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Sample GSM90528 Query DataSets for GSM90528
Status Public on Jan 04, 2006
Title BY4741 mock (3)
Sample type RNA
 
Channel 1
Source name BY4741 tot. RNA extract (3)
Organism Saccharomyces cerevisiae
Characteristics BY4741 tot. RNA extract (3)
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name BY4741 RNA-IP (3)
Organism Saccharomyces cerevisiae
Characteristics BY4741 RNA-IP (3)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: RNA coimmunoprecipitation, IP Controls
Image: http://smd.stanford.edu/MicroArray/gifs/2003-01/37361.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
1 109 36 99 31 10 5 99 32 103 32 0 1 0 0 30 17 25 5 23 25 8 16 15 1 2 .5 null .505 .462 3.427 80 442 .277 .5 100 2680 17720 31 41 51 61 -50 328 282 46 4.55 291 9 .22 null 2.186 null
2 115 35 108 32 7 3 110 32 112 33 2 0 0 0 30 13 27 5 16 18 7 10 10 2 2.333 .429 null .291 .333 3.305 80 430 .182 .52 100 2850 17720 31 41 68 78 -50 319 291 27 3.9 291 0 .256 null 1.964 null
3 119 40 110 32 9 8 110 35 115 32 0 3 0 0 36 17 27 5 21 31 10 18 17 3 1.125 .889 null .302 .32 3.282 80 432 .193 .47 100 3030 17730 32 42 86 96 -50 364 291 73 8.089 319 27 .124 null 3.016 null
4 117 33 112 31 5 2 111 30 115 31 -1 -1 0 0 30 12 24 5 18 17 10 11 7 -2 2.5 .4 null .24 .224 3.119 80 420 .133 .43 100 3200 17730 32 42 103 113 -50 300 282 18 3.64 273 -9 .275 null 1.864 null
5 117 44 113 33 4 11 108 35 117 34 -5 2 0 0 34 25 27 5 17 27 8 21 15 -3 .364 2.75 null .447 .38 2.929 80 432 .337 .53 100 3370 17730 32 42 120 130 -50 400 300 100 25.027 319 18 .04 null 4.645 null
6 155 40 125 33 30 7 141 35 142 35 16 2 0 0 71 21 53 8 22 17 5 12 37 18 4.286 .233 .125 .183 .179 3.122 80 357 .155 .69 100 3540 17730 32 42 137 147 -50 364 300 64 2.123 319 18 .471 1.138 1.086 .186
7 223 52 127 38 96 14 218 48 143 40 91 10 0 0 61 16 47 11 82 46 46 15 110 101 6.857 .146 .11 .135 .133 2.619 156 672 .102 .48 140 3690 17740 31 45 150 164 -100 473 346 127 1.327 437 91 .753 1 .408 0
8 225 53 144 41 81 12 196 46 153 42 52 5 0 0 97 25 43 10 60 30 20 17 93 57 6.75 .148 .096 .17 .157 3.365 80 441 .178 .76 100 3880 17730 32 42 171 181 -50 482 373 109 1.348 419 46 .742 .875 .431 -.193
9 231 53 123 39 108 14 218 46 136 40 95 7 0 0 72 20 42 9 93 32 58 20 122 102 7.714 .13 .074 .099 .102 2.314 80 507 .114 .53 110 4080 17740 32 43 190 201 -100 482 355 127 1.18 419 64 .848 .671 .238 -.577
10 656 90 116 40 540 50 679 87 127 42 563 47 0 0 154 25 36 9 100 97 97 92 590 610 10.8 .093 .083 .087 .084 1.542 80 426 .086 .82 110 4250 17750 33 44 207 218 0 819 364 455 .843 792 428 1.187 .76 -.247 -.396
11 207 47 131 39 76 8 197 44 143 40 66 5 0 0 54 13 41 10 77 31 35 11 84 71 9.5 .105 .076 .142 .133 2.836 80 388 .152 .59 100 4390 17730 32 42 222 232 -50 428 355 73 .958 400 46 1.044 .689 -.062 -.537
12 239 54 129 40 110 14 229 50 145 42 100 10 0 0 102 19 48 9 87 55 55 20 124 110 7.857 .127 .1 .101 .109 2.09 120 592 .092 .53 130 4580 17750 32 45 239 252 -100 491 364 127 1.158 455 91 .863 .91 .212 -.136
13 2015 249 131 36 1884 213 2194 264 194 43 2063 228 0 0 832 72 219 24 95 98 92 96 2097 2291 8.845 .113 .111 .123 .108 1.828 120 415 .102 .94 120 4750 17750 33 45 257 269 0 2266 328 1938 1.029 2403 2075 .972 1.006 .041 .008
14 14219 1038 136 38 14083 1000 4043 653 188 44 3907 615 0 0 15417 1016 177 23 83 80 74 71 15083 4522 14.083 .071 .157 .091 .072 2.232 208 906 .065 .96 160 4900 17760 32 48 270 286 0 9446 346 9101 .646 5943 5597 1.547 1.433 -.63 .519
15 53585 5806 144 45 53441 5761 56922 6095 184 49 56778 6050 2 0 12104 1134 95 22 100 100 100 100 59202 62828 9.276 .108 .107 .11 .107 1.328 80 483 .106 .98 110 5080 17750 33 44 290 301 0 52838 410 52428 .981 55468 55058 1.019 .97 -.028 -.044
16 2475 243 138 35 2337 208 2570 249 164 40 2432 214 0 0 762 47 82 21 100 100 100 100 2545 2646 11.236 .089 .088 .093 .086 1.39 80 496 .082 .95 110 5260 17750 33 44 308 319 0 2211 319 1893 .81 2266 1948 1.235 .801 -.304 -.321
17 1084 120 139 36 945 84 1084 120 149 38 945 84 0 0 276 26 55 8 100 100 100 100 1029 1029 11.25 .089 .089 .089 .084 1.541 80 420 .078 .86 100 5430 17750 34 44 326 336 0 1092 328 764 .809 1092 764 1.236 .809 -.306 -.306
18 11965 1218 148 36 11817 1182 12414 1231 154 37 12266 1195 0 0 2996 295 51 8 100 100 100 100 12999 13461 9.997 .1 .097 .101 .099 1.198 80 483 .098 .96 110 5600 17750 33 44 342 353 0 11085 328 10757 .91 11203 10875 1.099 .887 -.136 -.174
19 1629 154 176 41 1453 113 1635 154 197 43 1459 113 0 0 444 29 76 12 100 100 100 100 1566 1572 12.858 .078 .077 .079 .074 1.389 80 468 .073 .91 110 5770 17760 34 45 359 370 0 1401 373 1028 .708 1401 1028 1.413 .705 -.499 -.505
20 1396 160 161 39 1235 121 1393 159 181 40 1232 120 0 0 415 37 71 10 100 100 100 100 1356 1352 10.207 .098 .097 .101 .094 1.544 80 479 .09 .93 110 5940 17750 33 44 376 387 0 1456 355 1101 .892 1447 1092 1.122 .886 -.165 -.174

Total number of rows: 9984

Table truncated, full table size 2135 Kbytes.




Supplementary data files not provided
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