NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM90523 Query DataSets for GSM90523
Status Public on Jan 04, 2006
Title Puf5 IP (1)
Sample type RNA
 
Channel 1
Source name Puf5 extract tot. RNA
Organism Saccharomyces cerevisiae
Characteristics Puf5 extract tot. RNA
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name RNA-IP PUF5
Organism Saccharomyces cerevisiae
Characteristics RNA-IP PUF5
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/32101.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
1 566 489 90 64 476 425 544 454 91 64 454 390 0 0 121 157 14 13 100 100 100 100 901 844 1.12 .893 .859 .869 .865 1.22 52 366 .898 .94 90 1830 18700 45 54 30 39 0 619 81 538 1.13 575 494 .885 1.087 .177 .121
2 27345 19694 97 70 27248 19624 32690 22381 99 72 32593 22311 0 0 11202 7292 18 17 100 100 100 100 46872 54904 1.389 .72 .685 .768 .716 1.421 80 452 .701 .98 100 2000 18690 44 54 47 57 0 24929 89 24841 .912 28330 28242 1.097 .866 -.133 -.207
3 39413 28677 102 73 39311 28604 47190 32908 105 77 47088 32835 0 0 15406 9427 21 21 100 100 100 100 67915 79923 1.374 .728 .697 .825 .712 1.639 80 452 .703 .98 100 2180 18690 44 54 65 75 0 36300 92 36208 .921 41656 41563 1.086 .883 -.119 -.18
4 2546 1593 99 71 2447 1522 2604 1711 102 71 2505 1640 0 0 819 491 19 17 100 100 100 100 3969 4145 1.608 .622 .655 .613 .615 1.397 80 440 .616 .98 100 2360 18690 44 54 83 93 0 2016 90 1927 .787 2166 2076 1.27 .829 -.345 -.271
5 1476 1141 101 73 1375 1068 1508 1148 102 75 1407 1075 0 0 357 275 15 17 100 100 100 100 2443 2482 1.287 .777 .764 .783 .77 1.265 80 440 .769 .97 100 2530 18690 44 54 100 110 0 1444 92 1352 .983 1453 1361 1.017 .967 -.024 -.048
6 14139 11152 103 76 14036 11076 15552 12110 104 77 15449 12034 0 0 4666 3571 15 16 100 100 100 100 25112 27483 1.267 .789 .779 .808 .784 1.282 80 441 .788 .98 100 2710 18690 44 54 118 128 0 14116 96 14020 .999 15329 15233 1.001 .986 -.002 -.02
7 1515 1119 104 75 1411 1044 1504 1099 106 77 1400 1024 0 0 261 202 20 19 100 100 100 100 2455 2424 1.352 .74 .731 .742 .724 1.187 52 368 .723 .98 90 2870 18680 43 52 134 143 0 1416 95 1322 .937 1391 1296 1.068 .926 -.095 -.111
8 875 598 104 76 771 522 808 497 106 77 704 421 0 0 208 298 19 14 100 100 100 100 1293 1125 1.477 .677 .598 .632 .61 1.384 52 378 .73 .9 90 3050 18680 43 52 152 161 0 757 96 661 .857 629 533 1.167 .757 -.223 -.402
9 861 780 107 77 754 703 837 737 108 77 730 660 0 0 226 273 16 14 100 100 100 100 1457 1390 1.073 .932 .904 .915 .886 1.205 52 378 .945 .97 90 3220 18680 43 52 169 178 0 987 97 890 1.18 933 835 .847 1.144 .239 .195
10 544 436 103 73 441 363 491 277 104 74 388 204 0 0 231 391 15 13 100 100 100 100 804 592 1.215 .823 .526 .629 .567 1.674 52 379 1.082 .82 90 3390 18680 43 52 186 195 0 552 92 459 1.042 351 258 .96 .666 .059 -.587
11 1857 1477 105 75 1752 1402 1712 1419 105 75 1607 1344 0 0 372 309 15 13 100 100 100 100 3154 2951 1.25 .8 .836 .798 .792 1.161 52 378 .779 .97 90 3560 18680 43 52 203 212 0 1870 95 1775 1.013 1796 1701 .987 1.059 .019 .082
12 1468 1423 107 75 1361 1348 1465 1405 107 77 1358 1330 0 0 341 328 16 14 100 100 100 100 2709 2688 1.01 .99 .979 1.007 .976 1.251 80 462 .984 .98 100 3740 18680 43 53 221 231 0 1801 95 1706 1.254 1778 1684 .798 1.24 .326 .31
13 1723 1339 107 74 1616 1265 1731 1265 107 76 1624 1191 0 0 237 230 16 14 100 100 100 100 2881 2815 1.277 .783 .733 .78 .756 1.212 52 350 .765 .96 90 3900 18680 43 52 237 246 0 1695 94 1601 .991 1601 1508 1.009 .928 -.013 -.107
14 6332 25561 103 76 6229 25485 8357 32752 104 77 8254 32676 0 0 4140 17317 15 16 100 100 100 100 31714 40930 .244 4.091 3.959 4.143 4.001 1.769 120 618 4.211 .98 120 4080 18680 42 54 254 266 0 32356 96 32259 5.179 41458 41362 .193 5.011 2.373 2.325
15 1036 16089 102 74 934 16015 1122 17600 103 75 1020 17526 0 0 320 5156 14 17 100 100 100 100 16949 18546 .058 17.147 17.182 16.59 17.499 1.44 80 456 17.907 .95 100 4260 18680 43 53 273 283 0 20366 94 20272 21.705 22278 22185 .046 21.75 4.44 4.443
16 1247 979 102 67 1145 912 1260 888 102 69 1158 821 0 0 166 296 16 13 100 100 100 100 2057 1979 1.255 .797 .709 .774 .722 1.241 52 364 .805 .93 90 4430 18680 43 52 290 299 0 1239 85 1154 1.008 1124 1039 .992 .897 .012 -.156
17 802 468 98 65 704 403 785 408 99 66 687 343 0 0 222 288 15 13 100 100 100 100 1107 1030 1.747 .572 .499 .504 .497 1.579 80 452 .659 .85 100 4600 18680 43 53 307 317 0 592 82 510 .725 516 434 1.38 .632 -.465 -.662
18 1338 998 96 65 1242 933 1466 1035 97 65 1370 970 0 0 503 397 14 12 100 100 100 100 2175 2340 1.331 .751 .708 .755 .721 1.607 80 452 .747 .95 100 4770 18680 43 53 324 334 0 1263 82 1181 .951 1310 1228 1.052 .896 -.073 -.158
19 2178 1195 97 65 2081 1130 2407 1319 99 66 2310 1254 0 0 707 394 22 20 100 100 100 100 3211 3564 1.842 .543 .543 .537 .533 1.597 80 464 .53 .95 100 4950 18680 43 53 342 352 0 1513 82 1430 .687 1670 1587 1.455 .687 -.541 -.541
20 361 270 98 66 263 204 305 185 100 69 207 119 0 0 204 272 22 21 100 98 100 90 467 326 1.289 .776 .575 .614 .584 1.711 80 439 1.076 .83 100 5130 18680 43 53 360 370 0 342 84 258 .982 234 151 1.018 .728 -.026 -.459

Total number of rows: 10752

Table truncated, full table size 2312 Kbytes.




Supplementary data files not provided

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap