 .575 2.233 120 587 .374 .69 130 3420 10040 77 90 139 152 0 419 131 288 .805 427 296 1.242 .885 -.313 -.176
6 534 414 87 89 447 325 495 437 113 92 408 348 0 0 198 120 83 27 99 100 95 99 772 756 1.375 .727 .853 .732 .748 1.858 120 578 .629 .78 130 3620 10040 77 90 159 172 0 625 134 490 1.097 659 525 .912 1.287 .133 .364
7 413 249 88 97 325 152 403 252 120 113 315 155 0 0 144 64 106 91 95 86 78 28 477 470 2.138 .468 .492 .45 .492 2.031 120 547 .377 .73 120 3820 10030 77 89 180 192 0 376 146 229 .706 380 234 1.417 .742 -.503 -.43
8 806 738 91 114 715 624 836 758 125 131 745 644 0 0 321 251 106 127 97 97 92 89 1339 1389 1.146 .873 .864 .907 .925 1.885 156 640 .845 .87 140 4020 10030 76 90 199 213 0 1113 172 941 1.317 1144 972 .759 1.304 .397 .383
9 845 1462 83 105 762 1357 849 1418 121 114 766 1313 0 0 375 564 133 50 95 100 92 99 2119 2079 .562 1.781 1.714 1.831 1.849 1.638 120 616 1.885 .79 130 4210 10040 77 90 218 231 0 2206 158 2047 2.687 2139 1981 .372 2.586 1.426 1.371
10 333 419 80 97 253 322 279 355 114 101 199 258 0 0 200 230 105 36 76 95 45 90 575 457 .786 1.273 1.296 1.23 1.384 2.594 120 602 1.239 .56 130 4420 10040 77 90 239 252 0 632 146 486 1.92 536 389 .521 1.956 .941 .968
11 339 369 90 105 249 264 304 295 122 117 214 190 0 0 180 199 92 67 77 88 55 67 513 404 .943 1.06 .888 1.059 1 2.99 80 464 1.07 .64 110 4610 10020 76 87 259 270 0 557 158 398 1.6 445 287 .625 1.339 .678 .422
12 334 210 85 113 249 97 328 190 116 120 243 77 0 0 176 82 89 55 77 65 59 39 346 320 2.567 .39 .317 .432 .453 2.955 120 566 .235 .53 130 4800 10030 76 89 277 290 0 317 170 146 .588 287 116 1.701 .478 -.767 -1.065
13 355 228 84 105 271 123 262 167 114 104 178 62 0 0 288 130 82 36 69 70 51 46 394 240 2.203 .454 .348 .528 .447 3.95 120 567 .347 .69 120 5000 10050 79 91 298 310 0 344 158 186 .685 252 94 1.46 .526 -.546 -.928
14 411 393 84 98 327 295 390 388 113 97 306 290 0 0 206 145 84 39 91 98 76 93 622 596 1.108 .902 .948 .932 .909 2.009 156 603 .758 .73 140 5210 10040 77 91 318 332 0 593 148 445 1.361 585 438 .735 1.43 .445 .516
15 2742 755 83 97 2659 658 2704 665 120 95 2621 568 0 0 1672 452 103 40 100 97 97 93 3317 3189 4.041 .247 .217 .235 .253 1.969 120 532 .227 .88 130 5400 10040 77 90 337 350 0 1139 146 993 .373 1003 857 2.678 .327 -1.421 -1.613
16 398 686 82 92 316 594 353 595 117 92 271 503 0 0 238 376 99 39 82 100 61 95 910 774 .532 1.88 1.856 2.01 1.909 2.39 156 649 1.983 .73 140 5610 10040 77 91 358 372 0 1035 139 896 2.836 898 759 .353 2.8 1.504 1.486
17 370 399 80 94 290 305 289 349 116 98 209 255 0 0 255 270 102 49 74 86 50 70 595 464 .951 1.052 1.22 1.026 1.13 2.325 120 597 1.032 .76 130 5810 10050 78 91 378 391 0 602 142 460 1.587 527 385 .63 1.841 .666 .88
18 471 394 93 104 378 290 277 287 126 105 184 183 0 0 372 301 91 42 76 82 50 70 668 367 1.303 .767 .995 .753 .874 2.826 80 456 .679 .7 100 5990 10020 77 87 398 408 0 594 157 438 1.157 433 276 .864 1.5 .211 .585
19 413 197 84 91 329 106 389 205 119 91 305 114 0 0 227 66 98 38 90 82 74 70 435 419 3.104 .322 .374 .347 .375 1.984 120 712 .21 .57 130 6220 10040 77 90 419 432 0 297 137 160 .486 309 172 2.057 .564 -1.041 -.826
20 259 135 89 98 170 37 238 135 136 103 149 37 0 0 168 52 122 34 53 53 23 26 207 186 4.595 .218 .248 .366 .39 3.332 52 327 .083 .27 80 6410 10020 78 86 441 449 0 204 148 56 .328 204 56 3.045 .375 -1.607 -1.416

Total number of rows: 6912

Table truncated, full table size 1469 Kbytes.




Supplementary data files not provided
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