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Sample GSM328845 Query DataSets for GSM328845
Status Public on Oct 28, 2008
Title Dhh1_(1)_cDNA_Mg _RBP40paper
Sample type RNA
 
Channel 1
Source Name total RNA extract
Organism(s) Saccharomyces cerevisiae
Characteristics total RNA extract
Extracted molecule total RNA
Extraction protocol not provided
Label Cy3
Label protocol Gerber et al. (2004) PLoS Biology; The protocol can be accessed from the web-site; Protocol Type = Extract preparation; Performer: Andre,,Gerber
 
Channel 2
Source Name affinity purified RNA
Organism(s) Saccharomyces cerevisiae
Characteristics affinity purified RNA
Extracted molecule total RNA
Extraction protocol not provided
Label Cy5
Label protocol Gerber et al. (2004) PLoS Biology; The protocol can be accessed from the web-site; Protocol Type = Extract preparation; Performer: Andre,,Gerber
 
 
Hybridization protocol not provided
Scan protocol Scanning software = AxImageIO; Scanner Make = Axon Instruments (V1.00)
Description Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2006-11/71150.gif
Genotype: Dhh1
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 Oct 09, 2008
Contact name Daniel Hogan
Organization name Stanford University
Street address 279 Campus Dr B439
City Stanford
State/province CA
ZIP/Postal code 94025
Country USA
 
Platform ID GPL7455
Series (1)
GSE13135 RBP40_arrays

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
1 854 261 150 113 704 148 756 240 154 123 606 127 0 0 332 99 41 64 100 80 100 49 852 733 4.757 .21 .21 .197 .207 2.24 208 1660 .171 .58 85 1295 20415 86 103 74 91 0 1469 636 833 1.184 1351 715 .845 1.18 .243 .239
2 13834 927 148 113 13686 814 10419 817 153 122 10271 704 0 0 9670 489 42 63 100 99 100 97 14500 10975 16.813 .059 .069 .061 .061 1.454 208 1660 .053 .95 85 1470 20410 85 102 109 126 0 5219 636 4583 .335 4600 3963 2.986 .386 -1.578 -1.374
3 6215 368 147 114 6068 254 3431 265 151 122 3284 151 0 0 7975 329 42 62 100 72 99 58 6322 3435 23.89 .042 .046 .044 .047 2.442 208 1512 .039 .92 80 1650 20415 87 103 146 162 0 2072 642 1430 .236 1492 850 4.243 .259 -2.085 -1.95
4 1045 265 148 111 897 154 717 259 152 119 569 148 0 0 921 139 48 59 91 69 83 58 1051 717 5.825 .172 .26 .226 .193 3.249 156 1272 .134 .72 75 1835 20400 84 99 183 198 0 1492 625 867 .967 1458 833 1.035 1.464 -.049 .55
5 410 181 145 111 265 70 218 153 148 121 73 42 0 0 426 106 41 62 64 41 44 22 335 115 3.786 .264 .575 .517 .602 4.706 316 2328 .184 .52 100 2015 20410 84 104 217 237 -50 1019 625 394 1.487 861 236 .672 3.239 .573 1.696
6 6639 507 150 116 6489 391 6550 496 154 123 6400 380 0 0 1103 151 40 62 100 99 100 97 6880 6780 16.596 .06 .059 .056 .058 1.541 208 1660 .058 .87 85 2205 20410 85 102 256 273 0 2854 653 2201 .339 2792 2139 2.948 .334 -1.56 -1.581
7 1016 297 149 109 867 188 879 288 151 119 730 179 0 0 351 112 41 61 100 88 100 70 1055 909 4.612 .217 .245 .199 .211 2.063 208 1642 .188 .67 85 2385 20410 85 102 292 309 0 1672 614 1058 1.221 1621 1008 .819 1.38 .288 .465
8 216 151 142 109 74 42 183 140 145 117 41 31 0 0 115 76 40 60 50 34 24 13 116 72 1.762 .568 .756 .958 .872 4.003 316 2262 .805 .28 100 2560 20410 84 104 326 346 -50 850 614 236 3.195 788 175 .313 4.257 1.676 2.09
9 225 159 145 111 80 48 192 145 147 119 47 34 0 0 119 84 39 62 54 34 27 16 128 81 1.667 .6 .723 1.013 .894 4.291 316 2301 .872 .38 100 2745 20410 84 104 363 383 -50 895 625 270 3.378 816 191 .296 4.073 1.756 2.026
10 434 225 155 119 279 106 350 202 161 128 195 83 0 0 227 115 45 67 86 57 72 36 385 278 2.632 .38 .426 .437 .432 2.712 80 560 .387 .56 50 2940 20410 89 99 407 417 0 1267 670 597 2.139 1137 467 .468 2.396 1.097 1.261
11 380 238 156 109 224 129 320 213 160 120 164 104 0 0 183 113 40 61 86 69 76 44 353 268 1.736 .576 .634 .588 .6 3.011 156 1140 .551 .6 70 3110 20420 89 103 439 453 0 1340 614 726 3.242 1199 586 .308 3.57 1.697 1.836
12 436 267 150 118 286 149 385 251 154 128 235 133 0 0 157 108 42 65 100 76 98 51 435 368 1.919 .521 .566 .499 .554 2.281 156 1272 .562 .59 75 3280 20400 84 99 472 487 0 1503 664 839 2.933 1413 749 .341 3.186 1.552 1.672
13 705 318 157 114 548 204 686 300 163 125 529 186 0 0 177 128 44 64 100 88 100 69 752 715 2.686 .372 .352 .322 .37 2.102 208 1512 .366 .7 80 3465 20410 86 102 509 525 0 1790 642 1148 2.096 1689 1047 .477 1.979 1.067 .985
14 11405 805 172 117 11233 688 11855 808 180 127 11683 691 0 0 5578 340 59 64 100 98 100 96 11921 12374 16.327 .061 .059 .06 .061 1.71 208 1512 .057 .94 80 3650 20410 86 102 546 562 0 4532 659 3873 .345 4549 3890 2.9 .333 -1.536 -1.586
15 1264 366 164 118 1100 248 1289 355 169 126 1125 237 0 0 331 135 44 63 100 91 100 80 1348 1362 4.435 .225 .211 .201 .224 2.147 156 1272 .215 .75 75 3840 20410 86 101 584 599 0 2061 664 1396 1.269 1999 1334 .788 1.186 .344 .246
16 629 342 159 117 470 225 650 330 162 124 491 213 0 0 140 129 43 63 100 93 100 78 695 704 2.089 .479 .434 .423 .475 1.967 208 1660 .512 .75 85 4020 20410 85 102 619 636 0 1925 659 1267 2.695 1858 1199 .371 2.442 1.43 1.288
17 695 376 161 121 534 255 670 359 170 130 509 238 0 0 142 131 84 69 100 93 100 79 789 747 2.094 .478 .468 .421 .471 1.817 156 1272 .49 .77 75 4205 20415 87 102 657 672 0 2117 681 1436 2.688 2021 1340 .372 2.632 1.427 1.396
18 2185 357 152 112 2033 245 2410 349 159 122 2258 237 0 0 736 137 75 63 100 92 100 80 2278 2495 8.298 .121 .105 .116 .127 1.849 208 1512 .109 .76 80 4385 20400 84 100 693 709 0 2010 631 1379 .678 1965 1334 1.474 .591 -.56 -.759
19 797 257 137 107 660 150 674 235 143 117 537 128 0 0 385 114 44 60 100 78 100 53 810 665 4.4 .227 .238 .216 .23 2.356 208 1512 .196 .65 80 4570 20400 84 100 730 746 0 1447 602 844 1.28 1323 721 .782 1.342 .356 .424
20 465 255 141 109 324 146 429 239 146 118 288 130 0 0 165 113 42 59 100 75 98 51 470 418 2.219 .451 .451 .373 .457 2.573 156 1140 .479 .67 70 4760 20405 86 100 769 783 0 1436 614 822 2.537 1346 732 .394 2.541 1.343 1.346

Total number of rows: 9216

Table truncated, full table size 2004 Kbytes.




Supplementary data files not provided
Raw data included within Sample table
Processed data included within Sample table
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