NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM95013 Query DataSets for GSM95013
Status Public on Feb 03, 2006
Title glucose pulse (0.2g/l) on galactose chemostat (t=30min)
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=30min
Organism Saccharomyces cerevisiae
Characteristics t=30min
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Chemostat, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58959.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 2372 1948 102 67 2270 1881 2022 1697 103 69 1920 1630 0 0 1184 1011 20 20 100 100 100 100 4151 3550 1.207 .829 .849 .813 .818 1.188 52 382 .83 .975 90 1370 19990 38 47 44 53 0 3057 105 2952 1.3 2663 2558 .769 1.332 .379 .414 .414
2 18294 18656 100 70 18194 18586 18469 18727 101 72 18369 18657 0 0 3860 4267 17 21 100 100 100 100 36780 37026 .979 1.022 1.016 1.018 1.025 1.093 52 403 1.03 .985 90 1550 19990 38 47 62 71 0 29274 110 29164 1.603 29385 29275 .624 1.594 .681 .672 .672
3 21002 14684 103 72 20899 14612 20502 14881 105 76 20399 14809 0 0 5887 5063 19 27 100 100 100 100 35511 35208 1.43 .699 .726 .678 .706 1.173 52 409 .714 .985 90 1740 19980 37 46 81 90 0 23041 113 22928 1.097 23350 23237 .912 1.139 .134 .188 .188
4 3365 2640 105 76 3260 2564 2374 2198 113 85 2269 2122 0 0 2199 1911 89 83 100 100 100 100 5824 4391 1.271 .787 .935 .734 .75 1.316 52 414 .805 .967 90 1920 19980 37 46 99 108 0 4142 119 4023 1.234 3449 3330 .81 1.467 .303 .553 .553
5 6256 5033 102 74 6154 4959 6385 5129 102 76 6283 5055 0 0 1389 1378 17 22 100 100 100 100 11113 11338 1.241 .806 .805 .791 .785 1.131 52 406 .815 .982 90 2110 19980 37 46 118 127 0 7897 116 7781 1.264 8048 7932 .791 1.262 .338 .336 .336
6 33406 54976 100 78 33306 54898 36483 59842 101 85 36383 59764 0 5 8779 13395 19 47 100 100 100 100 88204 96147 .607 1.648 1.643 1.675 1.662 1.103 52 394 1.624 .992 90 2280 19980 37 46 135 144 0 86264 122 86142 2.586 93899 93777 .387 2.577 1.371 1.366 1.366
7 5354 4327 102 78 5252 4249 5338 4247 103 81 5236 4169 0 0 792 793 25 32 100 100 100 100 9501 9405 1.236 .809 .796 .804 .804 1.077 52 340 .814 .989 80 2480 19980 38 46 156 164 0 6790 122 6667 1.269 6664 6542 .788 1.249 .344 .321 .321
8 489 328 98 73 391 255 404 296 99 78 306 223 0 0 318 175 19 25 100 91 100 91 646 529 1.533 .652 .729 .687 .736 2.246 12 104 .589 .858 50 2680 19990 40 45 177 182 0 515 115 400 1.023 464 350 .977 1.144 .033 .193 .193
9 5482 1552 95 77 5387 1475 1990 528 97 79 1895 451 0 0 6747 1933 17 23 100 100 100 100 6862 2346 3.652 .274 .238 .251 .247 1.395 52 416 .274 .937 90 2840 19970 36 45 191 200 0 2435 121 2314 .43 828 708 2.328 .373 -1.219 -1.421 -1.421
10 188 120 97 80 91 40 113 86 99 81 16 6 0 0 258 125 18 22 47 28 26 15 131 22 2.275 .44 .375 .793 .75 3.118 80 508 .466 .827 100 3040 19960 35 45 211 221 -50 188 126 63 .69 135 9 1.45 .588 -.536 -.765
11 5373 4594 103 82 5270 4512 4746 4027 104 84 4643 3945 0 0 2255 1930 19 23 100 100 100 100 9782 8588 1.168 .856 .85 .856 .856 1.102 52 386 .864 .983 90 3210 19970 36 45 228 237 0 7209 129 7080 1.343 6319 6190 .744 1.333 .426 .415 .415
12 1874 1742 103 82 1771 1660 1362 1268 104 85 1259 1186 0 0 1502 1460 20 29 100 100 100 100 3431 2445 1.067 .937 .942 .874 .83 1.324 52 412 .95 .965 90 3400 19960 35 44 247 256 0 2733 129 2605 1.471 1990 1861 .68 1.478 .557 .564 .564
13 1142 1987 98 80 1044 1907 568 553 99 82 470 473 0 0 1370 3920 18 27 100 100 100 100 2951 943 .547 1.827 1.006 1.106 .929 2.144 52 408 5.063 .203 90 3590 19970 36 45 266 275 0 3118 126 2992 2.866 868 742 .349 1.579 1.519 .659 .659
14 2260 2410 98 85 2162 2325 533 520 100 87 435 435 0 0 3964 4400 19 25 95 98 93 95 4487 870 .93 1.075 1 1.122 1 1.928 80 482 1.105 .976 100 3780 19970 36 46 285 295 0 3782 133 3648 1.687 816 683 .593 1.569 .755 .65 .65
15 592 543 104 87 488 456 251 217 106 89 147 130 0 0 731 687 24 28 98 90 94 82 944 277 1.07 .934 .884 .854 .899 1.611 52 392 .939 .978 90 3950 19960 35 44 302 311 0 852 137 716 1.466 340 204 .682 1.388 .552 .473 .473
16 671 498 104 87 567 411 455 306 105 90 351 219 0 0 546 417 19 26 100 100 100 100 978 570 1.38 .725 .624 .697 .714 1.327 32 230 .818 .921 70 4140 19950 35 42 322 329 0 781 137 645 1.137 480 344 .879 .979 .186 -.031 -.031
17 530 384 106 86 424 298 372 301 106 89 266 215 0 0 383 256 18 25 100 90 98 86 722 481 1.423 .703 .808 .681 .666 1.981 52 340 .666 .899 80 4320 19960 36 44 340 348 0 603 135 468 1.103 472 337 .907 1.268 .141 .343 .343
18 5071 3914 106 89 4965 3825 4270 3438 105 91 4164 3349 0 0 4069 3042 18 24 100 100 100 100 8790 7513 1.298 .77 .804 .833 .759 1.376 52 326 .757 .984 80 4510 19970 37 45 359 367 0 6142 140 6002 1.209 5395 5255 .827 1.262 .274 .336 .336
19 655 463 104 87 551 376 255 205 116 129 151 118 0 0 899 597 111 375 63 25 34 19 927 269 1.465 .682 .781 .698 .702 1.864 52 334 .664 .97 80 4690 19960 36 44 377 385 0 727 137 590 1.071 322 185 .934 1.226 .099 .294 .294
20 187 130 105 91 82 39 129 106 106 94 24 15 0 0 161 75 17 25 65 40 42 25 121 39 2.103 .476 .625 .822 .656 3.45 80 494 .461 .624 100 4870 19950 34 44 394 404 -50 204 143 61 .746 166 24 1.34 .981 -.422 -.028

Total number of rows: 10752

Table truncated, full table size 2435 Kbytes.




Supplementary data files not provided
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap