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Sample GSM343540 Query DataSets for GSM343540
Status Public on May 12, 2009
Title CFW100 RPL16a-ZZ total vs reference (4)
Sample type RNA
 
Channel 1
Source name Reference RNA
Organism Saccharomyces cerevisiae
Characteristics Reference RNA
Extracted molecule total RNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name Total RNA RPL16a-ZZ
Organism Saccharomyces cerevisiae
Characteristics Total RNA RPL16a-ZZ
Extracted molecule total RNA
Extraction protocol not provided
Label Cy5
Label protocol not provided
 
 
Hybridization protocol not provided
Scan protocol Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1880, 20000; Software: type: feature extraction; Performer: Regula,,Halbeisen
Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-10-20; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 400; Parameter Laser on time = 15670; Parameter Laser Power = 2.95; Parameter Scan Time = 13:57:52; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 24.69; Performer: Regula,,Halbeisen
Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-10-20; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 340; Parameter Scan Power = 100; Parameter Laser on time = 15669; Parameter Laser Power = 3.57; Parameter Scan Time = 13:57:52; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 24.69; Performer: Regula,,Halbeisen
Description Simple annotation: RNA coimmunoprecipitation, Condition media
Image: http://smd.stanford.edu/MicroArray/gifs/2006-10/70717.gif
Measurement: time(absolute) 20 m
Growth Condition: CFW
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 Nov 18, 2008
Last update date May 12, 2009
Contact name Andre Gerber
E-mail(s) andre.gerber@pharma.ethz.ch
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 GPL7662
Series (2)
GSE13653 Affinity purification of ribosomes and associated RNAs from stress-treated cells
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 1676 1850 138 91 1538 1759 1727 1931 142 94 1589 1840 0 0 336 405 29 25 100 100 100 100 3297 3429 .874 1.144 1.158 1.139 1.178 1.204 52 334 1.156 .98 80 2100 20230 19 27 18 26 0 3024 149 2875 1.869 3156 3007 .535 1.893 .902 .92
2 18036 27897 144 89 17892 27808 22863 34497 149 95 22719 34408 0 0 11922 17968 36 33 100 100 100 100 45700 57127 .643 1.554 1.515 1.633 1.567 1.237 80 495 1.538 1 100 2280 20230 18 28 35 45 0 45594 145 45449 2.54 56381 56236 .394 2.475 1.345 1.308
3 25649 20129 141 87 25508 20042 22769 18975 145 88 22628 18888 0 0 13348 11055 30 21 100 100 100 100 45550 41516 1.273 .786 .835 .757 .784 1.152 52 334 .798 1 80 2460 20220 18 26 54 62 0 32898 142 32756 1.284 31012 30870 .779 1.364 .361 .448
4 2325 1888 140 85 2185 1803 2393 1975 141 85 2253 1890 0 0 754 588 27 16 100 100 100 100 3988 4143 1.212 .825 .839 .836 .83 1.131 52 340 .822 .99 80 2640 20230 19 27 72 80 0 3086 139 2947 1.349 3228 3089 .741 1.371 .432 .455
5 1037 992 143 82 894 910 998 986 146 84 855 904 0 0 290 229 31 18 100 100 100 100 1804 1759 .982 1.018 1.057 1.037 1.001 1.239 32 236 .976 .97 70 2830 20220 18 25 91 98 0 1621 134 1487 1.664 1611 1477 .601 1.728 .734 .789
6 4572 11422 139 86 4433 11336 4747 11784 144 89 4608 11698 0 0 775 1982 29 26 100 100 100 100 15769 16306 .391 2.557 2.539 2.553 2.567 1.101 52 414 2.58 .99 90 3010 20220 17 26 108 117 0 18668 141 18527 4.179 19260 19119 .239 4.149 2.063 2.053
7 1470 1401 137 84 1333 1317 1526 1420 139 88 1389 1336 0 0 318 282 26 30 100 100 100 100 2650 2725 1.012 .988 .962 .997 .995 1.212 52 340 .984 .98 80 3190 20220 18 26 127 135 0 2290 137 2152 1.615 2321 2184 .619 1.572 .691 .653
8 1273 594 136 83 1137 511 1268 570 139 86 1132 487 0 0 477 241 29 16 100 100 100 100 1648 1619 2.225 .449 .43 .44 .438 1.258 32 176 .447 .95 60 3360 20230 20 26 145 151 0 971 136 835 .735 932 796 1.361 .703 -.445 -.508
9 697 331 139 87 558 244 660 343 141 88 521 256 0 0 332 113 27 18 100 100 96 96 802 777 2.287 .437 .491 .465 .48 1.506 32 176 .392 .92 60 3560 20210 18 24 165 171 0 541 142 399 .715 561 418 1.399 .803 -.485 -.316
10 848 365 131 90 717 275 734 351 134 92 603 261 0 0 589 215 27 19 100 78 100 75 992 864 2.607 .384 .433 .343 .392 1.691 32 176 .362 .95 60 3720 20230 20 26 181 187 0 597 147 449 .627 574 427 1.595 .707 -.674 -.499
11 1630 1204 138 89 1492 1115 1834 1370 140 92 1696 1281 0 0 829 572 29 21 98 94 94 92 2607 2977 1.338 .747 .755 .764 .752 1.427 52 340 .728 .98 80 3910 20220 18 26 199 207 0 1968 145 1822 1.221 2239 2094 .819 1.234 .289 .304
12 728 526 133 94 595 432 658 506 136 96 525 412 0 0 263 175 27 21 100 100 100 100 1027 937 1.377 .726 .785 .726 .735 1.242 52 340 .707 .97 80 4090 20220 18 26 217 225 0 860 154 706 1.187 827 673 .843 1.283 .247 .359
13 1076 995 137 96 939 899 1080 1000 138 98 943 904 0 0 321 276 27 21 100 100 100 100 1838 1847 1.044 .957 .959 .975 .972 1.205 52 340 .937 .98 80 4270 20230 19 27 235 243 0 1626 157 1469 1.565 1634 1477 .639 1.567 .646 .648
14 11471 7817 139 101 11332 7716 12793 7972 151 111 12654 7871 0 0 6294 4319 61 52 100 100 100 98 19048 20525 1.469 .681 .622 .681 .692 1.153 52 340 .679 1 80 4460 20210 17 25 254 262 0 12776 165 12611 1.113 13029 12864 .899 1.017 .154 .024
15 2635 1989 148 105 2487 1884 2957 2177 175 139 2809 2072 0 0 831 576 89 92 100 100 100 100 4371 4881 1.32 .758 .738 .773 .758 1.187 52 408 .736 .98 90 4640 20210 16 25 271 280 0 3251 172 3079 1.238 3558 3386 .808 1.206 .308 .27
16 1869 904 143 110 1726 794 2031 960 162 123 1888 850 0 0 562 230 64 42 100 100 100 98 2520 2738 2.174 .46 .45 .47 .46 1.253 52 408 .445 .97 90 4820 20210 16 25 289 298 0 1477 180 1298 .752 1569 1389 1.33 .736 -.411 -.443
17 1660 697 144 114 1516 583 2050 830 161 128 1906 716 0 0 1042 354 66 57 91 92 86 81 2099 2622 2.6 .385 .376 .479 .388 1.875 80 520 .364 .98 100 5010 20220 17 27 308 318 0 1139 186 953 .629 1357 1170 1.591 .614 -.67 -.704
18 3571 2519 148 117 3423 2402 3982 2755 183 152 3834 2638 0 0 1099 731 106 100 100 100 100 100 5825 6472 1.425 .702 .688 .707 .695 1.152 52 408 .69 .99 90 5200 20210 16 25 327 336 0 4117 191 3926 1.147 4503 4311 .872 1.125 .198 .169
19 1658 940 136 114 1522 826 1634 955 144 117 1498 841 0 0 573 287 42 33 100 100 100 100 2348 2339 1.843 .543 .561 .558 .548 1.276 52 340 .533 .98 80 5380 20220 18 26 346 354 0 1536 186 1350 .887 1561 1375 1.127 .918 -.173 -.124
20 1032 468 135 108 897 360 954 467 138 111 819 359 0 0 404 152 28 23 100 100 100 100 1257 1178 2.492 .401 .438 .407 .402 1.27 52 340 .384 .97 80 5570 20220 18 26 365 373 0 765 177 588 .656 763 587 1.525 .716 -.608 -.481

Total number of rows: 9216

Table truncated, full table size 2050 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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