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Sample GSM402431 Query DataSets for GSM402431
Status Public on May 12, 2009
Title Rpl16a-ZZ Gradient (4)
Sample type RNA
 
Channel 1
Source name Total RNA Rpl16a-ZZ
Organism Saccharomyces cerevisiae
Characteristics reference: Total RNA Rpl16a-ZZ
Extracted molecule total RNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name Gradient RNA Rpl16a-ZZ
Organism Saccharomyces cerevisiae
Characteristics test: Gradient RNA Rpl16a-ZZ
Extracted molecule total RNA
Extraction protocol not provided
Label Cy5
Label protocol not provided
 
 
Hybridization protocol not provided
Scan protocol GenePix 4200A
Description Simple annotation: RNA coimmunoprecipitation, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2009-01/82651.gif
Media: SC
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 May 12, 2009
Last update date May 12, 2009
Contact name Andre Gerber
E-mail(s) [email protected]
Phone +41 44 6337378
Fax +41 44 6337364
Organization name Swiss Federal Institute of Technology
Department Institute of Pharmaceutical Science
Street address Wolfgang Pauli Str. 10, HCI H396
City ETH Hoenggerberg, Zuerich
ZIP/Postal code ZH
Country Switzerland
 
Platform ID GPL8546
Series (2)
GSE13654 Affinity purification of ribosomes and associated RNAs using tagged Rpl16a and Rpl16b
GSE13682 Affinity purification of ribosomes and associated RNAs from stress-treated cells using tagged Rpl16a and Rpl16b

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
1 939 912 44 54 895 858 968 954 46 54 924 900 0 0 150 144 12 8 100 100 100 100 1753 1824 1.043 .959 .974 .959 .961 1.102 32 176 .965 .99 60 2150 6750 36 42 56 62 0 1423 84 1339 1.496 1488 1404 .669 1.52 .581 .604
2 160 118 43 54 117 64 161 118 45 55 118 64 0 0 29 18 15 11 100 100 100 100 181 182 1.828 .547 .542 .546 .559 1.392 32 176 .544 .89 60 2370 6750 36 42 78 84 0 184 84 100 .853 184 100 1.172 .846 -.229 -.241
3 393 358 45 54 348 304 391 370 50 56 346 316 0 0 99 107 36 12 100 100 100 100 652 662 1.145 .874 .913 .853 .848 1.234 32 236 .855 .97 70 2580 6740 34 41 98 105 0 559 84 474 1.363 577 493 .734 1.425 .447 .511
4 80 61 43 53 37 8 68 62 44 54 25 9 0 0 56 12 12 10 81 46 53 9 45 34 4.625 .216 .36 .441 .432 3.202 32 236 .129 .97 70 2810 6740 34 41 121 128 0 95 83 12 .337 97 14 2.964 .562 -1.568 -.832
5 51 54 42 54 9 0 49 53 43 54 7 -1 0 0 13 11 11 10 36 13 15 3 9 6 null null null .65 .545 4.653 80 560 .42 .13 100 3030 6740 33 43 142 152 -50 84 84 0 null 83 -2 null null null null
6 51 54 43 54 8 0 50 54 45 55 7 0 0 0 14 9 14 11 28 13 6 0 8 7 null null null .586 .625 3.315 80 560 .379 .49 100 3250 6740 33 43 164 174 -50 84 84 0 null 84 0 null null null null
7 408 419 44 55 364 364 400 421 62 62 356 366 0 0 100 92 140 54 100 100 84 100 728 722 1 1 1.028 1.004 1.087 1.242 32 236 .244 .81 70 3480 6750 35 42 188 195 0 654 86 568 1.56 657 571 .641 1.604 .642 .682
8 310 195 41 53 269 142 305 197 41 53 264 144 0 0 88 48 10 9 100 100 100 100 411 408 1.894 .528 .545 .524 .532 1.293 32 236 .522 .96 70 3700 6740 34 41 210 217 0 304 83 222 .824 307 225 1.214 .851 -.28 -.233
9 190 149 39 53 151 96 187 154 41 53 148 101 0 0 43 34 10 10 100 100 100 96 247 249 1.573 .636 .682 .614 .682 1.514 32 236 .652 .9 70 3920 6740 34 41 232 239 0 232 83 150 .992 240 158 1.008 1.065 -.012 .09
10 213 164 43 53 170 111 226 168 43 53 183 115 0 0 59 50 10 9 96 96 96 96 281 298 1.532 .653 .628 .654 .619 1.54 32 236 .661 .93 70 4150 6740 34 41 255 262 0 256 83 173 1.019 262 179 .982 .98 .027 -.029
11 1735 1678 43 55 1692 1623 1920 1845 45 55 1877 1790 0 0 518 475 14 9 100 100 100 100 3315 3667 1.043 .959 .954 .969 .963 1.114 32 236 .949 .99 70 4350 6750 35 42 275 282 0 2618 86 2532 1.497 2878 2793 .668 1.488 .582 .573
12 71 63 43 55 28 8 71 62 43 55 28 7 0 0 14 14 11 11 87 31 68 12 36 35 3.5 .286 .25 .404 .444 3.173 32 176 .273 .19 60 4580 6740 35 41 299 305 0 98 86 12 .446 97 11 2.243 .39 -1.166 -1.358
13 116 86 41 55 75 31 121 86 42 56 80 31 0 0 30 17 17 10 98 88 90 73 106 111 2.419 .413 .388 .372 .405 2.145 52 340 .426 .75 80 4800 6750 35 43 320 328 0 134 86 48 .645 134 48 1.551 .605 -.633 -.726
14 350 271 41 54 309 217 368 284 41 54 327 230 0 0 101 70 10 10 100 100 100 100 526 557 1.424 .702 .703 .7 .708 1.274 52 420 .702 .96 90 5010 6740 33 42 340 349 0 423 84 339 1.096 443 359 .913 1.097 .132 .134
15 230 191 41 53 189 138 230 194 41 54 189 141 0 0 49 33 9 10 100 100 100 100 327 330 1.37 .73 .746 .731 .724 1.326 52 340 .723 .94 80 5230 6750 35 43 363 371 0 298 83 215 1.139 303 220 .878 1.164 .188 .219
16 854 753 40 50 814 703 869 739 41 52 829 689 0 0 260 246 10 10 100 100 100 100 1517 1518 1.158 .864 .831 .849 .872 1.177 52 340 .872 .99 80 5450 6740 34 42 385 393 0 1175 78 1097 1.347 1153 1075 .742 1.297 .43 .375
17 316 299 43 51 273 248 319 306 43 52 276 255 0 0 80 69 10 9 100 100 100 100 521 531 1.101 .908 .924 .92 .902 1.255 52 340 .89 .96 80 5670 6750 35 43 407 415 0 466 80 387 1.417 477 398 .706 1.441 .503 .528
18 134 116 41 51 93 65 137 110 41 52 96 59 0 0 31 24 9 10 100 100 100 100 158 155 1.431 .699 .615 .692 .699 1.534 52 340 .679 .84 80 5890 6740 34 42 429 437 0 181 80 101 1.09 172 92 .917 .959 .125 -.061
19 292 237 39 52 253 185 298 252 41 53 259 200 0 0 88 59 10 9 100 100 100 100 438 459 1.368 .731 .772 .74 .738 1.352 32 236 .703 .95 70 6110 6730 33 40 451 458 0 370 81 289 1.141 393 312 .877 1.205 .19 .269
20 53 55 44 53 9 2 52 55 47 54 8 2 0 0 12 9 18 12 21 12 1 1 11 10 4.5 .222 .25 .592 .604 2.718 80 560 .459 .25 100 2150 6960 55 65 54 64 -50 86 83 3 .347 86 3 2.884 .39 -1.528 -1.358

Total number of rows: 10944

Table truncated, full table size 2236 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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