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Sample GSM90527 Query DataSets for GSM90527
Status Public on Jan 04, 2006
Title Puf3 IP (2)
Sample type RNA
 
Channel 1
Source name tot. RNA Puf3 (ex2)
Organism Saccharomyces cerevisiae
Characteristics tot. RNA Puf3 (ex2)
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name IP-RNA Puf3 (2)
Organism Saccharomyces cerevisiae
Characteristics IP-RNA Puf3 (2)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2002-06/30145.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 GPL3270
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
1 587 243 70 37 517 206 630 273 73 39 560 236 0 0 277 117 17 10 100 98 100 97 723 796 2.51 .398 .421 .37 .403 1.407 80 486 .392 .97 110 910 18340 32 43 17 28 0 675 103 572 1.107 758 656 .903 1.171 .146 .227
2 83 36 68 36 15 0 78 35 71 37 10 -1 0 0 18 9 17 10 38 11 11 3 15 9 null null null .621 .591 4.181 80 392 .156 .23 100 1080 18320 31 41 35 45 -50 100 100 0 null 97 null null null null null
3 18513 5401 67 35 18446 5366 9219 2431 74 38 9152 2396 0 0 16108 5090 35 12 100 100 100 100 23812 11548 3.438 .291 .262 .265 .288 1.824 156 629 .296 .97 140 1260 18330 30 44 51 65 0 15003 97 14906 .808 6753 6656 1.238 .727 -.307 -.46
4 1564 463 64 35 1500 428 1338 447 70 37 1274 412 0 0 1027 311 32 11 100 100 100 100 1928 1686 3.505 .285 .323 .273 .285 1.378 120 523 .286 .97 130 1430 18330 30 43 68 81 0 1286 97 1189 .793 1242 1144 1.262 .898 -.335 -.155
5 76 38 63 36 13 2 70 35 64 37 7 -1 0 0 23 14 10 8 40 20 18 13 15 6 6.5 .154 null .75 .5 3.858 80 384 .601 .47 100 1600 18310 30 40 87 97 -50 106 100 6 .427 97 null 2.34 null -1.227 null
6 76 42 65 36 11 6 70 37 66 37 5 1 0 0 23 16 10 8 37 26 18 18 17 6 1.833 .545 .2 .624 .613 3.285 80 425 .522 .39 100 1770 18310 30 40 104 114 -50 117 100 17 1.515 103 3 .66 .556 .599 -.848
7 943 362 65 36 878 326 746 317 67 36 681 281 0 0 473 177 15 8 100 100 100 99 1204 962 2.693 .371 .413 .356 .368 1.503 120 552 .364 .97 130 1960 18330 30 43 121 134 0 1006 100 906 1.031 881 781 .97 1.146 .045 .197
8 1369 513 66 36 1303 477 1351 556 68 37 1285 520 0 0 762 288 16 8 100 100 100 100 1780 1805 2.732 .366 .405 .356 .365 1.476 80 390 .361 .97 110 2130 18330 31 42 139 150 0 1425 100 1325 1.017 1544 1444 .983 1.124 .024 .169
9 273 175 67 35 206 140 229 155 67 36 162 120 0 0 146 94 11 8 100 100 99 98 346 282 1.471 .68 .741 .701 .68 1.609 120 525 .651 .95 120 2300 18330 31 43 156 168 0 486 97 389 1.888 431 333 .53 2.058 .917 1.041
10 597 289 70 36 527 253 579 280 72 37 509 244 0 0 229 110 17 8 100 100 100 100 780 753 2.083 .48 .479 .482 .493 1.595 52 327 .438 .93 90 2460 18320 31 40 173 182 0 803 100 703 1.334 778 678 .75 1.332 .415 .413
11 844 256 70 36 774 220 717 227 72 37 647 191 0 0 604 171 15 8 100 100 100 99 994 838 3.518 .284 .295 .281 .289 1.499 120 657 .277 .97 130 2640 18320 29 42 189 202 0 711 100 611 .79 631 531 1.267 .82 -.341 -.286
12 2142 915 68 36 2074 879 2329 998 70 37 2261 962 0 0 1032 454 11 8 100 100 100 100 2953 3223 2.359 .424 .425 .408 .435 1.432 80 463 .418 .97 110 2820 18310 29 40 208 219 0 2542 100 2442 1.177 2772 2672 .849 1.182 .235 .241
13 1330 451 68 37 1262 414 1020 349 70 37 952 312 0 0 920 296 11 8 100 100 100 100 1676 1264 3.048 .328 .328 .32 .318 1.415 120 533 .316 .96 120 2990 18310 29 41 225 237 0 1253 103 1150 .911 969 867 1.097 .91 -.134 -.135
14 10749 4101 73 38 10676 4063 6859 2764 74 39 6786 2726 0 0 9983 3709 12 8 100 100 100 100 14739 9512 2.628 .381 .402 .39 .383 1.474 120 541 .366 .97 120 3150 18330 31 43 241 253 0 11392 106 11286 1.057 7678 7572 .946 1.116 .08 .158
15 1170 450 71 37 1099 413 1064 382 72 38 993 345 0 0 680 287 12 8 100 100 100 100 1512 1338 2.661 .376 .347 .361 .356 1.375 120 629 .378 .96 130 3370 18320 29 42 262 275 0 1250 103 1147 1.044 1061 958 .958 .965 .062 -.051
16 507 202 68 37 439 165 375 178 69 37 307 141 0 0 342 122 10 8 100 98 100 97 604 448 2.661 .376 .459 .37 .363 1.726 120 591 .358 .96 130 3520 18300 27 40 277 290 0 561 103 458 1.044 494 392 .958 1.276 .062 .351
17 560 159 67 37 493 122 427 133 68 37 360 96 0 0 385 94 10 8 100 98 100 94 615 456 4.041 .247 .267 .241 .251 1.715 120 554 .241 .97 120 3700 18310 29 41 296 308 0 442 103 339 .687 369 267 1.455 .741 -.541 -.433
18 1649 609 66 37 1583 572 756 260 67 37 690 223 0 0 1564 530 10 8 100 100 100 100 2155 913 2.767 .361 .323 .371 .365 1.284 120 617 .344 .98 130 3870 18300 27 40 312 325 0 1692 103 1589 1.004 722 619 .996 .898 .005 -.156
19 1256 534 67 37 1189 497 876 354 68 38 809 317 0 0 871 377 10 8 100 100 100 100 1686 1126 2.392 .418 .392 .402 .399 1.381 120 644 .416 .97 130 4050 18300 27 40 330 343 0 1483 103 1381 1.161 983 881 .861 1.088 .216 .122
20 537 245 68 38 469 207 562 257 69 38 494 219 0 0 214 96 10 8 100 100 100 100 676 713 2.266 .441 .443 .454 .444 1.467 80 416 .436 .97 100 4220 18310 30 40 349 359 0 681 106 575 1.226 714 608 .816 1.231 .294 .3

Total number of rows: 9600

Table truncated, full table size 2059 Kbytes.




Supplementary data files not provided
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