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Sample GSM90529 Query DataSets for GSM90529
Status Public on Jan 04, 2006
Title BY4741 mock (4)
Sample type RNA
 
Channel 1
Source name BY4741 tot. RNA extract (4)
Organism Saccharomyces cerevisiae
Characteristics BY4741 tot. RNA extract (4)
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name BY4741 RNA-IP (4)
Organism Saccharomyces cerevisiae
Characteristics BY4741 RNA-IP (4)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: RNA coimmunoprecipitation, IP Controls
Image: http://smd.stanford.edu/MicroArray/gifs/2003-01/37362.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 96 36 82 29 14 7 82 31 84 29 0 2 0 0 44 18 18 4 23 28 15 17 21 2 2 .5 null .322 .253 2.902 80 464 .256 .74 100 2250 17610 36 46 20 30 -50 344 277 67 4.771 296 19 .21 null 2.254 null
2 118 37 91 30 27 7 96 30 95 31 5 0 0 0 64 21 24 6 30 21 15 16 34 5 3.857 .259 null .385 .379 3.143 80 428 .273 .79 100 2420 17610 36 46 37 47 -50 353 286 67 2.474 286 0 .404 null 1.307 null
3 98 36 85 30 13 6 85 32 89 31 0 2 0 0 45 14 21 5 15 22 11 12 19 2 2.167 .462 null .356 .333 3.692 80 428 .208 .69 100 2590 17610 36 46 54 64 -50 344 286 57 4.404 305 19 .227 null 2.139 null
4 94 32 87 29 7 3 88 30 89 30 1 1 0 0 27 10 17 4 18 20 7 13 10 2 2.333 .429 1 .351 .333 2.917 80 429 .2 .59 100 2760 17610 36 46 71 81 -50 305 277 29 4.09 286 10 .245 9.543 2.032 3.254
5 104 36 88 31 16 5 93 31 89 31 5 0 0 0 44 13 15 5 30 27 15 17 21 5 3.2 .313 null .434 .449 2.737 80 429 .226 .72 100 2930 17610 36 46 88 98 -50 344 296 48 2.982 296 0 .335 null 1.576 null
6 121 38 94 32 27 6 101 33 107 34 7 1 0 0 68 15 36 7 16 28 12 13 33 8 4.5 .222 .143 .447 .471 2.816 80 432 .171 .74 100 3100 17600 35 45 105 115 -50 363 305 57 2.121 315 10 .472 1.363 1.085 .447
7 166 45 115 35 51 10 153 41 118 37 38 6 0 0 63 14 37 8 50 37 17 15 61 44 5.1 .196 .158 .223 .219 2.99 80 444 .15 .7 100 3270 17600 35 45 122 132 -50 429 334 95 1.871 391 57 .534 1.507 .904 .591
8 154 45 104 35 50 10 136 41 109 35 32 6 0 0 70 16 30 7 51 41 18 17 60 38 5 .2 .188 .242 .222 2.711 80 426 .176 .75 100 3450 17600 35 45 140 150 -50 429 334 95 1.909 391 57 .524 1.789 .933 .839
9 156 41 101 33 55 8 135 37 103 33 34 4 0 0 81 19 25 6 63 33 30 15 63 38 6.875 .145 .118 .218 .22 2.966 80 432 .186 .84 100 3620 17600 35 45 157 167 -50 391 315 76 1.388 353 38 .72 1.123 .473 .167
10 471 77 107 36 364 41 472 71 112 36 365 35 0 0 62 19 30 6 100 100 100 100 405 400 8.878 .113 .096 .104 .097 1.471 52 354 .111 .88 90 3790 17610 36 45 174 183 0 735 344 391 1.075 678 334 .93 .915 .104 -.128
11 177 45 120 36 57 9 151 40 123 36 31 4 0 0 88 19 31 7 50 31 23 16 66 35 6.333 .158 .129 .217 .241 3.071 80 469 .176 .75 100 3960 17600 35 45 191 201 -50 429 344 86 1.507 382 38 .664 1.231 .591 .3
12 289 76 152 43 137 33 247 52 162 45 95 9 0 0 144 42 68 13 66 41 25 33 170 104 4.152 .241 .095 .175 .162 3.891 12 104 .197 .85 50 4130 17640 41 46 210 215 -100 725 410 315 2.299 496 86 .435 .904 1.201 -.145
13 1108 146 115 34 993 112 1102 143 119 35 987 109 0 0 181 28 35 8 100 100 100 100 1105 1096 8.866 .113 .11 .111 .11 1.359 80 498 .106 .93 110 4310 17620 36 47 225 236 0 1393 324 1069 1.076 1365 1040 .929 1.054 .106 .076
14 23378 1483 107 33 23271 1450 27682 1656 116 35 27575 1623 0 0 11735 706 38 8 100 100 100 99 24721 29198 16.049 .062 .059 .065 .061 1.569 120 499 .06 .97 120 4480 17620 36 48 242 254 0 14152 315 13837 .595 15803 15488 1.682 .562 -.75 -.832
15 47209 4790 116 36 47093 4754 60297 5816 126 38 60181 5780 16 0 22614 2162 43 9 100 100 100 100 51847 65961 9.906 .101 .096 .109 .101 1.489 120 526 .098 .98 120 4650 17620 36 48 259 271 0 45711 344 45367 .963 55502 55159 1.038 .917 -.054 -.126
16 1908 194 99 32 1809 162 1871 189 105 33 1772 157 0 0 398 34 28 7 100 100 100 100 1971 1929 11.167 .09 .089 .09 .088 1.191 80 449 .086 .97 110 4820 17620 36 47 276 287 0 1851 305 1546 .855 1804 1498 1.17 .846 -.227 -.242
17 1023 106 96 31 927 75 1023 104 98 31 927 73 0 0 175 19 20 4 100 100 100 100 1002 1000 12.36 .081 .079 .08 .082 1.333 80 485 .076 .94 110 4990 17610 35 46 293 304 0 1012 296 716 .772 992 697 1.295 .751 -.373 -.412
18 9465 1005 95 31 9370 974 10024 1047 99 31 9929 1016 0 0 2308 204 25 5 100 100 100 100 10344 10945 9.62 .104 .102 .106 .103 1.17 80 490 .099 .98 110 5160 17600 34 45 310 321 0 9591 296 9295 .992 9992 9696 1.008 .977 -.012 -.034
19 1397 141 95 31 1302 110 1366 143 98 32 1271 112 0 0 321 25 25 7 100 100 100 100 1412 1383 11.836 .084 .088 .084 .088 1.269 80 479 .081 .95 110 5340 17610 35 46 328 339 0 1346 296 1050 .806 1365 1069 1.24 .841 -.311 -.25
20 1007 122 96 31 911 91 981 119 99 32 885 88 0 0 193 24 20 6 100 100 100 100 1002 973 10.011 .1 .099 .098 .098 1.292 80 406 .096 .95 100 5510 17610 36 46 346 356 0 1164 296 868 .953 1136 840 1.049 .949 -.069 -.076

Total number of rows: 9984

Table truncated, full table size 2093 Kbytes.




Supplementary data files not provided
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