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Sample GSM90535 Query DataSets for GSM90535
Status Public on Jan 04, 2006
Title Puf5 IP (4)
Sample type RNA
 
Channel 1
Source name Puf5 tot. RNA extract (4)
Organism Saccharomyces cerevisiae
Characteristics Puf5 tot. RNA extract (4)
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name Puf5 RNA-IP (4)
Organism Saccharomyces cerevisiae
Characteristics Puf5 RNA-IP (4)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2003-01/36815.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
1 114 76 99 67 15 9 107 73 101 68 8 6 0 0 30 17 15 13 37 32 21 20 24 14 1.667 .6 .75 .674 .59 3.603 80 464 .295 .32 100 2620 18550 70 80 33 43 -50 231 204 27 1.825 222 18 .548 2.282 .868 1.19
2 123 75 101 67 22 8 115 72 103 68 14 5 0 0 36 19 16 13 45 31 22 16 30 19 2.75 .364 .357 .723 .75 3.487 80 443 .322 .3 100 2790 18550 70 80 50 60 -50 228 204 24 1.106 219 15 .904 1.087 .146 .12
3 191 132 105 71 86 61 161 109 106 72 56 38 0 0 93 71 16 14 75 75 66 58 147 94 1.41 .709 .679 .641 .629 2.123 12 104 .67 .75 50 2960 18570 74 79 69 74 -100 402 216 186 2.158 332 116 .463 2.064 1.11 1.046
4 118 77 101 68 17 9 107 74 103 70 6 6 0 0 35 20 12 13 38 28 25 15 26 12 1.889 .529 1 .636 .591 3.34 80 456 .428 .35 100 3130 18540 69 79 84 94 -50 234 207 27 1.611 225 18 .621 3.042 .688 1.605
5 118 78 102 69 16 9 113 77 103 70 11 8 0 0 27 22 13 13 47 38 17 15 25 19 1.778 .563 .727 1.218 1.25 3.201 80 432 .948 .42 100 3300 18540 69 79 101 111 -50 237 210 27 1.711 234 24 .584 2.213 .775 1.146
6 230 131 109 75 121 56 117 76 287 170 8 1 0 0 360 155 447 229 10 10 3 5 177 9 2.161 .463 .125 .621 .478 2.54 80 397 .492 .95 100 3470 18540 69 79 118 128 -50 399 228 170 1.408 231 3 .71 .38 .494 -1.395
7 1562 664 116 83 1446 581 1636 729 271 167 1520 646 0 0 881 303 405 203 82 82 73 73 2027 2166 2.489 .402 .425 .454 .408 1.658 156 563 .356 .91 140 3660 18560 69 83 135 149 -100 2020 253 1768 1.222 2218 1965 .818 1.293 .29 .371
8 1020 532 115 85 905 447 895 573 179 128 780 488 0 0 640 234 190 112 82 81 77 79 1352 1268 2.025 .494 .626 .565 .554 1.59 156 551 .302 .82 140 3830 18560 69 83 152 166 -100 1619 259 1360 1.503 1743 1485 .665 1.903 .588 .929
9 1828 704 122 88 1706 616 1297 597 201 148 1175 509 0 0 1409 453 168 132 95 92 92 73 2322 1684 2.769 .361 .433 .391 .352 1.851 80 397 .306 .87 100 4000 18530 68 78 171 181 0 2142 268 1874 1.099 1816 1549 .91 1.318 .136 .398
10 2216 805 135 97 2081 708 1847 670 205 152 1712 573 0 0 1553 519 167 134 100 91 98 72 2789 2285 2.939 .34 .335 .335 .332 1.608 80 463 .315 .9 110 4170 18540 68 79 187 198 0 2449 295 2154 1.035 2038 1743 .966 1.018 .05 .026
11 859 520 121 87 738 433 804 528 182 136 683 441 0 0 360 151 157 124 96 95 92 89 1171 1124 1.704 .587 .646 .604 .657 1.444 120 571 .557 .89 130 4340 18530 66 79 203 216 -100 1582 265 1317 1.785 1606 1342 .56 1.964 .836 .974
12 876 545 124 94 752 451 870 568 203 152 746 474 0 0 367 166 170 132 95 93 85 86 1203 1220 1.667 .6 .635 .609 .644 1.456 120 495 .556 .89 120 4510 18540 68 80 221 233 -100 1658 286 1372 1.825 1728 1442 .548 1.933 .868 .951
13 4433 2105 115 76 4318 2029 3250 1735 179 120 3135 1659 0 0 2873 1064 175 112 100 100 100 100 6347 4794 2.128 .47 .529 .501 .512 1.284 80 470 .418 .96 110 4680 18530 67 78 238 249 0 6404 231 6173 1.43 5279 5047 .699 1.61 .516 .687
14 16883 5222 110 75 16773 5147 17092 5169 175 112 16982 5094 0 0 8249 2504 213 118 95 98 95 95 21920 22076 3.259 .307 .3 .338 .303 1.918 120 587 .298 .97 130 4860 18530 66 79 255 268 0 15887 228 15659 .934 15726 15498 1.071 .913 -.099 -.132
15 49987 15944 117 81 49870 15863 57079 17862 226 152 56962 17781 31 0 19486 6903 244 152 96 98 96 96 65733 74743 3.144 .318 .312 .327 .317 1.861 120 540 .317 .97 130 5030 18530 66 79 272 285 0 48508 246 48262 .968 54343 54097 1.033 .95 -.047 -.074
16 5256 1346 113 74 5143 1272 3401 916 172 115 3288 842 0 0 3949 1016 176 114 99 96 96 89 6415 4130 4.043 .247 .256 .232 .239 1.56 120 470 .242 .96 120 5200 18540 68 80 290 302 0 4095 225 3870 .752 2787 2562 1.329 .779 -.41 -.36
17 1228 443 107 70 1121 373 1017 364 111 72 910 294 0 0 779 282 21 15 98 98 98 96 1494 1204 3.005 .333 .323 .321 .332 1.687 120 482 .337 .96 120 5370 18530 67 79 307 319 0 1348 213 1135 1.012 1107 894 .988 .983 .018 -.025
18 8472 1819 104 69 8368 1750 8383 1754 107 72 8279 1685 0 0 4057 998 16 20 97 94 97 93 10118 9964 4.782 .209 .204 .206 .209 1.497 120 475 .21 .95 120 5530 18530 67 79 323 335 0 5534 210 5324 .636 5336 5126 1.572 .619 -.652 -.692
19 1249 394 106 71 1143 323 1177 355 110 76 1071 284 0 0 569 172 31 27 100 98 98 95 1466 1355 3.539 .283 .265 .274 .271 1.607 120 496 .275 .95 120 5700 18520 66 78 340 352 0 1199 216 983 .86 1080 864 1.163 .807 -.218 -.31
20 2805 993 108 72 2697 921 2317 880 113 76 2209 808 0 0 1614 536 33 22 100 100 100 100 3618 3017 2.928 .341 .366 .343 .343 1.452 80 422 .316 .93 110 5870 18520 66 77 357 368 0 3021 219 2802 1.039 2677 2458 .963 1.113 .055 .154

Total number of rows: 9984

Table truncated, full table size 2214 Kbytes.




Supplementary data files not provided
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