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Sample GSM95009 Query DataSets for GSM95009
Status Public on Feb 03, 2006
Title glucose pulse (0.2g/l) on galactose chemostat (t=8min)
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=8min
Organism Saccharomyces cerevisiae
Characteristics t=8min
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Chemostat, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58955.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 3192 2163 111 127 3081 2036 2419 1600 112 130 2308 1473 0 0 2804 1937 19 32 95 97 91 90 5117 3781 1.513 .661 .638 .664 .653 1.297 80 476 .674 .99 100 2260 20740 49 59 77 87 0 2783 163 2619 .85 2058 1895 1.176 .821 -.234 -.284 -.284
2 15953 23220 114 134 15839 23086 16772 23957 118 137 16658 23823 0 0 6351 9306 27 36 100 100 100 100 38925 40481 .686 1.458 1.43 1.463 1.474 1.107 80 496 1.459 .991 100 2440 20750 50 60 95 105 0 29873 172 29700 1.875 30821 30648 .533 1.84 .907 .88 .88
3 17935 12877 119 138 17816 12739 18372 12565 164 155 18253 12427 0 0 5274 3713 365 154 100 100 100 100 30555 30680 1.399 .715 .681 .716 .709 1.083 52 386 .704 .99 90 2630 20750 50 59 114 123 0 16566 178 16389 .92 16165 15987 1.087 .876 -.12 -.191 -.191
4 3906 2844 117 135 3789 2709 2216 1660 119 138 2099 1525 0 0 3729 2783 39 38 100 100 100 100 6498 3624 1.399 .715 .727 .696 .702 1.163 52 408 .731 .993 90 2810 20750 50 59 132 141 0 3659 174 3485 .92 2136 1962 1.087 .935 -.121 -.097 -.097
5 6619 4967 120 137 6499 4830 6525 4772 121 138 6405 4635 0 0 2133 1475 19 32 100 100 100 100 11329 11040 1.346 .743 .724 .752 .746 1.123 52 408 .732 .986 90 2990 20750 50 59 150 159 0 6390 176 6214 .956 6139 5963 1.046 .931 -.065 -.103 -.103
6 23458 33477 123 139 23335 33338 22527 30646 128 168 22404 30507 0 0 7677 11207 39 210 100 100 100 100 56673 52911 .7 1.429 1.362 1.424 1.43 1.072 52 406 1.426 .996 90 3170 20740 49 58 168 177 0 43068 179 42890 1.838 39426 39247 .544 1.752 .878 .809 .809
7 4821 3017 121 139 4700 2878 4804 3054 121 141 4683 2915 0 0 1341 911 19 36 100 100 100 100 7578 7598 1.633 .612 .622 .604 .606 1.111 52 406 .617 .988 90 3360 20750 50 59 187 196 0 3881 179 3703 .788 3929 3750 1.269 .801 -.344 -.32 -.32
8 211 175 118 133 93 42 144 131 119 135 26 -2 0 0 244 162 20 29 57 26 35 15 135 24 2.214 .452 null .826 .667 4.351 80 485 .652 .854 100 3550 20750 50 60 206 216 0 225 171 54 .581 169 -3 1.721 null -.783 null null
9 3946 1882 122 131 3824 1751 1229 656 123 134 1107 525 0 0 5677 2500 21 31 97 95 95 95 5575 1632 2.184 .458 .474 .512 .467 1.54 80 450 .443 .988 100 3740 20770 52 62 225 235 0 2421 169 2253 .589 844 675 1.698 .61 -.763 -.713 -.713
10 317 223 119 132 198 91 140 133 120 135 21 1 0 0 480 266 19 30 53 33 41 22 289 22 2.176 .46 .048 .806 .585 2.895 80 457 .54 .925 100 3900 20760 51 61 241 251 0 287 170 117 .591 171 1 1.691 .061 -.758 -4.029 -4.029
11 4116 10921 124 143 3992 10778 3672 9415 129 150 3548 9272 0 0 1995 5754 29 69 100 100 100 100 14770 12820 .37 2.7 2.613 2.667 2.69 1.11 52 320 2.703 .99 80 4100 20750 51 59 262 270 0 14050 184 13866 3.473 12112 11928 .288 3.362 1.796 1.749 1.749
12 3362 1552 125 153 3237 1399 3084 1452 127 154 2959 1299 0 0 1655 749 23 37 100 100 100 100 4636 4258 2.314 .432 .439 .424 .421 1.173 52 326 .432 .973 80 4280 20760 52 60 280 288 0 1997 197 1800 .556 1868 1671 1.799 .565 -.847 -.824 -.824
13 1061 940 123 154 938 786 389 325 124 162 266 171 0 0 1366 1230 21 45 87 82 77 61 1724 437 1.193 .838 .643 .779 .809 2.449 80 486 .884 .985 100 4460 20760 51 61 297 307 0 1209 198 1011 1.078 418 220 .928 .827 .108 -.274 -.274
14 2424 2377 119 142 2305 2235 409 413 120 144 290 271 0 0 4918 4799 20 33 83 76 80 71 4540 561 1.031 .97 .934 .935 .974 1.754 80 462 .975 .997 100 4650 20770 52 62 316 326 0 3058 183 2875 1.247 531 349 .802 1.202 .319 .266 .266
15 627 575 118 133 509 442 237 235 119 137 119 102 0 0 902 786 19 34 90 78 86 66 951 221 1.152 .868 .857 .875 .899 1.81 80 481 .87 .983 100 4820 20760 51 61 333 343 0 740 171 569 1.117 302 131 .895 1.103 .16 .141 .141
16 1218 960 119 132 1099 828 1077 873 121 133 958 741 0 0 695 506 20 32 100 100 100 98 1927 1699 1.327 .753 .773 .752 .761 1.185 52 384 .742 .975 90 5010 20760 51 60 352 361 0 1235 170 1065 .969 1123 953 1.032 .995 -.045 -.007 -.007
17 624 564 119 135 505 429 367 325 120 136 248 190 0 0 700 608 20 33 85 70 71 58 934 438 1.177 .85 .766 .829 .899 1.941 80 492 .862 .969 100 5180 20770 52 62 369 379 0 726 174 552 1.093 418 244 .915 .986 .128 -.021 -.021
18 9076 5766 120 130 8956 5636 7692 4513 121 133 7572 4383 0 0 5217 3428 19 33 100 100 100 100 14592 11955 1.589 .629 .579 .624 .621 1.15 52 410 .637 .994 90 5380 20770 52 61 389 398 0 7418 167 7251 .81 5806 5639 1.235 .745 -.305 -.425 -.425
19 1265 703 126 140 1139 563 672 338 126 140 546 198 0 0 1352 715 21 33 100 100 96 84 1702 744 2.023 .494 .363 .489 .497 1.457 32 236 .516 .979 70 5550 20780 54 61 407 414 0 904 180 724 .636 435 255 1.573 .467 -.653 -1.1 -1.1
20 210 155 118 131 92 24 144 134 119 135 26 3 0 0 188 78 20 31 61 26 35 16 116 29 3.833 .261 .115 .495 .403 2.993 80 513 .376 .551 100 5730 20770 52 62 424 434 0 199 169 31 .336 172 4 2.98 .148 -1.575 -2.752 -2.752

Total number of rows: 10752

Table truncated, full table size 2506 Kbytes.




Supplementary data files not provided
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