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Sample GSM90521 Query DataSets for GSM90521
Status Public on Jan 04, 2006
Title Puf1 IP (2)
Sample type RNA
 
Channel 1
Source name Puf1 tot. RNA extract (2)
Organism Saccharomyces cerevisiae
Characteristics Puf1 tot. RNA extract (2)
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name Puf1 RNA-IP (2)
Organism Saccharomyces cerevisiae
Characteristics Puf1 RNA-IP (2)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2003-01/36819.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
1 135 49 124 47 11 2 132 48 127 48 8 1 0 0 24 9 22 7 26 13 10 5 13 9 5.5 .182 .125 .325 .368 3.362 80 456 .032 .08 100 2900 17390 42 52 33 43 -50 246 236 10 .912 241 5 1.097 .627 -.133 -.674
2 142 54 127 49 15 5 136 52 129 49 9 3 0 0 37 14 24 7 25 27 12 16 20 12 3 .333 .333 .379 .363 3.863 80 407 .101 .28 100 3070 17390 42 52 50 60 -50 271 246 25 1.672 261 15 .598 1.672 .741 .741
3 167 58 126 49 41 9 142 55 130 50 16 6 0 0 87 21 24 9 36 35 20 16 50 22 4.556 .22 .375 .4 .462 3.036 80 432 .104 .39 100 3240 17390 42 52 67 77 -50 291 246 45 1.101 276 30 .908 1.881 .139 .911
4 141 54 126 51 15 3 135 53 129 51 9 2 0 0 33 10 27 9 27 17 10 7 18 11 5 .2 .222 .347 .38 3.506 80 420 .083 .2 100 3410 17390 42 52 84 94 -50 271 256 15 1.003 266 10 .997 1.115 .005 .157
5 145 56 127 51 18 5 136 52 130 52 9 1 0 0 41 14 28 9 30 28 17 13 23 10 3.6 .278 .111 .34 .352 3.323 80 444 .096 .25 100 3580 17390 42 52 101 111 -50 281 256 25 1.393 261 5 .718 .557 .478 -.843
6 160 62 141 55 19 7 143 57 178 62 2 2 0 0 70 27 95 22 10 12 2 6 26 4 2.714 .368 1 .303 .247 3.565 80 444 .211 .61 100 3760 17390 42 52 119 129 -50 311 276 35 1.848 286 10 .541 5.016 .886 2.326
7 248 85 154 60 94 25 214 79 236 71 60 19 0 0 136 35 611 46 1 16 0 6 119 79 3.76 .266 .317 .326 .281 2.75 80 440 .199 .8 100 3930 17380 41 51 136 146 -50 426 301 125 1.334 396 95 .75 1.588 .416 .667
8 286 88 141 56 145 32 290 86 190 62 149 30 0 0 95 23 535 39 0 32 0 3 177 179 4.531 .221 .201 .216 .223 2.06 156 572 .181 .73 140 4120 17410 42 56 153 167 -100 441 281 161 1.107 431 150 .903 1.01 .147 .014
9 374 100 140 56 234 44 286 91 154 59 146 35 0 0 633 41 55 15 77 74 61 54 278 181 5.318 .188 .24 .249 .268 2.284 208 840 .036 .4 160 4260 17410 41 57 166 182 -100 502 281 221 .943 456 176 1.06 1.202 -.084 .266
10 595 184 150 59 445 125 555 176 193 64 405 117 0 0 219 55 265 17 80 98 31 93 570 522 3.56 .281 .289 .286 .302 2.037 80 400 .231 .82 100 4460 17380 41 51 189 199 0 923 296 627 1.409 883 587 .71 1.449 .495 .535
11 250 89 152 60 98 29 238 86 176 63 86 26 0 0 112 26 69 16 57 70 23 31 127 112 3.379 .296 .302 .29 .264 2.583 80 354 .168 .69 100 4610 17380 41 51 204 214 -50 446 301 145 1.484 431 130 .674 1.516 .57 .601
12 233 83 147 58 86 25 225 79 170 62 78 21 0 0 107 30 68 17 55 54 28 32 111 99 3.44 .291 .269 .277 .286 1.978 120 550 .189 .72 120 4780 17370 39 51 220 232 -100 416 291 125 1.458 396 105 .686 1.35 .544 .433
13 4652 1167 143 57 4509 1110 4963 1249 162 60 4820 1192 0 0 1255 286 61 16 100 100 100 100 5619 6012 4.062 .246 .247 .25 .248 1.394 80 506 .22 .91 110 4970 17380 40 51 239 250 0 5853 286 5567 1.235 6265 5979 .81 1.24 .304 .311
14 39714 6203 148 57 39566 6146 45266 6450 173 63 45118 6393 0 0 14647 1554 79 20 100 100 100 100 45712 51511 6.438 .155 .142 .176 .148 2.114 80 497 .132 .91 110 5140 17370 39 50 256 267 0 31112 286 30827 .779 32351 32065 1.284 .711 -.36 -.493
15 56952 15856 152 61 56800 15795 62609 16720 199 70 62457 16659 15 0 13350 2653 113 25 100 100 100 100 72595 79116 3.596 .278 .267 .288 .269 1.512 80 510 .253 .93 110 5310 17370 39 50 273 284 0 79529 306 79223 1.395 83863 83557 .717 1.338 .48 .42
16 3948 822 142 56 3806 766 3573 754 173 63 3431 698 0 0 1764 343 98 22 100 100 100 100 4572 4129 4.969 .201 .203 .206 .199 1.645 80 483 .179 .87 110 5490 17380 40 51 291 302 0 4123 281 3842 1.009 3782 3501 .991 1.02 .014 .029
17 2234 489 134 53 2100 436 2124 490 137 54 1990 437 0 0 853 196 26 8 100 98 98 97 2536 2427 4.817 .208 .22 .19 .214 1.786 80 470 .203 .88 110 5650 17380 40 51 307 318 0 2453 266 2187 1.041 2458 2192 .96 1.101 .058 .139
18 20573 5141 133 53 20440 5088 21792 5369 137 54 21659 5316 0 0 5605 1485 32 9 100 100 100 100 25528 26975 4.017 .249 .245 .249 .245 1.56 80 444 .225 .9 100 5830 17370 40 50 326 336 0 25786 266 25520 1.249 26929 26664 .801 1.231 .32 .3
19 2857 601 132 53 2725 548 2792 606 136 55 2660 553 0 0 1174 260 28 14 100 97 100 97 3273 3213 4.973 .201 .208 .185 .215 1.887 80 468 .193 .85 110 6000 17370 39 50 342 353 0 3014 266 2749 1.009 3040 2774 .991 1.043 .012 .06
20 1827 411 135 53 1692 358 1820 430 138 56 1685 377 0 0 660 160 29 12 100 98 100 96 2050 2062 4.726 .212 .224 .201 .219 1.873 80 400 .198 .87 100 6170 17370 40 50 360 370 0 2061 266 1796 1.061 2157 1891 .942 1.122 .086 .166

Total number of rows: 9984

Table truncated, full table size 2183 Kbytes.




Supplementary data files not provided
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