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Sample GSM90531 Query DataSets for GSM90531
Status Public on Jan 04, 2006
Title Puf1 IP (3)
Sample type RNA
 
Channel 1
Source name Puf1 tot. RNA extract (3)
Organism Saccharomyces cerevisiae
Characteristics Puf1 tot. RNA extract (3)
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name Puf1 RNA-IP (3)
Organism Saccharomyces cerevisiae
Characteristics Puf1 RNA-IP (3)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2003-01/36821.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
1 125 45 120 44 5 1 124 45 121 44 4 1 0 0 19 6 20 7 20 18 3 1 6 5 5 .2 .25 .387 .333 3.02 80 450 .108 .3 100 2680 16310 70 80 19 29 -50 209 204 5 .929 209 5 1.077 1.161 -.107 .215
2 144 48 127 46 17 2 130 48 130 47 3 2 0 0 44 8 23 8 23 18 16 5 19 5 8.5 .118 .667 .342 .286 3.336 80 427 .112 .4 100 2850 16300 69 79 36 46 -50 223 214 9 .546 223 9 1.83 3.096 -.872 1.63
3 154 52 140 49 14 3 142 51 143 49 2 2 0 0 45 11 28 9 30 22 13 8 17 4 4.667 .214 1 .238 .256 3.01 80 437 .16 .54 100 3030 16300 69 79 54 64 -50 241 228 14 .995 237 9 1.005 4.644 -.007 2.215
4 173 55 157 52 16 3 169 53 159 53 12 1 0 0 37 10 29 9 30 23 11 10 19 13 5.333 .188 .083 .302 .295 3.42 80 414 .155 .51 100 3200 16300 69 79 71 81 -50 255 241 14 .871 246 5 1.148 .387 -.2 -1.37
5 173 54 167 57 6 -3 165 52 171 57 -2 -5 0 0 33 12 33 9 16 11 8 8 3 -7 null null null .383 .396 3.187 80 432 .127 .38 100 3370 16290 68 78 88 98 -50 251 265 -14 null 241 -23 null null null null
6 198 60 179 60 19 0 177 59 206 64 -2 -1 0 0 60 9 78 17 15 3 5 0 19 -3 null null null .222 .198 3.27 80 398 .142 .69 100 3540 16290 68 78 105 115 -50 279 279 0 null 274 -5 null null null null
7 363 93 190 60 173 33 357 92 215 64 167 32 0 0 111 25 83 18 82 77 50 40 206 199 5.242 .191 .192 .191 .201 1.646 120 479 .194 .88 130 3700 16320 69 82 119 132 -100 432 279 153 .886 427 149 1.129 .89 -.175 -.168
8 350 83 187 58 163 25 342 83 199 60 155 25 0 0 93 17 61 13 89 76 69 44 188 180 6.52 .153 .161 .154 .159 1.795 120 392 .152 .82 120 3870 16310 69 81 137 149 -100 385 269 116 .712 385 116 1.404 .749 -.489 -.417
9 308 76 176 56 132 20 331 78 195 58 155 22 0 0 89 17 74 14 73 67 52 32 152 177 6.6 .152 .142 .163 .167 1.962 156 651 .159 .83 140 4020 16320 69 83 151 165 -100 353 260 93 .704 362 102 1.421 .659 -.507 -.601
10 963 209 195 61 768 148 902 195 227 64 707 134 0 0 335 66 90 15 100 100 98 100 916 841 5.189 .193 .19 .193 .192 1.174 80 448 .193 .98 100 4240 16280 67 77 175 185 0 971 283 687 .895 906 622 1.117 .88 -.16 -.184
11 312 78 228 64 84 14 328 76 251 66 100 12 0 0 119 19 90 15 51 43 22 17 98 112 6 .167 .12 .124 .143 2.238 80 391 .139 .81 100 4400 16270 66 76 191 201 -50 362 297 65 .774 353 56 1.292 .557 -.37 -.844
12 332 81 242 67 90 14 308 77 269 69 66 10 0 0 128 21 97 18 41 35 17 13 104 76 6.429 .156 .152 .162 .159 2.04 80 444 .143 .81 100 4570 16260 65 75 208 218 -50 376 311 65 .722 358 46 1.384 .704 -.469 -.507
13 3170 832 244 71 2926 761 3236 839 269 73 2992 768 0 0 443 104 96 17 100 100 100 100 3687 3760 3.845 .26 .257 .261 .261 1.068 80 504 .259 1 110 4750 16260 64 75 225 236 0 3864 330 3534 1.208 3896 3567 .828 1.192 .272 .253
14 27455 3675 216 68 27239 3607 27236 3625 249 71 27020 3557 0 0 5304 669 107 19 100 100 100 100 30846 30577 7.552 .132 .132 .133 .132 1.047 80 458 .131 1 110 4920 16250 63 74 242 253 0 17067 316 16751 .615 16835 16519 1.626 .611 -.701 -.71
15 49033 16648 196 63 48837 16585 61163 18919 247 69 60967 18856 17 0 21082 6926 126 21 99 100 99 100 65422 79823 2.945 .34 .309 .373 .338 1.49 120 553 .335 .99 120 5100 16250 63 75 260 272 0 77314 293 77022 1.577 87861 87569 .634 1.436 .657 .522
16 3208 630 178 58 3030 572 3438 660 207 61 3260 602 0 0 1136 209 94 15 98 100 97 99 3602 3862 5.297 .189 .185 .197 .185 1.299 120 523 .187 .99 120 5270 16250 63 75 277 289 0 2926 269 2656 .877 3065 2796 1.141 .858 -.19 -.222
17 1281 303 174 56 1107 247 1283 303 177 57 1109 247 0 0 186 52 31 9 100 100 100 100 1354 1356 4.482 .223 .223 .222 .219 1.125 80 453 .222 .99 110 5440 16240 62 73 294 305 0 1407 260 1147 1.036 1407 1147 .965 1.034 .051 .049
18 11668 2421 167 55 11501 2366 11845 2439 170 56 11678 2384 0 0 1914 413 32 12 100 100 100 100 13867 14062 4.861 .206 .204 .205 .206 1.058 80 476 .205 1 110 5600 16240 62 73 310 321 0 11243 255 10988 .955 11327 11071 1.047 .948 -.066 -.077
19 1942 390 158 53 1784 337 1961 389 162 54 1803 336 0 0 360 70 30 11 100 100 100 100 2121 2139 5.294 .189 .186 .189 .191 1.09 80 469 .188 .99 110 5780 16230 61 72 328 339 0 1811 246 1565 .877 1807 1560 1.14 .865 -.189 -.208
20 1977 486 161 53 1816 433 1947 477 165 54 1786 424 0 0 442 95 34 8 100 100 100 100 2249 2210 4.194 .238 .237 .24 .238 1.108 80 469 .234 .99 110 5950 16230 61 72 345 356 0 2257 246 2011 1.107 2215 1969 .903 1.103 .147 .141

Total number of rows: 9984

Table truncated, full table size 2170 Kbytes.




Supplementary data files not provided
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