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Sample GSM343544 Query DataSets for GSM343544
Status Public on May 12, 2009
Title CFW100 RPL16a-ZZ total vs reference (2)
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 = 840, 19440; 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 = 2006-09-20; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 450; Parameter Laser on time = 14880; Parameter Laser Power = 2.91; Parameter Scan Time = 10:52:24; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 24.25; 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 = 2006-09-20; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 390; Parameter Scan Power = 100; Parameter Laser on time = 14880; Parameter Laser Power = 3.60; Parameter Scan Time = 10:52:24; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 24.25; Performer: Regula,,Halbeisen
Description Simple annotation: RNA coimmunoprecipitation, Condition media
Image: http://smd.stanford.edu/MicroArray/gifs/2006-10/70535.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 2220 1493 401 151 1819 1342 2178 1438 414 161 1777 1287 0 0 566 508 115 54 100 100 100 100 3161 3064 1.355 .738 .724 .717 .726 1.285 52 306 .748 .96 80 930 19890 41 49 5 13 0 2014 204 1811 .995 1940 1736 1.005 .977 -.007 -.033
2 36358 32220 406 151 35952 32069 37793 33801 413 155 37387 33650 0 0 11721 9692 93 41 100 100 100 100 68021 71037 1.121 .892 .9 .922 .878 1.181 52 412 .88 1 90 1110 19890 40 49 22 31 0 43472 204 43268 1.203 45605 45401 .831 1.214 .267 .28
3 30955 16077 415 152 30540 15925 29906 15017 425 157 29491 14865 1 0 15751 9240 99 41 100 100 100 100 46465 44356 1.918 .521 .504 .523 .525 1.194 52 414 .533 .99 90 1310 19880 39 48 42 51 0 21691 205 21486 .704 20261 20056 1.421 .68 -.507 -.556
4 3453 2266 382 153 3071 2113 3363 2078 398 157 2981 1925 0 0 1026 822 114 36 100 100 100 100 5184 4906 1.453 .688 .646 .679 .679 1.212 52 340 .7 .98 80 1490 19880 40 48 61 69 0 3057 206 2851 .928 2804 2597 1.077 .871 -.107 -.199
5 1886 1417 353 159 1533 1258 1819 1264 373 162 1466 1105 0 0 523 500 115 37 100 100 100 100 2791 2571 1.219 .821 .754 .811 .792 1.268 32 236 .808 .95 70 1680 19870 39 46 80 87 0 1912 215 1697 1.107 1705 1491 .903 1.017 .147 .024
6 7830 14612 341 162 7489 14450 8247 15113 354 169 7906 14951 0 0 2450 5341 94 57 100 100 100 100 21939 22857 .518 1.929 1.891 1.887 1.956 1.134 52 420 1.933 .99 90 1860 19870 38 47 97 106 0 19715 219 19496 2.603 20391 20172 .384 2.551 1.38 1.351
7 2662 2276 339 161 2323 2115 2799 2238 357 195 2460 2077 0 0 775 696 110 175 100 100 100 98 4438 4537 1.098 .91 .844 .901 .9 1.251 52 416 .902 .96 90 2050 19870 38 47 116 125 0 3071 217 2854 1.228 3020 2802 .814 1.139 .297 .188
8 1905 900 330 171 1575 729 1877 950 346 177 1547 779 0 0 938 441 94 59 93 93 90 90 2304 2326 2.16 .463 .504 .474 .426 1.965 32 176 .437 .9 60 2230 19880 41 47 136 142 0 1214 231 984 .624 1282 1051 1.601 .679 -.679 -.558
9 1380 568 336 155 1044 413 1251 577 359 162 915 422 0 0 774 272 112 42 96 96 90 87 1457 1337 2.528 .396 .461 .42 .416 1.666 32 176 .338 .9 60 2400 19880 41 47 153 159 0 766 209 557 .534 778 569 1.874 .622 -.906 -.684
10 2187 1042 341 149 1846 893 2201 1017 378 168 1860 868 0 0 557 219 241 110 100 100 100 100 2739 2728 2.067 .484 .467 .498 .441 1.5 12 104 .443 .94 50 2600 19870 40 45 173 178 0 1406 201 1205 .653 1372 1171 1.532 .63 -.616 -.667
11 2715 1971 341 150 2374 1821 2817 2104 364 159 2476 1954 0 0 1490 1164 124 49 92 96 88 92 4195 4430 1.304 .767 .789 .733 .77 1.358 52 340 .769 .98 80 2780 19860 38 46 190 198 0 2659 202 2457 1.035 2839 2636 .966 1.065 .05 .091
12 1235 655 343 155 892 500 1196 642 369 166 853 487 0 0 385 228 139 59 98 100 98 96 1392 1340 1.784 .561 .571 .564 .55 1.425 52 340 .526 .9 80 2960 19850 37 45 208 216 0 884 209 675 .756 866 657 1.322 .77 -.403 -.377
13 1820 1312 347 158 1473 1154 1720 1254 366 172 1373 1096 0 0 537 500 127 70 100 100 98 100 2627 2469 1.276 .783 .798 .76 .77 1.327 52 412 .785 .97 90 3140 19850 36 45 225 234 0 1770 213 1557 1.057 1692 1479 .946 1.077 .08 .107
14 18474 10203 342 154 18132 10049 14529 7832 376 167 14187 7678 0 0 15099 8510 151 74 100 100 100 100 28181 21865 1.804 .554 .541 .54 .548 1.205 52 334 .556 .99 80 3330 19840 36 44 245 253 0 13766 208 13558 .748 10567 10359 1.337 .73 -.419 -.454
15 2470 2022 343 154 2127 1868 1349 1143 368 163 1006 989 0 0 1810 1482 135 46 98 100 95 99 3995 1995 1.139 .878 .983 .958 .93 1.396 120 665 .844 .98 120 3520 19830 33 45 262 274 0 2728 208 2520 1.185 1542 1334 .844 1.326 .245 .408
16 2858 2337 398 186 2460 2151 2735 1263 819 1152 2337 1077 0 0 2951 7356 1910 4984 73 3 3 3 4611 3414 1.144 .874 .461 .572 .486 1.763 52 316 2.169 .95 80 3690 19830 35 43 281 289 0 3153 251 2902 1.18 1704 1453 .848 .622 .238 -.686
17 2823 1676 454 227 2369 1449 3230 1139 1037 1487 2776 912 0 0 1777 2469 1950 4672 61 7 11 2 3818 3688 1.635 .612 .329 .465 .374 1.873 80 497 1.594 .78 100 3890 19830 34 44 300 310 0 2261 306 1955 .825 1537 1230 1.212 .443 -.277 -1.174
18 6549 5346 364 168 6185 5178 6988 5653 430 232 6624 5485 0 0 1944 1629 216 194 100 100 100 100 11363 12109 1.194 .837 .828 .853 .828 1.181 52 326 .833 .99 80 4060 19830 35 43 318 326 0 7213 227 6986 1.13 7627 7400 .885 1.117 .176 .16
19 2168 1112 348 155 1820 957 2036 1021 361 160 1688 866 0 0 710 436 103 44 100 100 100 100 2777 2554 1.902 .526 .513 .511 .524 1.296 52 340 .524 .96 80 4250 19830 35 43 337 345 0 1500 209 1291 .709 1378 1168 1.41 .692 -.495 -.531
20 1644 656 330 137 1314 519 1580 691 343 143 1250 554 0 0 678 222 92 37 100 100 100 98 1833 1804 2.532 .395 .443 .407 .414 1.337 52 340 .366 .95 80 4440 19820 34 42 356 364 0 885 185 700 .533 932 747 1.876 .598 -.908 -.742

Total number of rows: 9216

Table truncated, full table size 2108 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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