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Sample GSM94990 Query DataSets for GSM94990
Status Public on Feb 03, 2006
Title glucose pulse (2g/l) on galactose chemostat (t=240min)
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=240min
Organism Saccharomyces cerevisiae
Characteristics t=240min
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Chemostat, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58920.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
1 935 945 100 103 835 842 655 687 100 106 555 584 0 0 688 706 18 32 100 100 100 98 1677 1139 .992 1.008 1.052 .98 1.001 1.34 52 337 1.012 .964 90 1640 19760 47 56 39 48 0 1021 111 910 1.09 742 631 .918 1.137 .124 .185 .185
2 10150 8675 100 114 10050 8561 9791 8504 101 117 9691 8390 0 0 2339 2075 18 32 100 100 100 100 18611 18081 1.174 .852 .866 .849 .858 1.087 52 329 .849 .988 80 1830 19760 48 56 59 67 0 9374 123 9251 .92 9189 9066 1.086 .935 -.12 -.096 -.096
3 10413 14423 99 110 10314 14313 9726 13478 105 125 9627 13368 0 0 2946 4050 86 153 100 100 100 100 24627 22995 .721 1.388 1.389 1.387 1.392 1.086 52 332 1.363 .99 80 2020 19750 47 55 78 86 0 15585 119 15466 1.5 14564 14445 .667 1.5 .585 .585 .585
4 780 891 100 117 680 774 504 511 102 122 404 394 0 0 716 859 17 37 100 100 100 98 1454 798 .879 1.138 .975 1.03 1.114 1.381 52 414 1.167 .967 90 2200 19760 47 56 95 104 0 963 126 836 1.23 552 426 .813 1.054 .299 .076 .076
5 1987 2008 99 114 1888 1894 1921 1945 99 118 1822 1831 0 0 444 439 17 34 100 100 100 100 3782 3653 .997 1.003 1.005 1.005 1.001 1.098 52 402 1 .984 90 2390 19750 46 55 114 123 0 2170 123 2047 1.084 2102 1979 .923 1.086 .116 .119 .119
6 19243 19166 100 125 19143 19041 19619 19427 100 129 19519 19302 0 0 2136 2266 18 39 100 100 100 100 38184 38821 1.005 .995 .989 .994 .999 1.049 52 403 .989 .995 90 2570 19750 46 55 132 141 0 20710 135 20575 1.075 20992 20857 .93 1.069 .104 .096 .096
7 1969 1916 100 132 1869 1784 2097 1981 102 136 1997 1849 0 0 439 434 18 37 100 100 100 100 3653 3846 1.048 .955 .926 .956 .946 1.115 52 414 .942 .982 90 2750 19750 46 55 150 159 0 2070 143 1928 1.031 2141 1998 .97 1 .045 .001 .001
8 408 398 107 125 301 273 311 350 120 138 204 225 0 0 252 197 40 55 100 91 91 83 574 429 1.103 .907 1.103 1.033 .96 1.598 12 104 .913 .771 50 2920 19770 50 55 169 174 0 430 135 295 .98 378 243 1.02 1.192 -.029 .253 .253
9 782 626 101 138 681 488 307 306 105 143 206 168 0 0 1132 797 70 64 92 80 71 59 1169 374 1.395 .717 .816 .649 .617 1.752 52 420 .705 .965 90 3130 19750 46 55 188 197 0 676 149 527 .774 331 182 1.291 .881 -.369 -.182 -.182
10 140 142 98 134 42 8 111 134 99 134 13 0 0 0 99 60 18 35 41 23 30 11 50 13 5.25 .19 null 1.044 .971 4.049 80 488 .619 .273 100 3330 19740 45 55 208 218 0 153 145 9 .206 145 0 4.859 null -2.281 null null
11 1540 1407 95 125 1445 1282 1443 1341 98 131 1348 1216 0 0 640 559 42 60 100 100 100 100 2727 2564 1.127 .887 .902 .889 .881 1.174 52 380 .871 .97 90 3490 19740 45 54 224 233 0 1520 135 1385 .959 1449 1314 1.043 .975 -.061 -.037 -.037
12 581 591 96 116 485 475 534 488 96 121 438 372 0 0 343 358 15 37 100 100 100 92 960 810 1.021 .979 .849 .956 .955 1.356 52 332 .986 .937 80 3680 19750 47 55 244 252 0 639 125 513 1.058 527 402 .945 .918 .082 -.124 -.124
13 559 596 92 119 467 477 415 399 93 121 323 280 0 0 460 469 15 34 100 98 100 98 944 603 .979 1.021 .867 1.059 1.053 1.48 52 414 1.019 .951 90 3860 19740 45 54 261 270 0 644 129 515 1.104 431 303 .906 .937 .142 -.094 -.094
14 1478 1350 95 121 1383 1229 273 279 96 124 178 158 0 0 2426 2106 23 35 93 84 84 62 2612 336 1.125 .889 .888 .851 .995 1.598 32 176 .871 .981 60 4040 19750 48 54 281 287 0 1459 131 1328 .96 301 171 1.041 .959 -.059 -.06 -.06
15 535 449 100 119 435 330 533 493 105 125 433 374 0 0 298 238 34 35 91 83 91 83 765 807 1.318 .759 .864 .763 .709 1.763 12 104 .787 .858 50 4210 19750 48 53 298 303 0 485 129 357 .82 533 404 1.22 .933 -.287 -.1 -.1
16 211 176 92 115 119 61 138 138 127 212 46 23 0 0 185 118 506 1059 7 0 0 0 180 69 1.951 .513 .5 .701 .691 2.91 80 507 .624 .601 100 4430 19740 45 55 318 328 0 190 124 66 .554 149 25 1.805 .54 -.852 -.888 -.888
17 165 151 92 114 73 37 118 122 93 118 26 8 0 0 161 118 17 32 60 30 37 15 110 34 1.973 .507 .308 .672 .722 3.247 80 466 .727 .681 100 4610 19740 45 55 336 346 0 163 123 40 .548 132 9 1.826 .332 -.869 -1.589 -1.589
18 1843 2309 94 113 1749 2196 1702 1934 95 120 1608 1821 0 0 1249 1559 16 34 100 100 98 98 3945 3429 .796 1.256 1.132 1.279 1.273 1.35 52 318 1.251 .983 80 4780 19740 46 54 354 362 0 2495 122 2373 1.357 2090 1968 .737 1.224 .44 .291 .291
19 415 367 93 120 322 247 218 194 94 123 125 74 0 0 467 408 16 32 93 68 90 53 569 199 1.304 .767 .592 .742 .802 2.796 32 170 .85 .937 60 4960 19740 47 53 373 379 0 397 130 267 .829 210 80 1.206 .64 -.271 -.645 -.645
20 131 134 94 124 37 10 114 130 96 127 20 6 0 0 77 40 17 39 51 25 31 5 47 26 3.7 .27 .3 1.017 1.089 4.686 80 506 .479 .025 100 5160 19740 45 55 391 401 0 145 134 11 .292 140 6 3.424 .324 -1.776 -1.625 -1.625

Total number of rows: 10752

Table truncated, full table size 2429 Kbytes.




Supplementary data files not provided
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