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Sample GSM402433 Query DataSets for GSM402433
Status Public on May 12, 2009
Title Rpl16b-ZZ in SC (1)
Sample type RNA
 
Channel 1
Source name Total RNA Rpl16b-ZZ
Organism Saccharomyces cerevisiae
Characteristics reference: Total RNA Rpl16b-ZZ
Extracted molecule total RNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name IP RNA (RA) Rpl16b-ZZ
Organism Saccharomyces cerevisiae
Characteristics test: IP RNA (RA) Rpl16b-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/2008-08/80812.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 2043 1849 36 71 2007 1778 2070 1827 36 71 2034 1756 0 0 480 406 6 16 100 100 100 100 3785 3790 1.129 .886 .863 .89 .87 1.121 32 176 .884 .99 60 2140 6730 22 28 63 69 0 2820 108 2712 1.351 2787 2679 .74 1.317 .434 .397
2 309 269 35 71 274 198 313 270 35 73 278 199 0 0 82 80 7 13 100 100 100 93 472 477 1.384 .723 .716 .67 .713 1.42 32 176 .751 .95 60 2360 6720 21 27 85 91 0 410 108 302 1.102 412 304 .907 1.092 .14 .127
3 2018 1528 35 72 1983 1456 2242 1693 36 73 2207 1621 0 0 694 558 7 14 100 100 100 100 3439 3828 1.362 .734 .734 .705 .723 1.186 32 236 .744 .99 70 2590 6720 20 27 107 114 0 2331 110 2221 1.12 2582 2473 .893 1.12 .163 .164
4 79 100 33 69 46 31 79 101 34 70 46 32 0 0 14 15 8 14 100 84 96 53 77 78 1.484 .674 .696 .613 .7 1.789 32 176 .773 .59 60 2810 6730 22 28 130 136 0 153 105 47 1.028 154 49 .973 1.061 .04 .086
5 53 92 34 72 19 20 51 91 34 72 17 19 0 0 12 18 6 16 87 53 68 9 39 36 .95 1.053 1.118 1.146 1.056 2.7 32 176 2.949 .44 60 3030 6730 22 28 152 158 0 140 110 31 1.606 139 29 .623 1.705 .683 .77
6 42 75 34 72 8 3 37 75 34 72 3 3 0 0 12 14 7 14 41 23 27 3 11 6 2.667 .375 1 1.43 1.4 3.154 80 554 1.068 .26 100 3240 6730 20 30 171 181 -50 114 110 5 .572 114 5 1.748 1.525 -.806 .609
7 891 781 34 70 857 711 877 786 35 74 843 716 0 0 205 168 6 15 100 100 100 100 1568 1559 1.205 .83 .849 .83 .853 1.151 32 176 .827 .99 60 3470 6740 23 29 196 202 0 1191 107 1085 1.266 1199 1092 .79 1.296 .34 .374
8 847 687 33 71 814 616 905 742 34 72 872 671 0 0 292 223 6 14 100 100 100 100 1430 1543 1.321 .757 .769 .745 .769 1.24 32 236 .756 .98 70 3690 6730 21 28 217 224 0 1048 108 940 1.154 1132 1024 .866 1.174 .207 .231
9 402 329 34 70 368 259 436 333 34 70 402 263 0 0 98 87 7 15 100 100 100 100 627 665 1.421 .704 .654 .689 .695 1.308 32 176 .711 .95 60 3910 6740 23 29 240 246 0 502 107 395 1.074 508 401 .931 .998 .102 -.003
10 569 388 34 69 535 319 596 396 35 70 562 327 0 0 137 104 9 13 100 100 100 100 854 889 1.677 .596 .582 .575 .59 1.277 32 236 .613 .97 70 4140 6740 22 29 262 269 0 592 105 487 .91 604 499 1.099 .888 -.137 -.172
11 4040 3067 36 72 4004 2995 4335 3505 40 75 4299 3433 0 0 1337 1205 28 21 100 100 100 100 6999 7732 1.337 .748 .799 .692 .756 1.321 32 236 .779 .99 70 4360 6740 22 29 284 291 0 4678 110 4569 1.141 5346 5237 .876 1.218 .19 .285
12 100 98 33 70 67 28 99 94 34 71 66 24 0 0 21 20 5 14 100 62 100 40 95 90 2.393 .418 .364 .328 .344 2.362 32 176 .465 .57 60 4580 6740 23 29 307 313 0 149 107 43 .637 143 37 1.569 .555 -.65 -.85
13 387 246 34 69 353 177 405 253 35 70 371 184 0 0 89 71 6 15 100 100 100 100 530 555 1.994 .501 .496 .474 .5 1.321 32 236 .51 .93 70 4790 6750 23 30 327 334 0 375 105 270 .765 386 281 1.307 .757 -.387 -.403
14 764 621 35 71 729 550 771 637 35 72 736 566 0 0 139 121 6 15 100 100 100 100 1279 1302 1.325 .754 .769 .747 .753 1.165 32 236 .756 .98 70 5020 6750 23 30 350 357 0 947 108 839 1.151 972 863 .869 1.173 .203 .23
15 815 785 35 70 780 715 800 809 36 72 765 739 0 0 112 112 7 15 100 100 100 100 1495 1504 1.091 .917 .966 .914 .913 1.138 32 236 .909 .99 70 5230 6750 23 30 371 378 0 1197 107 1091 1.398 1234 1127 .715 1.474 .484 .559
16 3442 3205 35 69 3407 3136 3629 3415 36 70 3594 3346 0 0 1788 1737 7 15 100 100 100 100 6543 6940 1.086 .92 .931 .916 .923 1.254 52 340 .935 .99 80 5450 6760 24 32 393 401 0 4889 105 4784 1.404 5209 5104 .712 1.42 .49 .506
17 1225 713 35 70 1190 643 1454 825 36 70 1419 755 0 0 550 316 7 13 100 100 100 100 1833 2174 1.851 .54 .532 .534 .546 1.242 52 340 .546 .99 80 5670 6760 24 32 415 423 0 1088 107 981 .824 1258 1152 1.213 .812 -.279 -.301
18 685 362 35 70 650 292 731 378 36 70 696 308 0 0 159 93 6 14 100 100 100 100 942 1004 2.226 .449 .443 .433 .456 1.256 32 236 .462 .98 70 5900 6750 23 30 438 445 0 552 107 445 .685 577 470 1.459 .675 -.545 -.567
19 863 654 35 70 828 584 900 652 36 72 865 582 0 0 147 133 12 16 100 100 100 100 1412 1447 1.418 .705 .673 .698 .691 1.148 32 236 .72 .98 70 6120 6760 24 31 460 467 0 998 107 891 1.076 995 888 .929 1.026 .106 .037
20 59 87 32 67 27 20 58 89 33 70 26 22 0 0 10 19 7 15 96 65 93 25 47 48 1.35 .741 .846 1.034 .958 1.879 32 176 1.798 .38 60 2150 6940 43 49 64 70 0 133 102 31 1.13 136 34 .885 1.291 .176 .368

Total number of rows: 10944

Table truncated, full table size 2330 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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