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Sample GSM87460 Query DataSets for GSM87460
Status Public on Dec 15, 2005
Title wt_hypo_osmotic_shock_30min
Sample type RNA
 
Channel 1
Source name wt (mid-lgo on YPD, 30C, OD 0.36)
Organism Saccharomyces cerevisiae
Characteristics wt (mid-lgo on YPD, 30C, OD 0.36)
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name wt, 30min after transfer to regular YPD
Organism Saccharomyces cerevisiae
Characteristics wt, 30min after transfer to regular YPD
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Mutants, osmotic
Image: http://smd.stanford.edu/MicroArray/gifs/2002-10/34350.gif
Measurement: time(absolute) 30 m
name: 34350_Time
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 Dec 13, 2005
Last update date Sep 22, 2006
Organization Stanford Microarray Database (SMD)
E-mail(s) array@genome.stanford.edu
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 (1)
GSE3812 Response of yeast cells to stress

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 3531 5276 100 133 3431 5143 3707 5441 123 157 3607 5308 0 0 790 1182 72 95 100 100 100 100 8574 8915 .667 1.499 1.472 1.501 1.519 1.147 120 783 1.492 .98 130 2300 9880 113 126 63 76 0 6207 156 6051 1.764 6401 6245 .567 1.731 .818 .792
2 2436 2780 104 125 2332 2655 2409 2749 129 155 2305 2624 0 0 437 554 78 102 100 100 100 100 4987 4929 .878 1.139 1.138 1.136 1.136 1.188 120 628 1.137 .98 120 2490 9870 113 125 83 95 0 3271 147 3124 1.339 3234 3087 .747 1.339 .422 .421
3 288 308 94 105 194 203 270 302 118 126 176 197 0 0 88 80 69 73 96 97 80 75 397 373 .956 1.046 1.119 1.073 1.09 1.543 120 688 1.03 .83 120 2690 9870 113 125 103 115 0 362 124 239 1.231 355 232 .812 1.317 .3 .397
4 3932 4046 93 103 3839 3943 4013 4109 114 123 3920 4006 0 0 782 853 75 72 100 100 100 100 7782 7926 .974 1.027 1.022 1.026 1.024 1.116 120 638 .998 .98 120 2890 9870 113 125 123 135 0 4760 121 4639 1.208 4834 4713 .828 1.202 .273 .266
5 337 362 93 100 244 262 308 336 119 120 215 236 0 0 143 162 91 81 95 95 59 73 506 451 .931 1.074 1.098 1.042 1.072 1.62 120 656 1.108 .89 120 3100 9870 113 125 144 156 0 426 118 308 1.263 395 278 .792 1.291 .337 .369
6 591 763 86 86 505 677 576 759 125 125 490 673 0 0 127 170 210 286 98 97 79 79 1182 1163 .746 1.341 1.373 1.33 1.36 1.266 120 625 1.351 .94 120 3300 9870 113 125 164 176 0 898 101 796 1.577 893 792 .634 1.616 .657 .692
7 191 187 81 81 110 106 177 179 99 90 96 98 0 0 81 68 67 41 75 85 27 63 216 194 1.038 .964 1.021 .908 .981 2.306 120 634 .739 .74 120 3500 9850 111 123 184 196 0 220 95 125 1.134 211 115 .882 1.201 .181 .264
8 2962 2186 91 93 2871 2093 3081 2257 112 106 2990 2164 0 0 607 445 72 58 100 100 100 100 4964 5154 1.372 .729 .724 .731 .733 1.125 120 651 .717 .98 120 3700 9870 113 125 204 216 0 2572 109 2462 .858 2655 2546 1.166 .851 -.222 -.232
9 913 1173 97 103 816 1070 923 1155 120 121 826 1052 0 0 164 214 72 78 100 100 100 100 1886 1878 .763 1.311 1.274 1.313 1.313 1.183 80 589 1.29 .95 110 3900 9850 111 122 224 235 0 1380 121 1259 1.543 1359 1238 .648 1.498 .625 .583
10 397 346 100 104 297 242 380 335 126 118 280 231 0 0 143 109 96 67 94 94 74 85 539 511 1.227 .815 .825 .838 .833 1.569 120 695 .726 .86 120 4110 9870 113 125 245 257 0 407 122 285 .959 394 272 1.043 .971 -.061 -.043
11 522 454 96 92 426 362 513 435 114 105 417 343 0 0 156 142 61 52 100 100 98 98 788 760 1.177 .85 .823 .842 .854 1.342 80 566 .84 .92 110 4310 9860 112 123 265 276 0 534 108 426 1 512 404 1 .968 0 -.047
12 260 238 90 89 170 149 238 225 107 101 148 136 0 0 89 88 58 49 90 90 68 71 319 284 1.141 .876 .919 .846 .865 1.715 80 608 .853 .8 110 4510 9850 111 122 285 296 0 280 105 175 1.031 265 160 .97 1.081 .044 .112
13 453 472 86 84 367 388 462 462 103 94 376 378 0 0 117 121 58 41 100 100 98 100 755 754 .946 1.057 1.005 1.063 1.027 1.367 80 583 1.035 .89 110 4720 9860 112 123 306 317 0 555 99 456 1.244 544 445 .804 1.183 .315 .242
14 578 745 94 92 484 653 585 769 116 103 491 677 0 0 130 193 65 49 98 99 96 99 1137 1168 .741 1.349 1.379 1.349 1.373 1.301 120 648 1.386 .94 120 4920 9860 112 124 326 338 0 876 108 768 1.587 905 796 .63 1.622 .667 .698
15 3478 5087 104 108 3374 4979 3481 5148 136 142 3377 5040 0 0 889 1151 140 102 100 100 100 100 8353 8417 .678 1.476 1.492 1.5 1.467 1.22 120 645 1.445 .98 130 5110 9870 112 125 344 357 0 5985 127 5858 1.736 6056 5929 .576 1.756 .796 .812
16 738 1074 102 110 636 964 734 1057 132 141 632 947 0 0 204 249 102 105 100 100 98 100 1600 1579 .66 1.516 1.498 1.549 1.55 1.268 120 612 1.478 .93 120 5310 9870 113 125 365 377 0 1264 129 1134 1.783 1244 1114 .561 1.763 .834 .818
17 381 390 96 93 285 297 369 374 114 102 273 281 0 0 109 140 64 48 98 98 96 97 582 554 .96 1.042 1.029 1.009 1.062 1.387 80 532 1.069 .89 110 5510 9870 113 124 385 396 0 459 109 349 1.226 440 331 .816 1.211 .294 .276
18 880 967 86 85 794 882 895 932 104 99 809 847 0 0 232 282 58 63 100 100 98 100 1676 1656 .9 1.111 1.047 1.119 1.099 1.273 80 585 1.114 .97 110 5700 9850 111 122 404 415 0 1138 100 1038 1.307 1096 996 .765 1.232 .386 .301
19 310 284 85 81 225 203 295 265 103 95 210 184 0 0 93 101 53 52 96 96 92 82 428 394 1.108 .902 .876 .865 .899 1.474 80 603 .919 .88 110 5900 9850 111 122 424 435 0 334 95 239 1.061 312 216 .942 1.031 .086 .044
20 322 263 86 77 236 186 308 251 102 86 222 174 0 0 97 86 49 37 100 98 92 91 422 396 1.269 .788 .784 .752 .751 1.495 80 572 .778 .86 110 6100 9870 113 124 444 455 0 309 91 219 .927 295 205 1.078 .922 -.109 -.117

Total number of rows: 6912

Table truncated, full table size 1502 Kbytes.




Supplementary data files not provided
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