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Sample GSM343537 Query DataSets for GSM343537
Status Public on May 12, 2009
Title CFW RPL16a-ZZ IP poly 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 IP RNA RPL16a-ZZ CFW
Organism Saccharomyces cerevisiae
Characteristics IP RNA RPL16a-ZZ CFW
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 = 960, 20080; 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 = 2006-05-26; 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 = 11896; Parameter Laser Power = 2.93; Parameter Scan Time = 11:10:04; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 25.31; 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 = 2006-05-26; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 420; Parameter Scan Power = 100; Parameter Laser on time = 11896; Parameter Laser Power = 3.60; Parameter Scan Time = 11:10:04; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 25.31; Performer: Regula,,Halbeisen
Description Simple annotation: RNA coimmunoprecipitation, Condition media
Image: http://smd.stanford.edu/MicroArray/gifs/2006-05/68680.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 3174 4602 499 170 2675 4432 3309 4650 505 175 2810 4480 0 0 1099 1828 103 43 100 100 96 100 7107 7290 .604 1.657 1.594 1.661 1.647 1.209 52 340 1.65 .97 80 1240 20370 25 33 24 32 0 4402 163 4239 1.585 4448 4285 .631 1.525 .664 .609
2 40558 49162 502 165 40056 48997 51727 65535 519 182 51225 65370 8 58 24639 24948 225 72 100 100 97 100 89053 116595 .818 1.223 1.276 1.428 1.208 1.555 80 537 1.163 .98 110 1430 20380 24 35 41 52 0 47025 158 46867 1.17 62686 62528 .855 1.221 .227 .288
3 28445 43357 518 170 27927 43187 32653 61570 544 183 32135 61400 3 38 21572 27322 285 67 91 100 90 97 71114 93535 .647 1.546 1.911 1.893 1.722 1.705 80 474 1.452 .96 100 1610 20380 25 35 60 70 0 41472 163 41309 1.479 58893 58730 .676 1.828 .565 .87
4 3951 5057 495 166 3456 4891 4060 5202 506 169 3565 5036 0 0 1552 2116 102 37 100 100 100 100 8347 8601 .707 1.415 1.413 1.416 1.434 1.203 52 340 1.433 .97 80 1800 20370 25 33 80 88 0 4837 159 4678 1.354 4976 4817 .739 1.351 .437 .434
5 1508 1515 490 168 1018 1347 1516 1470 530 223 1026 1302 0 0 573 675 224 286 84 87 84 84 2365 2328 .756 1.323 1.269 1.431 1.322 1.457 32 236 1.385 .95 70 1980 20360 24 31 98 105 0 1449 161 1288 1.266 1406 1245 .79 1.214 .34 .28
6 6519 18500 451 163 6068 18337 8089 23473 492 180 7638 23310 0 0 4148 12160 657 115 78 100 68 100 24405 30948 .331 3.022 3.052 3.089 3.031 1.297 80 568 3.027 .98 110 2160 20360 22 33 114 125 0 17696 156 17540 2.891 22452 22297 .346 2.919 1.531 1.546
7 2114 1841 393 164 1721 1677 2420 1958 464 195 2027 1794 0 0 908 931 786 154 82 88 61 84 3398 3821 1.026 .974 .885 .908 .974 1.397 52 394 1.063 .95 90 2340 20350 22 31 133 142 0 1761 157 1604 .932 1873 1716 1.073 .847 -.101 -.24
8 1129 1003 334 157 795 846 633 319 467 174 299 162 0 0 987 1257 1742 162 21 50 1 38 1641 461 .94 1.064 .542 .784 .782 1.935 52 334 1.228 .94 80 2510 20360 24 32 151 159 0 959 150 809 1.018 305 155 .982 .518 .026 -.948
9 3386 1656 331 155 3055 1501 3262 1607 410 180 2931 1452 0 0 986 551 423 128 100 100 100 96 4556 4383 2.035 .491 .495 .472 .486 1.287 32 236 .482 .93 70 2690 20360 24 31 169 176 0 1584 148 1436 .47 1537 1389 2.128 .474 -1.089 -1.077
10 1209 999 346 165 863 834 1075 871 353 195 729 706 0 0 711 835 119 166 75 66 66 58 1697 1435 1.035 .966 .968 .559 .827 2.786 12 104 1.134 .91 50 2860 20380 27 32 187 192 0 956 158 798 .924 833 675 1.082 .926 -.113 -.11
11 1682 1483 318 159 1364 1324 1455 1303 319 164 1137 1144 0 0 729 842 72 54 100 100 100 100 2688 2281 1.03 .971 1.006 .936 .93 1.353 32 236 1.011 .96 70 3050 20360 24 31 205 212 0 1419 152 1266 .928 1246 1094 1.077 .962 -.107 -.055
12 1007 1418 298 157 709 1261 1011 1396 303 157 713 1239 0 0 438 885 63 33 98 94 90 92 1970 1952 .562 1.779 1.738 1.62 1.805 1.681 52 340 1.934 .95 80 3240 20360 24 32 224 232 0 1356 150 1206 1.701 1335 1185 .588 1.662 .767 .733
13 1549 2945 299 154 1250 2791 1622 3152 323 161 1323 2998 0 0 630 1453 167 69 88 90 86 88 4041 4321 .448 2.233 2.266 2.314 2.118 1.887 52 340 2.301 .96 80 3420 20360 24 32 242 250 0 2817 147 2670 2.136 3015 2868 .468 2.168 1.095 1.116
14 26719 25042 319 162 26400 24880 29659 27493 322 166 29340 27331 0 0 15247 15076 82 42 100 100 100 100 51280 56671 1.061 .942 .932 .885 .933 1.227 52 334 .955 .99 80 3600 20360 24 32 260 268 0 23953 155 23798 .901 26298 26143 1.109 .891 -.15 -.166
15 2869 3021 340 171 2529 2850 3047 3398 386 215 2707 3227 0 0 1118 1265 206 125 96 100 90 98 5379 5934 .887 1.127 1.192 1.118 1.171 1.298 52 400 1.104 .96 90 3770 20360 23 32 276 285 0 2890 164 2726 1.078 3250 3087 .928 1.14 .108 .189
16 1736 1400 332 176 1404 1224 1816 1396 372 213 1484 1220 0 0 399 381 193 108 100 100 100 100 2628 2704 1.147 .872 .822 .86 .863 1.281 52 400 .846 .91 90 3960 20360 23 32 295 304 0 1339 168 1171 .834 1335 1167 1.199 .786 -.262 -.347
17 1538 1328 317 172 1221 1156 1861 1597 356 204 1544 1425 0 0 822 793 196 106 77 78 71 73 2377 2969 1.056 .947 .923 .903 .945 1.798 80 494 .947 .96 100 4140 20360 23 33 313 323 0 1270 165 1106 .906 1528 1363 1.104 .883 -.143 -.18
18 3611 3711 316 158 3295 3553 3864 4489 340 192 3548 4331 0 0 2141 2433 126 104 96 97 93 86 6848 7879 .927 1.078 1.221 .961 1.068 1.611 80 492 1.104 .97 100 4320 20360 23 33 331 341 0 3550 151 3399 1.031 4294 4143 .97 1.168 .045 .224
19 1782 2290 295 151 1487 2139 1899 2271 299 155 1604 2120 0 0 829 1295 61 34 96 96 96 96 3626 3724 .695 1.438 1.322 1.366 1.345 1.28 52 340 1.481 .98 80 4510 20360 24 32 351 359 0 2190 144 2046 1.376 2172 2028 .727 1.264 .46 .338
20 1068 763 303 152 765 611 1028 772 308 157 725 620 0 0 440 359 65 36 92 96 88 92 1376 1345 1.252 .799 .855 .718 .76 1.562 52 340 .797 .94 80 4690 20360 24 32 369 377 0 730 145 584 .764 738 593 1.309 .818 -.388 -.29

Total number of rows: 9216

Table truncated, full table size 2110 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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