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Sample GSM343549 Query DataSets for GSM343549
Status Public on May 12, 2009
Title Sorbitol RPL16a-ZZ IP poly vs reference (1)
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 IP RNA RPL16a-ZZ
Organism Saccharomyces cerevisiae
Characteristics IP 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 = 800, 20320; 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 = 2006-08-09; 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 = 13920; Parameter Laser Power = 2.83; Parameter Scan Time = 11:31:53; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 25.63; 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 = 2006-08-09; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 430; Parameter Scan Power = 100; Parameter Laser on time = 13920; Parameter Laser Power = 3.61; Parameter Scan Time = 11:31:53; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 25.63; Performer: Regula,,Halbeisen
Description Simple annotation: RNA coimmunoprecipitation, Condition media
Image: http://smd.stanford.edu/MicroArray/gifs/2006-08/69658.gif
Measurement: time(absolute) 10 m
Growth Condition: Sorbitol
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 1525 2967 176 249 1349 2718 1482 3003 179 254 1306 2754 0 0 505 891 35 54 100 100 100 100 4067 4060 .496 2.015 2.109 2.031 2.053 1.315 52 334 2.05 .96 80 1010 20720 36 44 17 25 0 4332 364 3969 2.942 4385 4021 .34 3.079 1.557 1.622
2 27050 34612 176 237 26874 34375 32843 45464 180 242 32667 45227 0 5 18759 23497 39 54 100 100 100 98 61249 77894 .782 1.279 1.384 1.14 1.186 1.451 80 580 1.275 .98 110 1190 20710 33 44 33 44 0 50537 346 50191 1.868 66382 66036 .535 2.021 .901 1.015
3 20399 41774 180 240 20219 41534 18927 42874 483 342 18747 42634 0 11 12064 18099 3541 1108 98 100 88 100 61753 61381 .487 2.054 2.274 2.156 2.211 1.269 52 402 1.972 .96 90 1380 20710 34 43 53 62 0 60995 350 60644 2.999 62601 62250 .333 3.321 1.585 1.731
4 2798 3176 180 242 2618 2934 2581 3201 191 263 2401 2959 0 0 1010 954 130 240 100 100 100 100 5552 5360 .892 1.121 1.232 1.137 1.18 1.232 52 340 1.149 .95 80 1560 20710 35 43 72 80 0 4637 353 4284 1.636 4674 4320 .611 1.799 .71 .848
5 846 1121 198 238 648 883 833 1141 765 401 635 903 0 0 338 379 5252 1665 0 1 0 0 1531 1538 .734 1.363 1.422 1.456 1.367 1.562 52 334 1.357 .92 80 1750 20700 34 42 91 99 0 1637 348 1289 1.99 1666 1318 .503 2.076 .992 1.054
6 6961 11959 181 250 6780 11709 7402 12276 187 253 7221 12026 0 0 1428 3009 39 53 100 100 100 100 18489 19247 .579 1.727 1.665 1.716 1.698 1.218 52 334 1.817 .96 80 1920 20700 34 42 108 116 0 17461 365 17096 2.522 17924 17559 .397 2.432 1.334 1.282
7 1706 1305 176 250 1530 1055 1858 1363 179 253 1682 1113 0 0 609 479 33 49 100 100 100 94 2585 2795 1.45 .69 .662 .674 .658 1.326 52 340 .696 .94 80 2100 20690 33 41 126 134 0 1905 365 1540 1.007 1990 1625 .993 .966 .01 -.05
8 2015 1929 173 240 1842 1689 2460 1897 181 244 2287 1657 0 0 1095 1114 41 49 100 100 83 100 3531 3944 1.091 .917 .725 1.093 .896 1.711 12 104 .968 .94 50 2300 20710 36 41 147 152 0 2817 350 2466 1.339 2770 2419 .747 1.058 .421 .081
9 1687 994 179 259 1508 735 1874 1153 181 260 1695 894 0 0 1105 461 28 71 91 91 91 75 2243 2589 2.052 .487 .527 .574 .54 1.564 12 104 .564 .88 50 2460 20710 36 41 163 168 0 1451 378 1073 .712 1684 1305 1.405 .77 -.491 -.377
10 1449 1833 183 244 1266 1589 1502 2134 227 329 1319 1890 0 0 619 718 208 382 100 100 91 83 2855 3209 .797 1.255 1.433 1.28 1.326 1.514 12 68 1.25 .93 40 2640 20710 37 41 182 186 0 2676 356 2320 1.833 3116 2760 .546 2.092 .874 1.065
11 1588 982 175 255 1413 727 1879 1041 177 255 1704 786 0 0 843 400 32 51 96 90 96 87 2140 2490 1.944 .515 .461 .566 .539 1.515 32 176 .465 .94 60 2840 20690 34 40 201 207 0 1434 372 1061 .751 1520 1148 1.331 .674 -.413 -.57
12 552 4414 172 248 380 4166 569 3949 174 249 397 3701 0 0 216 2213 32 51 98 100 94 100 4546 4098 .091 10.963 9.322 11.468 10.815 1.437 52 340 11.31 .94 80 3020 20680 32 40 218 226 0 6445 362 6083 16.007 5766 5404 .062 13.612 4.001 3.767
13 1031 1244 179 258 852 986 984 1336 194 275 805 1078 0 0 329 308 104 122 96 96 96 96 1838 1883 .864 1.157 1.339 1.195 1.131 1.314 32 236 1.208 .94 70 3200 20670 31 38 236 243 0 1816 377 1440 1.69 1951 1574 .592 1.955 .757 .967
14 9485 2818 173 246 9312 2572 628 447 175 253 455 201 0 0 15406 4193 35 53 95 81 88 70 11884 656 3.621 .276 .442 .366 .342 2.21 80 475 .268 .98 100 3380 20660 29 39 253 263 0 4115 359 3755 .403 653 293 2.48 .645 -1.31 -.633
15 1424 793 174 244 1250 549 636 471 178 251 462 227 0 0 1394 586 41 52 99 89 97 73 1799 689 2.277 .439 .491 .425 .45 2.212 156 970 .411 .94 150 3560 20650 25 40 268 283 0 1158 356 802 .641 688 331 1.559 .717 -.641 -.479
16 1532 1170 181 245 1351 925 1674 1382 192 254 1493 1137 0 0 933 639 53 57 96 91 88 81 2276 2630 1.461 .685 .762 .673 .66 1.813 80 500 .672 .95 100 3760 20660 29 39 291 301 0 1708 358 1351 1 2018 1660 1 1.112 0 .153
17 2302 1488 181 239 2121 1249 2453 1608 185 247 2272 1369 0 0 916 544 45 50 100 100 100 100 3370 3641 1.698 .589 .603 .591 .584 1.309 52 340 .595 .96 80 3950 20660 30 38 311 319 0 2173 349 1824 .86 2348 1999 1.163 .88 -.218 -.185
18 4272 7642 183 248 4089 7394 4736 8074 197 269 4553 7826 0 0 1430 2526 62 88 100 100 100 100 11483 12379 .553 1.808 1.719 1.841 1.756 1.236 52 404 1.826 .98 90 4130 20660 29 38 328 337 0 11158 362 10796 2.64 11789 11427 .379 2.51 1.401 1.328
19 1314 615 172 231 1142 384 1003 537 181 244 831 306 0 0 1155 333 49 65 84 76 73 63 1526 1137 2.974 .336 .368 .497 .359 3.04 52 340 .304 .93 80 4310 20660 30 38 347 355 0 898 337 561 .491 784 447 2.037 .538 -1.026 -.895
20 831 581 167 228 664 353 560 484 171 229 393 256 0 0 647 314 35 43 81 71 68 68 1017 649 1.881 .532 .651 .68 .594 1.614 32 236 .524 .91 70 4510 20660 30 37 367 374 0 848 333 515 .776 707 374 1.288 .951 -.365 -.072

Total number of rows: 9216

Table truncated, full table size 2076 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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