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Sample GSM90536 Query DataSets for GSM90536
Status Public on Jan 04, 2006
Title Puf2 IP (4)
Sample type RNA
 
Channel 1
Source name Puf2 tot. RNA extract (4)
Organism Saccharomyces cerevisiae
Characteristics Puf2 tot. RNA extract (4)
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name Puf2 RNA-IP (4)
Organism Saccharomyces cerevisiae
Characteristics Puf2 RNA-IP (4)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2003-01/36823.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
1 153 55 150 54 3 1 151 54 152 54 1 0 0 0 22 7 27 9 16 11 1 2 4 1 3 .333 null .358 .282 3.591 80 476 .192 .54 100 2930 17160 51 61 32 42 -50 324 318 6 1.961 318 0 .51 null .972 null
2 147 52 139 52 8 0 141 53 146 53 2 1 0 0 30 8 34 10 13 6 6 1 8 3 null null .5 .285 .273 3.054 80 432 .19 .54 100 3100 17160 51 61 49 59 -50 306 306 0 null 312 6 null 2.942 null 1.557
3 142 52 141 51 1 1 141 51 144 52 0 0 0 0 24 8 26 7 12 17 3 6 2 0 1 1 null .314 .323 2.571 80 420 .146 .46 100 3270 17160 51 61 66 76 -50 306 300 6 5.884 300 0 .17 null 2.557 null
4 151 54 142 52 9 2 149 54 143 53 7 2 0 0 27 8 25 7 23 21 6 7 11 9 4.5 .222 .286 .346 .35 2.628 80 420 .144 .46 100 3440 17160 51 61 83 93 -50 318 306 12 1.308 318 12 .765 1.681 .387 .749
5 156 55 141 52 15 3 149 56 142 52 8 4 0 0 38 7 23 7 30 28 15 3 18 12 5 .2 .5 .305 .258 3.514 80 432 .127 .47 100 3610 17160 51 61 100 110 -50 324 306 18 1.177 330 24 .85 2.942 .235 1.557
6 156 57 149 54 7 3 151 55 168 57 2 1 0 0 36 8 67 15 6 5 1 1 10 3 2.333 .429 .5 .294 .294 3.569 80 390 .204 .74 100 3780 17160 51 61 117 127 -50 335 318 18 2.522 324 6 .397 2.942 1.334 1.557
7 341 93 161 57 180 36 344 94 183 62 183 37 0 0 150 29 71 16 79 75 69 60 216 220 5 .2 .202 .229 .209 1.785 120 534 .185 .92 130 3940 17190 52 65 131 144 -100 547 335 212 1.177 553 218 .85 1.19 .235 .251
8 370 111 175 60 195 51 333 103 193 65 158 43 0 0 156 37 63 16 91 91 76 67 246 201 3.824 .262 .272 .265 .265 1.732 80 411 .234 .92 110 4120 17190 53 64 150 161 -100 653 353 300 1.539 606 253 .65 1.601 .622 .679
9 318 96 187 63 131 33 301 94 202 68 114 31 0 0 100 23 63 17 81 77 42 42 164 145 3.97 .252 .272 .255 .249 1.662 80 462 .214 .88 110 4280 17190 53 64 166 177 -100 565 371 194 1.482 553 182 .675 1.6 .568 .678
10 1109 237 189 63 920 174 1139 240 209 69 950 177 0 0 246 49 77 19 100 100 100 100 1094 1127 5.287 .189 .186 .188 .191 1.132 80 448 .184 .98 100 4480 17170 52 62 187 197 0 1395 371 1024 1.113 1412 1041 .899 1.096 .154 .133
11 317 100 179 63 138 37 306 96 202 68 127 33 0 0 90 22 76 17 85 87 30 43 175 160 3.73 .268 .26 .263 .256 1.601 80 438 .219 .84 110 4640 17190 53 64 202 213 -100 588 371 218 1.578 565 194 .634 1.529 .658 .613
12 335 104 180 63 155 41 321 100 200 69 141 37 0 0 92 24 68 19 93 87 57 42 196 178 3.78 .265 .262 .269 .26 1.605 80 468 .228 .85 110 4820 17190 53 64 220 231 -100 612 371 241 1.556 588 218 .643 1.544 .638 .627
13 4376 705 179 59 4197 646 4400 698 193 64 4221 639 0 0 1833 304 62 16 100 100 100 100 4843 4860 6.497 .154 .151 .152 .153 1.173 80 499 .153 .99 110 4990 17160 50 61 237 248 0 4148 347 3801 .906 4107 3760 1.104 .891 -.143 -.167
14 40919 3596 203 63 40716 3533 41728 3517 232 69 41525 3454 0 0 11782 1168 101 21 100 100 100 100 44249 44979 11.524 .087 .083 .086 .086 1.096 80 482 .087 1 110 5160 17160 50 61 254 265 0 21159 371 20788 .511 20694 20323 1.959 .489 -.97 -1.031
15 62774 9232 219 70 62555 9162 65535 9507 260 79 65316 9437 76 0 7918 1691 118 27 100 100 100 100 71717 74753 6.828 .146 .144 .145 .146 1.134 80 519 .146 .99 110 5330 17160 50 61 271 282 0 54321 412 53909 .862 55939 55527 1.16 .85 -.215 -.234
16 4304 744 188 64 4116 680 3726 673 220 70 3538 609 0 0 1554 246 94 23 100 100 100 100 4796 4147 6.053 .165 .172 .166 .166 1.077 80 483 .162 .99 110 5500 17170 51 62 288 299 0 4378 377 4001 .972 3960 3583 1.029 1.013 -.041 .018
17 2022 336 181 61 1841 275 1971 327 185 62 1790 266 0 0 594 78 39 9 100 100 100 100 2116 2056 6.695 .149 .149 .151 .151 1.115 80 428 .143 .99 100 5670 17170 52 62 306 316 0 1977 359 1618 .879 1924 1565 1.138 .874 -.186 -.194
18 18961 2150 186 61 18775 2089 18411 2008 189 62 18225 1947 0 0 4455 579 38 10 100 100 100 100 20864 20172 8.988 .111 .107 .11 .111 1.063 80 497 .112 1 110 5840 17160 50 61 322 333 0 12651 359 12292 .655 11815 11456 1.527 .629 -.611 -.67
19 2162 415 173 60 1989 355 2011 387 176 61 1838 327 0 0 825 135 38 11 100 100 100 100 2344 2165 5.603 .178 .178 .18 .181 1.122 80 478 .172 .99 110 6010 17160 50 61 339 350 0 2442 353 2089 1.05 2277 1924 .952 1.047 .071 .066
20 1912 413 166 60 1746 353 1914 430 172 60 1748 370 0 0 533 122 39 9 100 100 100 100 2099 2118 4.946 .202 .212 .199 .201 1.107 80 480 .2 .99 110 6180 17170 51 62 356 367 0 2430 353 2077 1.19 2530 2177 .841 1.245 .25 .317

Total number of rows: 9984

Table truncated, full table size 2184 Kbytes.




Supplementary data files not provided
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