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Sample GSM90537 Query DataSets for GSM90537
Status Public on Jan 04, 2006
Title Puf3 IP (4)
Sample type RNA
 
Channel 1
Source name Puf3 tot. RNA extract (4)
Organism Saccharomyces cerevisiae
Characteristics Puf3 tot. RNA extract (4)
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name Puf3 RNA-IP (4)
Organism Saccharomyces cerevisiae
Characteristics Puf3 RNA-IP (4)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2003-01/36807.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
1 177 180 186 180 -9 0 164 175 200 186 -22 -5 0 0 47 39 67 43 6 15 1 1 -9 -27 null null null .585 .725 2.91 80 450 .522 .44 100 2740 17290 92 102 37 47 -50 718 718 0 null 698 -20 null null null null
2 243 193 180 175 63 18 206 185 192 179 26 10 0 0 123 53 62 42 33 26 18 10 81 36 3.5 .286 .385 .541 .467 3.927 80 444 .341 .51 100 2910 17280 91 101 54 64 -50 770 698 72 1.14 738 40 .877 1.534 .189 .618
3 1797 491 179 174 1618 317 1358 382 185 176 1179 208 0 0 1350 353 55 39 100 98 100 92 1935 1387 5.104 .196 .176 .175 .166 1.781 52 346 .21 .87 90 3080 17280 91 100 71 80 0 1959 694 1265 .782 1524 830 1.279 .704 -.355 -.507
4 185 173 179 173 6 0 179 168 189 175 0 -5 0 0 51 37 57 36 12 20 2 3 6 -5 null null null .854 .967 4.205 80 433 .233 .23 100 3250 17280 91 101 88 98 -50 690 690 0 null 670 -20 null null null null
5 183 167 176 171 7 -4 173 163 187 172 -3 -8 0 0 58 31 59 33 10 8 5 2 3 -11 null null null .787 .851 4.292 80 440 .162 .26 100 3420 17280 91 101 105 115 -50 666 682 -16 null 650 -32 null null null null
6 160 173 170 180 -10 -7 158 172 177 185 -12 -8 0 0 41 34 46 43 12 7 0 0 -17 -20 null null null .904 1 3.937 80 418 .358 .17 100 3600 17270 90 100 123 133 -50 690 718 -28 null 686 -32 null null null null
7 1154 654 170 189 984 465 756 595 178 194 586 406 0 0 765 241 48 44 100 100 100 98 1449 992 2.116 .473 .693 .552 .55 1.657 80 418 .386 .91 100 3760 17270 90 100 139 149 0 2609 754 1855 1.885 2374 1620 .53 2.764 .915 1.467
8 1626 572 174 189 1452 383 563 360 186 196 389 171 0 0 2388 531 58 47 100 90 100 81 1835 560 3.791 .264 .44 .329 .33 2.181 80 454 .218 .94 100 3940 17270 90 100 157 167 0 2282 754 1528 1.052 1436 682 .95 1.754 .074 .81
9 2181 621 187 197 1994 424 444 271 206 209 257 74 0 0 3183 673 70 54 86 53 63 44 2418 331 4.703 .213 .288 .269 .256 2.272 52 363 .192 .92 90 4120 17260 89 98 175 184 0 2477 786 1692 .848 1081 295 1.179 1.149 -.237 .2
10 1875 609 190 182 1685 427 635 392 209 189 445 210 0 0 2557 524 77 42 100 96 100 86 2112 655 3.946 .253 .472 .306 .304 1.864 52 347 .182 .93 90 4280 17260 89 98 191 200 0 2430 726 1704 1.011 1564 838 .989 1.883 .016 .913
11 2054 503 176 178 1878 325 392 257 193 186 216 79 0 0 3555 579 69 45 90 71 73 43 2203 295 5.778 .173 .366 .297 .28 2.972 80 479 .155 .94 110 4450 17270 89 100 207 218 0 2007 710 1297 .69 1025 315 1.448 1.459 -.534 .545
12 2315 718 172 186 2143 532 1343 542 187 194 1171 356 0 0 2152 462 65 51 100 96 100 91 2675 1527 4.028 .248 .304 .256 .265 1.463 80 420 .22 .93 100 4620 17260 89 99 225 235 0 2864 742 2122 .99 2162 1420 1.01 1.213 -.014 .278
13 4882 1292 199 189 4683 1103 4423 1262 221 197 4224 1073 0 0 2272 454 94 48 100 100 100 100 5786 5297 4.246 .236 .254 .237 .25 1.53 80 497 .219 .91 110 4790 17260 88 99 241 252 0 5154 754 4400 .94 5035 4281 1.064 1.013 -.09 .019
14 28645 2985 196 185 28449 2800 29168 3036 235 193 28972 2851 0 0 6749 702 383 49 100 100 100 100 31249 31823 10.16 .098 .098 .099 .098 1.311 80 440 .095 .96 100 4970 17260 89 99 260 270 0 11909 738 11171 .393 12112 11374 2.547 .393 -1.349 -1.349
15 62941 7157 163 178 62778 6979 65535 7592 191 184 65372 7414 67 0 6541 2112 363 47 100 100 100 100 69757 72786 8.995 .111 .113 .105 .116 1.437 80 483 .111 .93 110 5140 17260 88 99 276 287 0 28553 710 27843 .444 30288 29578 2.255 .452 -1.173 -1.144
16 5251 1338 154 166 5097 1172 5270 1308 163 171 5116 1142 0 0 1521 353 45 41 100 100 100 100 6269 6258 4.349 .23 .223 .23 .227 1.201 80 407 .22 .97 100 5300 17250 88 98 293 303 0 5338 662 4676 .917 5218 4556 1.09 .891 -.124 -.167
17 2228 821 151 164 2077 657 2252 829 159 167 2101 665 0 0 610 173 39 34 100 100 100 100 2734 2766 3.161 .316 .317 .316 .319 1.328 80 440 .304 .96 100 5470 17250 88 98 310 320 0 3275 654 2621 1.262 3307 2653 .792 1.263 .336 .337
18 12957 2189 141 163 12816 2026 13390 2283 148 165 13249 2120 0 0 2959 522 35 33 100 100 100 100 14842 15369 6.326 .158 .16 .157 .162 1.227 80 440 .152 .96 100 5650 17250 88 98 328 338 0 8733 650 8083 .631 9108 8458 1.586 .638 -.665 -.648
19 2709 974 142 159 2567 815 2732 1031 148 166 2590 872 0 0 830 249 39 36 100 98 100 98 3382 3462 3.15 .317 .337 .321 .318 1.408 80 440 .301 .93 100 5820 17250 88 98 345 355 0 3886 634 3251 1.267 4113 3479 .789 1.343 .341 .426
20 3171 897 149 174 3022 723 2389 746 159 175 2240 572 0 0 1769 513 118 42 100 96 98 96 3745 2812 4.18 .239 .255 .216 .233 1.584 80 454 .248 .95 110 6000 17240 86 97 362 373 0 3579 694 2884 .954 2976 2282 1.048 1.019 -.067 .027

Total number of rows: 9984

Table truncated, full table size 2236 Kbytes.




Supplementary data files not provided
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