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Sample GSM72034 Query DataSets for GSM72034
Status Public on Aug 26, 2005
Title 03II01 batch p3
Sample type RNA
 
Channel 1
Source name "DBY10085 Chemostat: D=.25, [D]=2.4"
Organism Saccharomyces cerevisiae
Characteristics "DBY10085 Chemostat: D=.25, [D]=2.4"
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name DBY10085 Batch timepoint 3
Organism Saccharomyces cerevisiae
Characteristics DBY10085 Batch timepoint 3
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Starvation, Diauxic shift
Image: http://smd.stanford.edu/MicroArray/gifs/2003-02/38147.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) [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 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 2588 1253 193 240 2395 1013 2770 1190 211 257 2577 950 0 0 790 447 76 114 100 99 100 98 3408 3527 2.364 .423 .369 .413 .397 1.553 120 689 .417 .89 120 2180 10220 44 56 48 60 0 1262 242 1020 .426 1199 957 2.347 .371 -1.231 -1.429
2 1425 2041 186 247 1239 1794 1558 2079 206 263 1372 1832 0 0 440 662 86 110 95 98 95 96 3033 3204 .691 1.448 1.335 1.444 1.421 1.996 120 695 1.511 .91 130 2380 10210 42 55 67 80 0 2056 249 1807 1.458 2094 1845 .686 1.345 .544 .428
3 460 492 195 239 265 253 482 472 211 263 287 233 0 0 160 204 81 230 86 50 79 15 518 520 1.047 .955 .812 .844 .903 2.952 120 680 1.31 .57 130 2580 10210 42 55 87 100 0 496 241 255 .962 475 235 1.04 .818 -.056 -.29
4 3031 3011 198 236 2833 2775 3410 3179 214 262 3212 2943 0 0 1007 913 71 232 99 98 98 96 5608 6155 1.021 .98 .916 1.008 .946 1.542 120 679 .958 .95 130 2780 10220 43 56 107 120 0 3033 238 2795 .987 3202 2964 1.014 .923 -.019 -.116
5 416 442 198 234 218 208 410 412 216 253 212 178 0 0 147 180 84 136 85 60 66 28 426 390 1.048 .954 .84 .764 .89 2.861 120 638 1.284 .64 120 2980 10220 44 56 128 140 0 445 236 210 .961 415 179 1.041 .846 -.057 -.242
6 776 1461 193 229 583 1232 797 1490 209 248 604 1261 0 0 207 437 76 109 96 99 95 97 1815 1865 .473 2.113 2.088 2.151 2.047 1.658 120 722 2.237 .89 130 3190 10210 42 55 148 161 0 1472 231 1241 2.128 1501 1270 .47 2.103 1.09 1.072
7 400 501 199 245 201 256 413 488 219 265 214 243 0 0 144 214 84 117 83 72 67 50 457 457 .785 1.274 1.136 .969 1.061 2.515 156 832 1.693 .61 140 3390 10210 42 56 168 182 0 505 247 258 1.283 492 245 .78 1.144 .359 .194
8 3594 5650 196 242 3398 5408 3920 5959 212 257 3724 5717 0 0 1123 1690 72 112 100 100 100 100 8806 9441 .628 1.592 1.535 1.668 1.55 1.462 120 609 1.583 .96 120 3600 10220 44 56 190 202 0 5691 244 5447 1.603 6002 5758 .624 1.546 .681 .629
9 1006 850 192 241 814 609 1034 836 209 255 842 595 0 0 268 285 68 116 96 95 95 90 1423 1437 1.337 .748 .707 .743 .705 2.056 120 703 .804 .84 130 3790 10220 43 56 208 221 0 856 243 613 .754 842 599 1.327 .712 -.408 -.491
10 648 550 195 237 453 313 671 537 212 250 476 300 0 0 215 191 74 109 91 85 90 68 766 776 1.447 .691 .63 .65 .651 2.282 120 629 .765 .69 120 3990 10220 44 56 229 241 0 554 239 315 .696 541 302 1.437 .635 -.523 -.656
11 953 1350 205 241 748 1109 996 1381 222 252 791 1140 0 0 310 422 82 107 94 98 92 97 1857 1931 .674 1.483 1.441 1.445 1.392 1.51 120 645 1.514 .9 130 4190 10220 43 56 248 261 0 1360 243 1117 1.493 1391 1148 .67 1.452 .579 .538
12 494 486 204 241 290 245 515 424 223 250 311 183 0 0 210 254 88 108 82 70 74 43 535 494 1.184 .845 .588 .78 .869 2.703 156 838 1.089 .59 140 4390 10210 42 56 268 282 0 490 243 247 .851 427 184 1.175 .593 -.233 -.755
13 696 580 191 221 505 359 735 587 211 232 544 366 0 0 305 267 86 109 87 81 85 67 864 910 1.407 .711 .673 .68 .765 2.159 80 466 .703 .71 100 4600 10220 45 55 291 301 0 584 223 362 .716 591 369 1.397 .678 -.482 -.561
14 917 1587 191 230 726 1357 999 1663 216 244 808 1433 0 0 398 637 93 107 85 95 85 91 2083 2241 .535 1.869 1.774 1.715 1.803 1.688 120 700 1.981 .87 130 4790 10210 42 55 308 321 0 1598 232 1367 1.883 1675 1443 .531 1.786 .913 .837
15 1977 1640 192 229 1785 1411 2240 1710 216 247 2048 1481 0 0 1032 805 94 110 85 89 83 87 3196 3529 1.265 .79 .723 .817 .775 2.128 156 785 .779 .94 140 4990 10220 43 57 328 342 0 1652 231 1421 .796 1722 1492 1.256 .728 -.329 -.457
16 1406 1622 196 231 1210 1391 1628 1662 231 254 1432 1431 0 0 665 788 127 122 85 88 85 88 2601 2863 .87 1.15 .999 1.148 1.113 1.918 120 690 1.133 .88 130 5190 10210 42 55 348 361 0 1634 233 1401 1.158 1674 1441 .864 1.007 .212 .009
17 1291 1974 201 244 1090 1730 1412 2076 236 266 1211 1832 0 0 536 836 125 134 86 94 86 92 2820 3043 .63 1.587 1.513 1.503 1.526 1.619 120 573 1.643 .9 120 5390 10220 44 56 369 381 0 1988 246 1743 1.599 2091 1845 .626 1.524 .677 .608
18 1260 1456 201 250 1059 1206 1410 1494 238 274 1209 1244 0 0 892 906 127 135 78 83 76 80 2265 2453 .878 1.139 1.029 1.082 1.083 2.198 120 684 1.078 .85 130 5590 10220 43 56 388 401 0 1467 252 1215 1.147 1505 1253 .872 1.036 .198 .052
19 521 554 200 237 321 317 517 530 231 258 317 293 0 0 260 249 130 119 80 79 57 61 638 610 1.013 .988 .924 .92 .954 2.506 120 693 .902 .59 130 5790 10220 43 56 408 421 0 558 239 319 .995 534 295 1.005 .931 -.008 -.103
20 576 628 204 228 372 400 560 578 229 245 356 350 0 0 347 340 112 109 76 79 67 70 772 706 .93 1.075 .983 .935 .879 2.235 120 729 1.033 .72 130 5980 10220 43 56 427 440 0 633 230 403 1.083 582 353 .923 .99 .115 -.014

Total number of rows: 6912

Table truncated, full table size 1562 Kbytes.




Supplementary data files not provided
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