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Sample GSM90525 Query DataSets for GSM90525
Status Public on Jan 04, 2006
Title Puf2 IP (1)
Sample type RNA
 
Channel 1
Source name Puf2 tot. RNA extract (1)
Organism Saccharomyces cerevisiae
Characteristics Puf2 tot. RNA extract (1)
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name Puf2 RNA-IP (1)
Organism Saccharomyces cerevisiae
Characteristics Puf2 RNA-IP (1)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/34715.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 GPL3269
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
1 502 190 55 28 447 162 517 197 56 29 462 169 0 0 107 46 9 7 100 100 100 100 609 631 2.759 .362 .366 .356 .365 1.402 52 368 .337 .92 90 2080 18130 40 49 43 52 0 528 78 450 1.007 547 469 .993 1.016 .01 .023
2 39858 7808 56 32 39802 7776 46911 9294 59 34 46855 9262 0 0 17130 3211 17 11 100 100 100 100 47578 56117 5.119 .195 .198 .215 .198 2.391 80 512 .178 .92 110 2250 18130 39 50 59 70 0 21689 89 21600 .543 25817 25728 1.843 .549 -.882 -.865
3 36065 14468 59 32 36006 14436 39253 15980 66 34 39194 15948 0 0 11215 5174 27 12 100 100 100 100 50442 55142 2.494 .401 .407 .4 .41 2.433 80 452 .376 .89 100 2430 18130 40 50 78 88 0 40189 89 40100 1.114 44389 44300 .898 1.13 .155 .177
4 3094 1017 57 32 3037 985 3118 1117 59 32 3061 1085 0 0 851 383 15 9 100 100 100 100 4022 4146 3.083 .324 .354 .282 .354 2.433 80 426 .297 .86 100 2610 18130 40 50 96 106 0 2825 89 2736 .901 3103 3014 1.11 .985 -.151 -.022
5 1990 606 59 30 1931 576 1931 639 60 31 1872 609 0 0 676 189 10 9 100 100 100 98 2507 2481 3.352 .298 .325 .309 .315 1.965 80 428 .258 .87 100 2780 18130 40 50 113 123 0 1683 83 1600 .829 1775 1692 1.207 .904 -.271 -.146
6 21073 7509 69 31 21004 7478 23146 7973 71 31 23077 7942 0 0 8062 2399 17 11 100 100 100 100 28482 31019 2.809 .356 .344 .405 .367 2.187 80 470 .316 .91 110 2950 18130 39 50 129 140 0 20858 86 20772 .989 22147 22061 1.011 .956 -.016 -.065
7 2725 1007 63 32 2662 975 2909 1084 65 32 2846 1052 0 0 778 355 13 8 100 100 100 98 3637 3898 2.73 .366 .37 .359 .386 2.267 80 450 .356 .93 100 3120 18120 39 49 147 157 0 2797 89 2708 1.017 3011 2922 .983 1.027 .025 .038
8 771 279 59 27 712 252 763 286 59 27 704 259 0 0 103 60 8 7 100 100 100 100 964 963 2.825 .354 .368 .344 .36 1.308 52 379 .356 .93 90 3300 18110 38 47 165 174 0 775 75 700 .983 794 719 1.017 1.022 -.025 .031
9 1572 675 58 32 1514 643 1538 671 58 32 1480 639 0 0 274 125 8 7 100 100 100 100 2157 2119 2.355 .425 .432 .423 .437 1.179 52 371 .403 .95 90 3470 18110 38 47 182 191 0 1875 89 1786 1.18 1864 1775 .848 1.199 .238 .262
10 395 134 58 29 337 105 393 141 58 30 335 112 0 0 85 35 10 9 100 98 100 98 442 447 3.21 .312 .334 .295 .314 1.611 52 379 .297 .9 90 3640 18110 38 47 199 208 0 372 81 292 .865 392 311 1.155 .929 -.208 -.107
11 2456 938 56 30 2400 908 2625 971 58 31 2569 941 0 0 1091 295 10 9 96 100 96 100 3308 3510 2.643 .378 .366 .468 .377 2.836 80 462 .34 .94 100 3820 18120 39 49 217 227 0 2606 83 2522 1.051 2697 2614 .952 1.017 .072 .025
12 2813 1118 57 31 2756 1087 3056 1137 60 32 2999 1106 0 0 1051 261 16 9 97 100 96 100 3843 4105 2.535 .394 .369 .495 .387 2.626 80 482 .359 .95 110 4000 18120 38 49 234 245 0 3106 86 3019 1.096 3158 3072 .913 1.024 .132 .035
13 2366 1062 57 30 2309 1032 2710 1230 65 34 2653 1200 0 0 1115 434 38 26 100 100 100 98 3341 3853 2.237 .447 .452 .503 .448 2.483 80 427 .411 .93 100 4160 18120 39 49 251 261 0 2950 83 2867 1.242 3417 3333 .805 1.256 .312 .329
14 18180 9298 57 33 18123 9265 19204 9883 64 37 19147 9850 0 0 7298 3376 35 25 100 100 100 100 27388 28997 1.956 .511 .514 .543 .507 2.399 80 474 .479 .93 100 4340 18120 39 49 269 279 0 25828 92 25736 1.42 27453 27361 .704 1.429 .506 .515
15 3229 1204 58 30 3171 1174 3177 1260 60 31 3119 1230 0 0 483 323 12 9 100 100 100 100 4345 4349 2.701 .37 .394 .347 .395 1.676 52 387 .364 .93 90 4520 18110 38 47 287 296 0 3344 83 3261 1.028 3500 3417 .972 1.095 .04 .132
16 1622 637 58 33 1564 604 1653 632 60 34 1595 599 0 0 334 123 13 8 100 100 100 100 2168 2194 2.589 .386 .376 .389 .399 1.259 52 394 .371 .96 90 4690 18110 38 47 304 313 0 1769 92 1678 1.073 1756 1664 .932 1.043 .101 .061
17 1317 432 58 31 1259 401 1335 463 59 31 1277 432 0 0 253 119 10 8 100 98 100 98 1660 1709 3.14 .319 .338 .302 .324 1.46 52 394 .312 .96 90 4870 18110 38 47 322 331 0 1200 86 1114 .885 1286 1200 1.13 .94 -.177 -.09
18 1270 619 57 32 1213 587 1415 689 58 32 1358 657 0 0 613 334 10 8 98 96 98 95 1800 2015 2.066 .484 .484 .431 .5 2.124 80 464 .488 .95 100 5050 18110 38 48 340 350 0 1719 89 1631 1.344 1914 1825 .744 1.344 .427 .426
19 2590 888 57 32 2533 856 2709 932 60 33 2652 900 0 0 1213 437 13 10 100 96 100 95 3389 3552 2.959 .338 .339 .349 .364 2.078 80 510 .323 .93 110 5220 18110 37 48 356 367 0 2467 89 2378 .939 2589 2500 1.065 .943 -.091 -.085
20 372 172 57 29 315 143 399 199 59 31 342 170 0 0 128 74 13 9 100 95 97 91 458 512 2.203 .454 .497 .471 .513 1.88 80 444 .441 .88 100 5400 18110 38 48 375 385 0 478 81 397 1.261 553 472 .793 1.381 .335 .465

Total number of rows: 10752

Table truncated, full table size 2264 Kbytes.




Supplementary data files not provided
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