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Sample GSM90518 Query DataSets for GSM90518
Status Public on Jan 04, 2006
Title Puf4 IP (3)
Sample type RNA
 
Channel 1
Source name Puf4 tot. RNA extract (3)
Organism Saccharomyces cerevisiae
Characteristics Puf4 tot. RNA extract (3)
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name Puf4 RNA-IP (3)
Organism Saccharomyces cerevisiae
Characteristics Puf4 RNA-IP (3)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2003-01/36826.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 Jan 03, 2006
Last update date Sep 22, 2006
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 GPL3300
Series (2)
GSE3968 Puf proteins, RNA co-immunopurification
GSE4393 Extensive association of functionally and cytotopically related mRNAs with Puf family RNA-binding proteins in yeast

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
1 127 42 118 40 9 2 122 42 120 40 4 2 0 0 18 6 16 5 27 32 10 13 11 6 4.5 .222 .5 .51 .462 3.521 80 444 .12 .31 100 2670 16860 53 63 18 28 -50 315 300 15 1.669 315 15 .599 3.754 .739 1.909
2 143 45 122 40 21 5 134 44 123 41 12 4 0 0 36 6 17 5 38 36 25 18 26 16 4.2 .238 .333 .278 .243 3.254 80 408 .106 .44 100 2840 16860 53 63 35 45 -50 338 300 38 1.788 330 30 .559 2.503 .838 1.324
3 138 44 126 41 12 3 129 44 141 44 3 3 0 0 30 6 150 26 0 0 0 0 15 6 4 .25 1 .309 .29 3.11 80 420 .104 .37 100 3010 16850 52 62 52 62 -50 330 308 23 1.877 330 23 .533 7.509 .909 2.909
4 135 44 127 42 8 2 127 43 141 44 0 1 0 0 25 7 150 26 0 0 0 0 10 1 4 .25 null .269 .25 2.626 80 420 .247 .88 100 3180 16850 52 62 69 79 -50 330 315 15 1.877 323 8 .533 null .909 null
5 145 46 126 41 19 5 134 45 128 42 8 4 0 0 34 8 17 6 36 38 21 13 24 12 3.8 .263 .5 .281 .231 2.626 80 446 .133 .45 100 3350 16850 52 62 86 96 -50 345 308 38 1.976 338 30 .506 3.754 .983 1.909
6 142 46 130 43 12 3 136 45 160 47 6 2 0 0 29 8 80 13 2 12 0 1 15 8 4 .25 .333 .306 .274 3.039 80 417 .153 .88 100 3530 16850 52 62 104 114 -50 345 323 23 1.877 338 15 .533 2.503 .909 1.324
7 323 74 139 45 184 29 328 74 166 48 189 29 0 0 114 22 77 13 85 82 72 57 213 218 6.345 .158 .153 .173 .16 1.853 120 483 .158 .91 130 3710 16870 52 65 120 133 -100 556 338 218 1.183 556 218 .845 1.152 .243 .204
8 330 76 142 45 188 31 323 73 160 47 181 28 0 0 70 16 54 10 100 95 90 75 219 209 6.065 .165 .155 .153 .167 1.447 80 381 .169 .89 110 3860 16860 52 63 136 147 -100 571 338 233 1.238 548 210 .808 1.162 .308 .216
9 346 75 152 47 194 28 303 70 185 51 151 23 0 0 202 24 102 15 81 78 20 25 222 174 6.929 .144 .152 .143 .155 1.594 80 468 .125 .92 110 4020 16860 52 63 152 163 -100 563 353 210 1.084 526 173 .923 1.144 .116 .194
10 1217 208 161 49 1056 159 1119 192 196 52 958 143 0 0 395 65 99 14 100 100 100 100 1215 1101 6.642 .151 .149 .148 .148 1.148 80 508 .153 .99 110 4220 16840 50 61 172 183 0 1562 368 1194 1.131 1442 1074 .885 1.121 .177 .165
11 289 66 163 49 126 17 237 64 184 50 74 15 0 0 123 18 62 11 60 53 38 32 143 89 7.412 .135 .203 .155 .145 2.148 80 357 .135 .88 100 4390 16840 51 61 190 200 -50 496 368 128 1.013 481 113 .987 1.522 .019 .606
12 295 72 150 45 145 27 297 73 167 48 147 28 0 0 63 13 55 11 91 85 73 64 172 175 5.37 .186 .19 .173 .18 1.779 156 597 .161 .84 140 4550 16840 49 63 204 218 -100 541 338 203 1.398 548 210 .715 1.43 .484 .516
13 5399 767 148 45 5251 722 5845 804 162 48 5697 759 0 0 2166 296 55 11 100 100 100 100 5973 6456 7.273 .137 .133 .14 .138 1.168 120 524 .136 .99 130 4730 16840 49 62 222 235 0 5759 338 5421 1.032 6037 5699 .969 1 .046 .001
14 41413 3289 153 48 41260 3241 46123 3566 188 53 45970 3518 7 0 20099 1660 102 18 100 98 100 98 44501 49488 12.731 .079 .077 .077 .075 1.214 120 485 .079 .99 120 4900 16840 50 62 240 252 0 24696 360 24336 .59 26776 26416 1.695 .575 -.762 -.799
15 46044 5866 152 49 45892 5817 52946 6336 211 58 52794 6287 30 0 20542 2788 116 20 100 100 100 100 51709 59081 7.889 .127 .119 .127 .127 1.151 120 545 .128 .99 120 5080 16830 49 61 258 270 0 44046 368 43678 .952 47575 47207 1.051 .894 -.071 -.161
16 5410 729 143 47 5267 682 5016 663 174 52 4873 616 0 0 1833 241 82 15 100 100 100 100 5949 5489 7.723 .129 .126 .129 .13 1.075 80 477 .128 1 110 5260 16830 49 60 276 287 0 5474 353 5121 .972 4978 4625 1.029 .949 -.041 -.075
17 2661 529 141 46 2520 483 2565 500 144 46 2424 454 0 0 696 133 26 6 100 100 100 100 3003 2878 5.217 .192 .187 .192 .192 1.078 80 448 .189 .99 110 5430 16830 49 60 293 304 0 3972 345 3627 1.439 3754 3409 .695 1.406 .525 .492
18 23673 2211 145 47 23528 2164 25632 2344 149 48 25487 2297 0 0 5007 467 29 8 100 100 100 100 25692 27784 10.872 .092 .09 .092 .092 1.061 80 467 .092 1 110 5590 16830 49 60 309 320 0 16602 353 16249 .691 17600 17247 1.448 .677 -.534 -.563
19 2928 314 146 47 2782 267 2869 307 152 48 2723 260 0 0 1094 102 49 9 100 100 100 100 3049 2983 10.419 .096 .095 .097 .096 1.127 80 469 .092 .99 110 5760 16820 48 59 326 337 0 2358 353 2005 .721 2305 1952 1.388 .717 -.473 -.48
20 2214 298 141 46 2073 252 2302 295 146 47 2161 249 0 0 519 68 49 7 100 100 100 100 2325 2410 8.226 .122 .115 .121 .123 1.132 80 458 .12 .99 110 5940 16820 48 59 344 355 0 2238 345 1892 .913 2215 1870 1.096 .865 -.132 -.209

Total number of rows: 9984

Table truncated, full table size 2171 Kbytes.




Supplementary data files not provided
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