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Sample GSM90520 Query DataSets for GSM90520
Status Public on Jan 04, 2006
Title Puf4 IP (1)
Sample type RNA
 
Channel 1
Source name Puf4 tot. RNA extract (1)
Organism Saccharomyces cerevisiae
Characteristics Puf4 tot. RNA extract (1)
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name Puf4 RNA-IP (1)
Organism Saccharomyces cerevisiae
Characteristics Puf4 RNA-IP (1)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/32245.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 GPL3269
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
1 718 355 151 92 567 263 693 278 159 94 542 186 0 0 281 271 37 16 98 97 97 92 830 728 2.156 .464 .343 .356 .351 1.935 80 445 .575 .83 100 1740 18980 37 47 25 35 0 634 164 470 .828 496 332 1.207 .613 -.272 -.706
2 39819 8242 158 99 39661 8143 47588 9450 162 101 47430 9351 0 0 15369 2937 29 19 100 100 100 100 47804 56781 4.871 .205 .197 .208 .2 1.512 80 427 .198 .98 100 1900 18970 36 46 41 51 0 14718 177 14541 .367 16875 16698 2.728 .352 -1.448 -1.506
3 47516 23398 163 99 47353 23299 55670 26685 168 102 55507 26586 8 0 19579 8203 31 20 100 100 100 100 70652 82093 2.032 .492 .479 .539 .481 1.649 80 438 .465 .97 100 2080 18970 36 46 59 69 0 41782 177 41605 .879 47652 47475 1.138 .855 -.187 -.226
4 3332 1275 153 89 3179 1186 3427 1346 157 91 3274 1257 0 0 802 359 28 17 100 100 100 100 4365 4531 2.68 .373 .384 .369 .356 1.356 80 440 .372 .97 100 2260 18970 36 46 77 87 0 2277 159 2118 .666 2404 2245 1.501 .686 -.586 -.545
5 2223 1226 152 89 2071 1137 2227 1199 157 91 2075 1110 0 0 445 259 50 17 100 100 100 100 3208 3185 1.821 .549 .535 .55 .546 1.208 52 368 .519 .96 90 2420 18960 35 44 93 102 0 2189 159 2030 .98 2141 1982 1.02 .955 -.029 -.066
6 21131 8045 156 92 20975 7953 22943 8701 161 92 22787 8609 0 0 6280 2184 44 17 100 100 100 100 28928 31396 2.637 .379 .378 .382 .375 1.433 80 470 .368 .97 100 2610 18960 35 45 112 122 0 14366 164 14202 .677 15538 15373 1.477 .675 -.563 -.568
7 2280 977 154 87 2126 890 2260 885 156 87 2106 798 0 0 257 281 22 14 100 100 100 100 3016 2904 2.389 .419 .379 .406 .389 1.22 52 362 .413 .95 90 2780 18960 35 44 129 138 0 1745 155 1589 .748 1580 1425 1.338 .677 -.42 -.564
8 1045 550 154 88 891 462 999 407 155 89 845 319 0 0 467 486 20 14 100 98 98 97 1353 1164 1.929 .519 .378 .419 .424 1.816 80 462 .671 .89 100 2960 18960 35 45 147 157 0 982 157 825 .926 727 570 1.08 .674 -.111 -.569
9 1280 834 158 91 1122 743 1145 507 160 92 987 416 0 0 605 727 20 15 100 100 100 100 1865 1403 1.51 .662 .421 .557 .523 1.501 52 370 .814 .91 90 3130 18950 34 43 164 173 0 1489 163 1327 1.183 905 743 .846 .753 .242 -.41
10 815 509 161 98 654 411 589 264 164 100 428 166 0 0 539 565 44 18 100 100 100 100 1065 594 1.591 .628 .388 .443 .428 1.646 52 378 .823 .93 90 3300 18950 34 43 181 190 0 909 175 734 1.122 471 296 .891 .693 .166 -.53
11 1746 18486 161 95 1585 18391 1819 20632 161 96 1658 20537 0 0 682 7060 24 16 93 100 92 100 19976 22195 .086 11.603 12.387 11.728 12.194 1.543 80 466 12.336 .92 100 3480 18950 34 44 199 209 0 33011 170 32841 20.72 36843 36673 .048 22.119 4.373 4.467
12 1713 976 161 93 1552 883 1796 939 163 94 1635 846 0 0 452 463 27 14 100 100 100 100 2435 2481 1.758 .569 .517 .537 .533 1.4 80 426 .617 .93 100 3660 18960 35 45 217 227 0 1743 166 1577 1.016 1677 1511 .984 .924 .023 -.114
13 2314 1129 162 95 2152 1034 2506 1150 168 98 2344 1055 0 0 585 419 33 20 100 100 100 100 3186 3399 2.081 .48 .45 .455 .466 1.491 80 426 .492 .95 100 3830 18960 35 45 234 244 0 2016 170 1846 .858 2054 1884 1.165 .804 -.221 -.315
14 23644 10555 158 95 23486 10460 25735 11267 169 106 25577 11172 0 0 7638 3364 103 120 100 100 100 100 33946 36749 2.245 .445 .437 .469 .443 1.564 80 441 .439 .98 100 4010 18960 35 45 252 262 0 18848 170 18679 .795 20120 19950 1.257 .78 -.33 -.358
15 2288 1385 147 81 2141 1304 2499 1463 156 92 2352 1382 0 0 716 331 100 118 100 100 100 100 3445 3734 1.642 .609 .588 .649 .586 1.429 80 462 .584 .95 100 4180 18950 34 44 269 279 0 2473 145 2329 1.088 2613 2468 .919 1.049 .121 .069
16 1378 638 146 79 1232 559 1362 595 147 79 1216 516 0 0 147 138 22 14 100 100 100 100 1791 1732 2.204 .454 .424 .446 .438 1.228 52 362 .444 .95 90 4360 18950 34 43 287 296 0 1139 141 998 .81 1063 921 1.234 .758 -.304 -.4
17 926 1080 136 72 790 1008 959 1114 138 73 823 1042 0 0 225 270 21 14 100 100 100 100 1798 1865 .784 1.276 1.266 1.313 1.266 1.392 80 452 1.283 .97 100 4520 18950 34 44 303 313 0 1929 129 1800 2.278 1989 1861 .439 2.261 1.188 1.177
18 1266 593 129 65 1137 528 1314 623 129 66 1185 558 0 0 387 218 18 13 100 98 100 98 1665 1743 2.153 .464 .471 .429 .468 1.674 80 452 .469 .97 100 4700 18950 34 44 321 331 0 1059 116 943 .829 1113 996 1.206 .841 -.27 -.25
19 2639 844 128 63 2511 781 2863 940 129 64 2735 877 0 0 857 256 18 13 100 100 100 100 3292 3612 3.215 .311 .321 .313 .317 1.45 80 440 .303 .98 100 4870 18950 34 44 338 348 0 1507 113 1395 .555 1679 1566 1.8 .573 -.848 -.804
20 429 177 130 63 299 114 408 153 132 63 278 90 0 0 85 68 20 12 100 100 100 100 413 368 2.623 .381 .324 .351 .332 1.408 52 370 .377 .87 90 5040 18940 33 42 355 364 0 316 113 204 .681 273 161 1.469 .578 -.555 -.791

Total number of rows: 10752

Table truncated, full table size 2376 Kbytes.




Supplementary data files not provided
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