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Sample GSM90533 Query DataSets for GSM90533
Status Public on Jan 04, 2006
Title Puf5 IP (3)
Sample type RNA
 
Channel 1
Source name Puf5 tot. RNA extract (3)
Organism Saccharomyces cerevisiae
Characteristics Puf5 tot. RNA extract (3)
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name Puf5 RNA-IP (3)
Organism Saccharomyces cerevisiae
Characteristics Puf5 RNA-IP (3)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2003-01/36814.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
1 209 134 190 129 19 5 191 135 197 134 1 6 0 0 106 30 35 35 20 7 7 3 24 7 3.8 .263 6 .687 .627 3.965 80 425 .313 .39 100 2940 16110 74 84 45 55 -50 595 572 22 1.168 599 27 .856 26.623 .224 4.735
2 804 385 200 123 604 262 514 269 203 129 314 146 0 0 609 293 41 32 95 81 86 66 866 460 2.305 .434 .465 .379 .411 1.734 80 421 .438 .93 110 3090 16130 75 86 59 70 0 1708 546 1163 1.925 1194 648 .52 2.063 .945 1.045
3 2227 533 202 122 2025 411 2017 483 207 124 1815 361 0 0 1151 295 39 25 100 97 100 95 2436 2176 4.927 .203 .199 .173 .195 1.809 80 446 .205 .93 100 3270 16120 75 85 78 88 0 2365 541 1824 .901 2143 1602 1.11 .883 -.151 -.18
4 759 259 214 128 545 131 710 228 218 128 496 100 0 0 469 107 42 25 87 78 78 68 676 596 4.16 .24 .202 .243 .251 2.682 32 170 .181 .74 60 3440 16110 76 82 97 103 0 1149 568 581 1.067 1012 444 .938 .895 .093 -.161
5 235 129 204 129 31 0 219 127 210 130 15 -2 0 0 73 28 43 25 36 18 20 5 31 13 null null null .433 .465 3.539 80 459 .257 .45 100 3620 16110 74 84 113 123 -50 572 572 0 null 564 -9 null null null null
6 205 129 199 131 6 -2 200 122 207 132 1 -9 0 0 36 29 42 29 15 15 5 5 4 -8 null null null .77 .829 2.569 80 413 .249 .26 100 3800 16110 74 84 131 141 -50 572 581 -9 null 541 -40 null null null null
7 1196 416 218 140 978 276 1209 424 222 146 991 284 0 0 356 103 44 32 100 100 100 97 1254 1275 3.543 .282 .287 .278 .289 1.353 80 396 .275 .94 100 3960 16120 75 85 147 157 0 1846 621 1225 1.252 1881 1260 .799 1.272 .324 .347
8 951 347 203 138 748 209 853 321 209 142 650 183 0 0 388 114 40 33 100 98 100 96 957 833 3.579 .279 .282 .277 .274 1.386 80 441 .272 .93 100 4130 16120 75 85 164 174 0 1540 612 927 1.24 1424 812 .807 1.249 .31 .321
9 1305 393 198 131 1107 262 809 275 203 134 611 144 0 0 1074 250 37 29 100 90 100 78 1369 755 4.225 .237 .236 .207 .249 1.94 52 302 .219 .91 80 4320 16120 76 84 184 192 0 1744 581 1163 1.05 1220 639 .952 1.046 .071 .065
10 1308 429 205 138 1103 291 1064 367 210 141 859 229 0 0 819 213 39 30 100 96 100 91 1394 1088 3.79 .264 .267 .253 .264 1.616 80 421 .254 .93 100 4490 16120 75 85 200 210 0 1904 612 1291 1.171 1628 1016 .854 1.183 .227 .242
11 642 234 220 145 422 89 583 211 221 146 363 66 0 0 344 102 36 31 98 68 95 51 511 429 4.742 .211 .182 .203 .216 1.949 80 391 .241 .85 100 4660 16130 76 86 217 227 0 1038 643 395 .936 936 293 1.069 .807 -.096 -.31
12 2481 953 210 135 2271 818 2264 943 214 138 2054 808 0 0 1016 388 37 29 100 100 100 100 3089 2862 2.776 .36 .393 .349 .357 1.38 80 461 .351 .93 110 4830 16120 74 85 233 244 0 4229 599 3630 1.598 4184 3585 .626 1.746 .677 .804
13 6800 2232 218 134 6582 2098 5498 2051 227 135 5280 1917 0 0 4092 971 52 28 100 100 100 100 8680 7197 3.137 .319 .363 .341 .341 1.377 80 450 .284 .95 110 5000 16110 73 84 250 261 0 9904 595 9309 1.414 9101 8506 .707 1.611 .5 .688
14 37922 7860 226 137 37696 7723 39608 8130 239 140 39382 7993 0 0 14638 2851 58 32 100 100 100 100 45419 47375 4.881 .205 .203 .216 .198 1.636 120 496 .197 .97 120 5170 16120 74 86 267 279 0 34877 608 34269 .909 36075 35467 1.1 .901 -.138 -.151
15 62748 17588 232 142 62516 17446 65535 17764 416 149 65303 17622 75 0 7299 4130 1564 36 100 100 100 100 79962 82925 3.583 .279 .27 .273 .277 1.308 80 434 .274 .94 110 5340 16120 74 85 284 295 0 78042 630 77412 1.238 78823 78193 .808 1.197 .308 .26
16 6379 1375 223 139 6156 1236 6780 1402 377 144 6557 1263 0 0 2756 525 1444 32 95 98 83 98 7392 7820 4.981 .201 .193 .203 .197 1.697 120 511 .174 .91 120 5510 16120 74 86 301 313 0 6101 617 5484 .891 6221 5604 1.122 .855 -.167 -.227
17 2639 666 209 131 2430 535 2470 658 216 134 2261 527 0 0 1126 282 47 28 100 97 100 95 2965 2788 4.542 .22 .233 .207 .218 1.628 120 481 .22 .96 120 5690 16120 74 86 319 331 0 2955 581 2374 .977 2920 2338 1.024 1.034 -.034 .049
18 16327 2808 199 128 16128 2680 15432 2682 206 130 15233 2554 0 0 7239 1250 42 25 100 99 100 99 18808 17787 6.018 .166 .168 .166 .158 1.686 120 479 .161 .96 120 5860 16120 74 86 336 348 0 12460 568 11892 .737 11901 11333 1.356 .744 -.44 -.427
19 3599 837 192 131 3407 706 3641 866 194 133 3449 735 0 0 1241 237 35 26 100 100 100 100 4113 4184 4.826 .207 .213 .212 .205 1.485 120 479 .199 .96 120 6030 16120 74 86 353 365 0 3714 581 3133 .919 3843 3261 1.088 .946 -.121 -.081
20 3399 791 188 130 3211 661 2762 652 191 132 2574 522 0 0 2539 568 32 27 100 95 100 94 3872 3096 4.858 .206 .203 .187 .191 1.721 120 433 .203 .94 120 6210 16120 74 86 371 383 0 3510 577 2933 .913 2893 2316 1.095 .9 -.131 -.152

Total number of rows: 9984

Table truncated, full table size 2250 Kbytes.




Supplementary data files not provided
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