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Sample GSM90538 Query DataSets for GSM90538
Status Public on Jan 04, 2006
Title BY4741 mock (1)
Sample type RNA
 
Channel 1
Source name BY4741 tot. RNA extract (1)
Organism Saccharomyces cerevisiae
Characteristics BY4741 tot. RNA extract (1)
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name BY4741 RNA-IP (1)
Organism Saccharomyces cerevisiae
Characteristics BY4741 RNA-IP (1)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: RNA coimmunoprecipitation, IP Controls
Image: http://smd.stanford.edu/MicroArray/gifs/2003-01/36816.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
1 190 107 190 93 0 14 179 91 210 102 -11 -2 0 0 63 53 97 44 5 13 1 6 14 -13 null null null .643 .506 5.013 80 443 .281 .49 100 2660 17260 41 51 21 31 -50 524 456 69 null 446 -10 null null null null
2 206 96 194 97 12 -1 202 92 217 105 8 -5 0 0 62 21 98 45 6 1 2 0 11 3 null null null .395 .366 2.663 80 401 .146 .38 100 2830 17260 41 51 38 48 -50 470 475 -5 null 451 -24 null null null null
3 187 87 151 83 36 4 176 85 162 85 25 2 0 0 59 20 52 21 26 17 8 5 40 27 9 .111 .08 .343 .351 3.058 80 421 .182 .51 100 3000 17260 41 51 55 65 -50 426 407 20 .544 416 10 1.837 .392 -.877 -1.351
4 160 82 145 80 15 2 146 80 160 85 1 0 0 0 51 18 58 23 13 13 5 2 17 1 7.5 .133 null .421 .465 4.264 80 433 .149 .37 100 3170 17260 41 51 72 82 -50 402 392 10 .653 392 0 1.531 null -.614 null
5 247 107 178 90 69 17 216 106 188 94 38 16 0 0 104 25 57 22 45 38 28 15 86 54 4.059 .246 .421 .34 .307 3.562 80 432 .155 .46 100 3350 17260 41 51 90 100 -50 524 441 83 1.207 519 78 .828 2.063 .271 1.045
6 239 104 189 100 50 4 191 92 566 177 2 -8 0 0 181 47 913 191 1 2 0 0 54 -6 12.5 .08 null .428 .533 3.546 80 397 .226 .96 100 3520 17260 41 51 107 117 -50 509 490 20 .392 451 -39 2.552 null -1.351 null
7 2893 608 216 110 2677 498 2947 625 753 213 2731 515 0 0 2174 324 1076 214 73 78 62 65 3175 3246 5.376 .186 .189 .224 .196 1.779 80 447 .163 .92 110 3700 17270 41 52 124 135 -100 2979 539 2440 .911 3062 2523 1.097 .924 -.134 -.114
8 2609 579 192 102 2417 477 2858 660 566 174 2666 558 0 0 1944 293 933 184 71 75 62 67 2894 3224 5.067 .197 .209 .253 .22 2.007 120 497 .168 .93 120 3870 17270 41 53 141 153 -100 2837 500 2337 .967 3233 2734 1.034 1.025 -.049 .036
9 671 225 176 99 495 126 513 174 628 193 337 75 0 0 595 142 932 200 10 18 2 2 621 412 3.929 .255 .223 .26 .276 1.891 80 422 .195 .9 100 4030 17250 40 50 158 168 -100 1102 485 617 1.247 852 367 .802 1.09 .318 .125
10 1416 349 182 103 1234 246 867 263 728 220 685 160 0 0 1371 218 961 213 32 40 13 13 1480 845 5.016 .199 .234 .205 .21 1.727 52 349 .187 .87 90 4210 17260 41 50 176 185 -100 1710 505 1205 .977 1288 784 1.024 1.144 -.034 .194
11 1985 503 176 101 1809 402 2141 576 444 157 1965 475 0 0 1402 230 716 160 70 76 61 65 2211 2440 4.5 .222 .242 .293 .234 2.236 120 576 .192 .93 130 4380 17260 39 52 191 204 -100 2464 495 1969 1.089 2822 2327 .919 1.184 .123 .244
12 1861 480 187 103 1674 377 2091 562 582 185 1904 459 0 0 1279 250 1005 202 65 70 49 60 2051 2363 4.44 .225 .241 .267 .232 2.072 120 519 .187 .93 120 4550 17250 39 51 209 221 -100 2352 505 1847 1.103 2753 2249 .906 1.181 .142 .24
13 2836 605 182 95 2654 510 2666 599 510 163 2484 504 0 0 812 152 944 187 98 97 87 83 3164 2988 5.204 .192 .203 .193 .197 1.183 80 476 .194 .95 110 4720 17250 39 50 226 237 0 2964 465 2498 .941 2935 2469 1.062 .994 -.087 -.009
14 40175 4829 197 96 39978 4733 39530 4868 377 146 39333 4772 0 0 9248 1133 636 146 100 100 100 100 44711 44105 8.447 .118 .121 .118 .119 1.113 80 419 .117 .98 100 4890 17250 40 50 244 254 0 23657 470 23187 .58 23848 23378 1.724 .594 -.786 -.751
15 57743 20913 208 107 57535 20806 65535 21865 553 205 65327 21758 65 0 16213 5731 758 187 100 100 98 100 78341 87085 2.765 .362 .333 .375 .349 1.531 80 530 .343 .96 110 5050 17240 38 49 259 270 0 102453 524 101929 1.772 107117 106593 .564 1.632 .825 .706
16 3579 636 187 102 3392 534 3352 641 416 174 3165 539 0 0 1220 184 528 159 100 97 96 88 3926 3704 6.352 .157 .17 .158 .15 1.493 80 454 .147 .94 100 5230 17250 40 50 278 288 0 3116 500 2616 .771 3140 2641 1.297 .834 -.375 -.261
17 1601 373 203 109 1398 264 1608 364 404 161 1405 255 0 0 488 105 634 148 92 90 60 33 1662 1660 5.295 .189 .181 .188 .188 1.303 80 427 .205 .87 100 5400 17250 40 50 295 305 0 1827 534 1293 .925 1783 1249 1.081 .889 -.112 -.17
18 12905 2790 215 108 12690 2682 13955 3057 375 144 13740 2949 0 0 5532 1279 632 140 95 95 93 93 15372 16689 4.732 .211 .215 .207 .21 1.23 80 444 .211 .97 100 5580 17240 39 49 313 323 0 13668 529 13139 1.035 14976 14447 .966 1.051 .05 .072
19 2232 494 181 100 2051 394 2162 493 217 106 1981 393 0 0 773 175 209 49 100 98 100 96 2445 2374 5.206 .192 .198 .188 .197 1.341 80 400 .189 .93 100 5750 17240 39 49 330 340 0 2420 490 1930 .941 2415 1925 1.063 .972 -.088 -.041
20 1736 381 171 89 1565 292 1530 329 217 97 1359 240 0 0 1366 297 246 63 78 78 75 71 1857 1599 5.36 .187 .177 .216 .186 1.917 80 420 .184 .87 100 5920 17240 39 49 347 357 0 1867 436 1431 .914 1612 1176 1.094 .865 -.13 -.209

Total number of rows: 9984

Table truncated, full table size 2195 Kbytes.




Supplementary data files not provided
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