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Sample GSM87461 Query DataSets for GSM87461
Status Public on Dec 15, 2005
Title wt_hypo_osmotic_shock_60min
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,60min after transfer to regular YPD
Organism Saccharomyces cerevisiae
Characteristics wt,60min after transfer to regular YPD
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Mutants, osmotic
Image: http://smd.stanford.edu/MicroArray/gifs/2002-10/34351.gif
Measurement: time(absolute) 60 m
name: 34351_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 1926 2573 69 66 1857 2507 1853 2450 82 77 1784 2384 0 0 748 1047 44 56 100 100 100 100 4364 4168 .741 1.35 1.336 1.35 1.319 1.179 120 844 1.348 .97 130 2240 9790 104 117 57 70 0 2957 76 2882 1.552 2816 2740 .644 1.536 .634 .619
2 2309 2413 68 66 2241 2347 2243 2217 85 85 2175 2151 0 0 811 1022 59 85 100 100 100 100 4588 4326 .955 1.047 .989 1.038 .976 1.26 120 643 1.064 .95 120 2460 9800 106 118 80 92 0 2774 76 2698 1.204 2548 2472 .831 1.137 .268 .185
3 317 350 67 67 250 283 273 300 81 79 206 233 0 0 152 180 52 60 99 100 93 89 533 439 .883 1.132 1.131 1.113 1.08 1.526 120 715 1.202 .9 130 2650 9800 105 118 98 111 0 402 77 325 1.301 345 268 .769 1.3 .38 .379
4 4072 3355 67 64 4005 3291 3801 3200 80 73 3734 3136 0 0 1594 1323 42 40 100 100 100 100 7296 6870 1.217 .822 .84 .818 .821 1.187 120 664 .82 .99 130 2850 9800 105 118 118 131 0 3856 74 3783 .945 3678 3605 1.059 .965 -.082 -.051
5 326 358 69 64 257 294 305 323 84 78 236 259 0 0 168 205 48 54 96 96 87 88 551 495 .874 1.144 1.097 1.108 1.117 1.594 120 639 1.176 .91 120 3040 9790 105 117 138 150 0 411 74 338 1.315 371 298 .761 1.261 .395 .335
6 643 828 69 67 574 761 631 780 83 79 562 713 0 0 204 237 58 58 100 100 99 100 1335 1275 .754 1.326 1.269 1.35 1.347 1.248 120 696 1.299 .96 130 3250 9800 105 118 158 171 0 952 77 875 1.524 897 820 .656 1.458 .608 .544
7 195 195 69 67 126 128 170 169 96 85 101 102 0 0 90 105 186 125 15 34 5 10 254 203 .984 1.016 1.01 .919 1.005 1.972 120 642 1.107 .85 120 3440 9790 105 117 178 190 0 224 77 147 1.168 194 117 .856 1.161 .224 .215
8 3270 2093 69 65 3201 2028 3191 2031 97 82 3122 1966 0 0 817 533 197 130 100 100 100 100 5229 5088 1.578 .634 .63 .636 .624 1.176 80 548 .621 .98 110 3640 9800 106 117 198 209 0 2406 75 2331 .728 2334 2260 1.373 .724 -.458 -.466
9 786 945 68 67 718 878 778 945 81 75 710 878 0 0 237 280 42 46 100 100 100 100 1596 1588 .818 1.223 1.237 1.231 1.21 1.264 120 690 1.243 .96 120 3840 9790 105 117 218 230 0 1086 77 1009 1.406 1086 1009 .711 1.421 .491 .507
10 269 223 67 65 202 158 249 208 80 73 182 143 0 0 129 93 42 47 97 93 91 76 360 325 1.278 .782 .786 .793 .798 1.582 80 560 .79 .88 110 4030 9790 105 116 237 248 0 256 75 182 .899 239 164 1.112 .903 -.154 -.147
11 365 275 69 65 296 210 355 259 81 71 286 194 0 0 155 104 42 30 96 97 94 95 506 480 1.41 .709 .678 .721 .713 1.955 120 646 .683 .91 120 4240 9790 105 117 258 270 0 316 75 241 .815 298 223 1.226 .78 -.294 -.359
12 151 117 71 65 80 52 133 108 82 71 62 43 0 0 71 49 40 30 71 66 35 32 132 105 1.538 .65 .694 .689 .675 2.285 120 751 .589 .7 130 4430 9780 103 116 276 289 0 134 75 60 .747 124 49 1.338 .797 -.421 -.327
13 246 232 71 65 175 167 213 204 82 69 142 139 0 0 113 124 37 25 92 93 81 86 342 281 1.048 .954 .979 .898 .873 2.015 80 548 1.037 .81 110 4630 9800 106 117 297 308 0 267 75 192 1.097 234 160 .912 1.125 .133 .17
14 555 572 71 67 484 505 571 600 83 71 500 533 0 0 166 175 36 26 98 99 95 95 989 1033 .958 1.043 1.066 1.036 1.025 1.334 120 675 1.068 .95 120 4840 9780 104 116 318 330 0 657 77 580 1.199 690 613 .834 1.225 .262 .293
15 1943 2535 71 67 1872 2468 2074 2505 86 73 2003 2438 0 0 740 779 46 28 98 100 98 100 4340 4441 .759 1.318 1.217 1.447 1.274 1.618 120 597 1.284 .97 120 5040 9800 106 118 338 350 0 2914 77 2837 1.515 2879 2802 .66 1.399 .6 .484
16 545 741 72 68 473 673 556 742 85 71 484 674 0 0 162 218 52 24 99 100 98 100 1146 1158 .703 1.423 1.393 1.453 1.413 1.324 120 663 1.475 .95 120 5240 9790 105 117 358 370 0 852 78 774 1.635 853 775 .611 1.601 .71 .679
17 274 263 70 65 204 198 252 234 81 68 182 169 0 0 109 117 37 20 100 100 93 100 402 351 1.03 .971 .929 .979 .949 1.628 80 526 1.021 .83 110 5440 9800 106 117 378 389 0 302 75 228 1.116 269 194 .896 1.067 .158 .094
18 515 525 71 68 444 457 509 528 86 73 438 460 0 0 142 165 47 30 99 100 99 99 901 898 .972 1.029 1.05 1.033 1.021 1.383 120 662 1.058 .95 120 5640 9790 105 117 398 410 0 603 78 525 1.183 607 529 .845 1.207 .243 .272
19 137 124 70 67 67 57 129 103 82 72 59 36 0 0 45 74 43 27 69 63 21 35 124 95 1.175 .851 .61 .703 .725 2.913 120 741 1.248 .59 130 5840 9790 104 117 417 430 0 143 77 66 .978 118 41 1.023 .701 -.032 -.512
20 254 188 69 65 185 123 256 184 80 70 187 119 0 0 76 46 40 25 97 97 93 95 308 306 1.504 .665 .636 .681 .663 1.692 80 562 .622 .86 110 6040 9780 104 115 438 449 0 216 75 141 .764 211 137 1.309 .731 -.388 -.451

Total number of rows: 6912

Table truncated, full table size 1464 Kbytes.




Supplementary data files not provided
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