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Sample GSM94993 Query DataSets for GSM94993
Status Public on Feb 03, 2006
Title glucose pulse (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/2005-01/58914.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 1754 1606 165 153 1589 1453 1316 1271 167 156 1151 1118 0 0 1171 999 23 45 100 100 100 100 3042 2269 1.094 .914 .971 .94 .945 1.287 52 388 .876 .956 90 1560 20000 43 52 31 40 0 2186 208 1978 1.245 1730 1522 .803 1.322 .316 .403 .403
2 16677 24384 165 161 16512 24223 17207 24552 166 163 17042 24391 0 0 4114 5962 22 47 100 100 100 100 40735 41433 .682 1.467 1.431 1.473 1.468 1.093 52 318 1.458 .993 80 1760 20000 44 52 52 60 0 33198 219 32979 1.997 33426 33207 .501 1.949 .998 .962 .962
3 38118 17679 169 162 37949 17517 39908 18133 169 164 39739 17971 1 0 19318 10254 23 51 100 100 100 100 55466 57710 2.166 .462 .452 .426 .453 1.308 52 328 .476 .985 80 1940 20010 45 53 70 78 0 24069 221 23849 .628 24687 24467 1.591 .616 -.67 -.7 -.7
4 2315 1728 170 160 2145 1568 1758 1247 170 167 1588 1087 0 0 2263 1683 23 52 100 93 97 86 3713 2675 1.368 .731 .685 .732 .724 1.461 80 480 .733 .955 100 2130 20010 44 54 88 98 0 2353 218 2135 .995 1698 1480 1.005 .932 -.007 -.102 -.102
5 3895 3454 167 159 3728 3295 4048 3487 168 164 3881 3328 0 0 524 511 23 51 100 100 100 100 7023 7209 1.131 .884 .858 .882 .884 1.111 52 321 .881 .981 80 2310 20000 44 52 107 115 0 4702 216 4486 1.203 4747 4531 .831 1.167 .267 .223 .223
6 23650 36466 168 166 23482 36300 25201 38507 169 173 25033 38341 0 0 5414 8718 25 58 100 100 100 100 59782 63374 .647 1.546 1.532 1.542 1.568 1.072 52 395 1.547 .995 90 2490 20000 43 52 124 133 0 49647 226 49421 2.105 52426 52200 .475 2.085 1.074 1.06 1.06
7 3399 2715 171 166 3228 2549 3475 2761 170 170 3304 2595 0 0 415 381 25 44 100 100 100 100 5777 5899 1.266 .79 .785 .787 .797 1.113 52 340 .786 .981 80 2670 20000 44 52 143 151 0 3696 226 3470 1.075 3759 3533 .93 1.069 .104 .097 .097
8 657 602 170 172 487 430 641 535 175 171 471 363 0 0 434 398 40 52 83 83 66 66 917 834 1.133 .883 .771 .913 .862 1.429 12 90 .946 .904 50 2860 19970 42 47 163 168 0 820 234 585 1.202 728 494 .832 1.049 .266 .069 .069
9 2933 1232 164 160 2769 1072 1793 831 166 163 1629 671 0 0 3004 1240 24 47 100 100 100 98 3841 2300 2.583 .387 .412 .38 .381 1.528 52 408 .397 .963 90 3040 20000 43 52 179 188 0 1677 218 1459 .527 1131 914 1.897 .561 -.924 -.834 -.834
10 286 248 162 159 124 89 192 188 164 160 30 29 0 0 292 223 23 45 56 37 37 22 213 59 1.393 .718 .967 1.362 .846 3.08 80 507 .772 .812 100 3230 19990 42 52 198 208 0 338 216 121 .977 256 39 1.023 1.316 -.033 .396 .396
11 2391 4595 161 162 2230 4433 2285 4355 163 163 2124 4193 0 0 1069 2019 24 48 100 100 100 100 6663 6317 .503 1.988 1.974 2.043 1.993 1.215 52 392 1.981 .97 90 3400 19990 42 51 215 224 0 6256 221 6035 2.706 5929 5709 .369 2.688 1.436 1.426 1.426
12 1245 883 162 163 1083 720 888 662 164 167 726 499 0 0 915 640 25 50 100 94 100 92 1803 1225 1.504 .665 .687 .616 .638 1.765 52 408 .674 .928 90 3580 19990 42 51 233 242 0 1202 222 980 .905 901 679 1.105 .936 -.144 -.096 -.096
13 1337 1182 161 157 1176 1025 781 823 161 161 620 666 0 0 1081 872 22 49 100 100 100 100 2201 1286 1.147 .872 1.074 .915 .855 1.417 52 414 .825 .961 90 3770 20000 43 52 252 261 0 1609 214 1395 1.187 1120 907 .843 1.462 .247 .548 .548
14 2928 4369 163 160 2765 4209 598 962 166 165 435 802 0 0 4170 6332 42 75 88 92 83 85 6974 1237 .657 1.522 1.844 1.684 1.559 2.164 80 488 1.522 .986 100 3970 20000 43 53 272 282 0 5948 218 5730 2.072 1310 1092 .483 2.51 1.051 1.328 1.328
15 672 802 163 162 509 640 445 553 167 173 282 391 0 0 635 727 46 82 73 73 63 65 1149 673 .795 1.257 1.387 1.562 1.413 1.962 52 382 1.194 .9 90 4130 19990 42 51 288 297 0 1092 221 871 1.712 753 532 .584 1.888 .776 .917 .917
16 709 760 162 158 547 602 531 549 164 164 369 391 0 0 510 529 23 51 100 96 98 92 1149 760 .909 1.101 1.06 1.127 1.191 1.765 52 420 1.059 .907 90 4320 19990 42 51 307 316 0 1035 215 820 1.498 747 532 .667 1.443 .583 .529 .529
17 585 564 163 153 422 411 286 279 163 158 123 126 0 0 643 610 22 48 84 82 69 65 833 249 1.027 .974 1.024 1.181 1.106 2.092 52 401 .95 .946 90 4510 19990 42 51 326 335 0 768 208 560 1.326 380 172 .754 1.395 .407 .48 .48
18 4272 2069 165 157 4107 1912 3620 1710 164 161 3455 1553 0 0 3073 1403 23 49 100 100 100 94 6019 5008 2.148 .466 .449 .471 .468 1.301 52 394 .457 .973 90 4680 19980 41 50 343 352 0 2817 214 2603 .634 2328 2114 1.578 .612 -.658 -.708 -.708
19 1160 670 162 156 998 514 573 368 163 159 411 212 0 0 1613 857 26 44 98 82 86 75 1512 623 1.942 .515 .516 .622 .547 2.585 52 340 .527 .948 80 4860 20000 44 52 362 370 0 912 212 700 .701 501 289 1.426 .702 -.512 -.51 -.51
20 262 236 165 158 97 78 197 228 165 162 32 70 0 0 148 98 33 57 48 57 28 25 175 102 1.244 .804 2.188 1.334 1.645 3.674 52 328 .755 .473 80 5060 20000 44 52 382 390 0 321 215 106 1.095 310 95 .913 2.978 .131 1.574 1.574

Total number of rows: 10752

Table truncated, full table size 2488 Kbytes.




Supplementary data files not provided
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