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Sample GSM90522 Query DataSets for GSM90522
Status Public on Jan 04, 2006
Title Puf3 IP (1)
Sample type RNA
 
Channel 1
Source name tot. RNA Puf3 (ex)
Organism Saccharomyces cerevisiae
Characteristics tot. RNA Puf3 (ex)
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name IP RNA Puf3 (1)
Organism Saccharomyces cerevisiae
Characteristics IP RNA Puf3 (1)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2002-06/29828.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 GPL3270
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
1 187 54 52 29 135 25 180 53 55 29 128 24 0 0 50 16 11 8 100 86 100 71 160 152 5.4 .185 .188 .184 .189 1.828 52 362 .178 .7 90 1100 18140 33 42 21 30 0 338 181 156 1.157 331 150 .864 1.172 .211 .229
2 60 28 53 28 7 0 57 26 54 28 4 -2 0 0 17 9 10 8 28 16 13 7 7 2 null null null .818 1 3.54 80 398 .216 .17 100 1270 18130 32 42 38 48 -50 175 175 0 null 163 null null null null null
3 8726 993 51 29 8675 964 5466 591 52 30 5415 562 0 0 7041 843 10 9 100 100 100 100 9639 5977 8.999 .111 .104 .105 .106 1.887 156 614 .107 .92 140 1460 18130 30 44 55 69 0 6206 181 6025 .695 3694 3513 1.44 .649 -.526 -.624
4 535 89 50 29 485 60 406 72 52 30 356 43 0 0 360 46 11 9 100 92 99 80 545 399 8.083 .124 .121 .124 .125 1.923 156 587 .109 .87 140 1610 18140 31 45 70 84 0 556 181 375 .773 450 269 1.293 .755 -.371 -.406
5 62 27 51 26 11 1 59 27 52 27 8 1 0 0 13 7 9 8 46 12 22 2 12 9 11 .091 .125 .642 .696 3.8 80 437 .033 .03 100 1790 18120 31 41 90 100 -50 169 163 6 .568 169 6 1.76 .781 -.816 -.356
6 58 32 49 29 9 3 55 32 50 30 6 3 0 0 17 9 8 8 36 25 20 7 12 9 3 .333 .5 .781 .625 3.779 80 392 .107 .09 100 1970 18120 31 41 108 118 -50 200 181 19 2.083 200 19 .48 3.125 1.059 1.644
7 351 81 49 27 302 54 245 62 50 27 196 35 0 0 227 49 8 8 100 86 99 75 356 231 5.593 .179 .179 .172 .179 2.022 156 580 .179 .89 140 2140 18130 30 44 123 137 0 506 169 338 1.118 388 219 .895 1.116 .16 .158
8 403 95 48 30 355 65 294 67 50 31 246 37 0 0 312 63 9 8 98 78 96 66 420 283 5.462 .183 .15 .193 .192 2.665 120 504 .176 .9 120 2320 18120 30 42 142 154 0 594 188 406 1.144 419 231 .874 .94 .195 -.089
9 182 59 50 28 132 31 132 52 54 29 82 24 0 0 108 30 23 9 96 73 76 56 163 106 4.258 .235 .293 .224 .26 2.288 156 736 .228 .83 140 2510 18130 30 44 160 174 0 369 175 194 1.468 325 150 .681 1.829 .554 .871
10 324 96 54 30 270 66 306 90 60 31 252 60 0 0 94 31 32 9 100 100 100 100 336 312 4.091 .244 .238 .23 .232 1.55 52 333 .234 .85 90 2670 18130 32 41 178 187 0 600 188 413 1.528 563 375 .655 1.488 .611 .573
11 600 86 57 30 543 56 377 66 59 31 320 36 0 0 462 50 15 9 100 88 100 73 599 356 9.696 .103 .113 .109 .113 1.968 120 594 .092 .85 130 2860 18150 32 45 195 208 0 538 188 350 .645 413 225 1.551 .703 -.634 -.508
12 825 173 55 28 770 145 966 190 58 30 911 162 0 0 362 85 24 11 100 96 100 92 915 1073 5.31 .188 .178 .164 .191 1.938 80 450 .185 .91 110 3020 18120 30 41 212 223 0 1081 175 906 1.177 1188 1013 .85 1.111 .235 .152
13 332 79 53 31 279 48 248 59 85 37 195 28 0 0 287 57 204 46 45 35 23 20 327 223 5.813 .172 .144 .186 .18 2.954 120 664 .154 .79 130 3200 18120 29 42 229 242 -100 494 194 300 1.075 369 175 .93 .897 .105 -.156
14 2253 364 45 26 2208 338 1261 125 106 40 1216 99 0 0 2359 403 291 64 80 59 59 48 2546 1315 6.533 .153 .081 .127 .123 2.596 52 317 .148 .86 90 3350 18090 28 37 246 255 0 2275 163 2113 .957 781 619 1.045 .509 -.064 -.975
15 287 76 40 27 247 49 266 65 55 30 226 38 0 0 177 41 77 14 78 76 61 61 296 264 5.041 .198 .168 .217 .198 2.578 52 337 .173 .78 80 3520 18130 33 41 264 272 0 475 169 306 1.24 406 238 .807 1.051 .31 .072
16 112 37 48 28 64 9 89 34 58 29 41 6 0 0 73 15 55 10 41 33 22 17 73 47 7.111 .141 .146 .208 .2 3.233 80 500 .13 .52 100 3720 18120 31 41 283 293 -50 231 175 56 .879 213 38 1.138 .915 -.186 -.129
17 424 56 54 30 370 26 449 55 59 31 395 25 0 0 165 18 26 9 98 78 96 63 396 420 14.231 .07 .063 .07 .068 2.328 52 318 .061 .65 80 3910 18120 32 40 303 311 0 350 188 163 .439 344 156 2.277 .396 -1.187 -1.338
18 253 66 56 30 197 36 215 51 60 31 159 21 0 0 179 39 22 10 82 71 76 51 233 180 5.472 .183 .132 .228 .203 2.985 80 506 .167 .77 110 4080 18120 30 41 318 329 0 413 188 225 1.142 319 131 .876 .825 .192 -.277
19 549 106 57 29 492 77 392 88 58 30 335 59 0 0 299 63 12 9 100 90 100 83 569 394 6.39 .157 .176 .131 .153 2.026 120 665 .159 .88 130 4250 18120 29 42 334 347 0 663 181 481 .978 550 369 1.022 1.101 -.032 .138
20 154 42 57 29 97 13 149 40 58 30 92 11 0 0 46 12 11 9 100 53 97 25 110 103 7.462 .134 .12 .131 .138 2.095 80 402 .131 .59 100 4420 18120 31 41 353 363 0 263 181 81 .838 250 69 1.194 .747 -.256 -.42

Total number of rows: 9600

Table truncated, full table size 1973 Kbytes.




Supplementary data files not provided
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