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Sample GSM343541 Query DataSets for GSM343541
Status Public on May 12, 2009
Title Menadione 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 = 680, 19840; 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 = 2006-08-29; 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 = 14408; Parameter Laser Power = 2.97; Parameter Scan Time = 14:59:58; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 24.94; 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 = 2006-08-29; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 360; Parameter Scan Power = 100; Parameter Laser on time = 14407; Parameter Laser Power = 3.62; Parameter Scan Time = 14:59:58; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 24.94; Performer: Regula,,Halbeisen
Description Simple annotation: RNA coimmunoprecipitation, Condition media
Image: http://smd.stanford.edu/MicroArray/gifs/2006-09/70013.gif
Measurement: time(absolute) 20 m
Growth Condition: Menadione
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 1429 725 247 80 1182 645 1455 729 315 126 1208 649 0 0 383 234 535 428 94 86 63 15 1827 1857 1.833 .546 .537 .542 .552 1.308 52 340 .529 .96 80 840 20020 14 22 12 20 0 1921 212 1709 1.446 1931 1719 .692 1.423 .532 .509
2 26474 18232 325 140 26149 18092 26716 18375 1650 1217 26391 18235 0 0 10359 7081 3686 2970 98 98 94 94 44241 44626 1.445 .692 .691 .685 .685 1.211 52 420 .705 .99 90 1030 20010 12 21 30 39 0 48301 371 47930 1.833 48680 48309 .546 1.831 .874 .872
3 22532 12287 273 96 22259 12191 20712 10668 1342 939 20439 10572 0 0 11044 6596 3715 2888 100 96 92 86 34450 31011 1.826 .548 .517 .534 .546 1.169 52 409 .566 .98 90 1220 20020 13 22 49 58 0 32551 254 32297 1.451 28262 28008 .689 1.37 .537 .455
4 2166 706 247 83 1919 623 1919 638 250 84 1672 555 0 0 765 257 38 16 100 100 100 100 2542 2227 3.08 .325 .332 .323 .332 1.199 52 340 .322 .98 80 1400 20020 14 22 68 76 0 1870 220 1650 .86 1690 1470 1.163 .879 -.217 -.185
5 1068 337 241 79 827 258 1048 320 242 81 807 241 0 0 418 142 38 16 100 98 98 96 1085 1048 3.205 .312 .299 .309 .31 1.399 52 327 .304 .94 80 1600 20010 13 21 88 96 0 893 209 684 .826 848 638 1.21 .791 -.275 -.338
6 5408 5530 233 78 5175 5452 5645 5885 236 82 5412 5807 0 0 1323 1404 40 21 100 100 100 100 10627 11219 .949 1.054 1.073 1.045 1.045 1.133 52 398 1.054 .99 90 1760 20020 13 22 103 112 0 14650 207 14444 2.791 15591 15384 .358 2.843 1.481 1.507
7 1653 513 231 79 1422 434 1717 516 235 80 1486 437 0 0 370 137 63 27 100 100 100 100 1856 1923 3.276 .305 .294 .3 .311 1.306 52 340 .304 .95 80 1950 20010 13 21 123 131 0 1359 209 1150 .809 1367 1158 1.237 .779 -.307 -.36
8 1391 384 236 81 1155 303 1268 368 299 100 1032 287 0 0 775 199 277 90 91 91 66 66 1458 1319 3.812 .262 .278 .263 .255 1.25 12 104 .312 .94 50 2120 20020 15 20 141 146 0 1017 215 803 .695 975 760 1.439 .737 -.525 -.441
9 1244 325 233 74 1011 251 1203 309 236 77 970 235 0 0 440 58 42 17 100 100 100 100 1262 1205 4.028 .248 .242 .264 .268 1.361 12 68 .185 .9 40 2310 20040 18 22 161 165 0 861 196 665 .658 819 623 1.52 .642 -.604 -.64
10 2592 1984 296 134 2296 1850 985 542 2434 1998 689 408 0 0 4774 4148 6160 5374 11 10 2 3 4146 1097 1.241 .806 .592 .566 .55 2.286 80 543 .898 .97 100 2500 20030 14 24 177 187 -100 5256 355 4901 2.135 1436 1081 .468 1.569 1.094 .65
11 1549 496 216 76 1333 420 1700 569 608 341 1484 493 0 0 836 287 2037 1291 21 0 0 0 1753 1977 3.174 .315 .332 .281 .313 1.647 52 411 .511 .95 90 2690 20010 12 21 196 205 0 1314 201 1113 .835 1507 1306 1.198 .88 -.261 -.184
12 868 244 208 71 660 173 825 244 211 73 617 173 0 0 289 77 36 14 100 100 100 100 833 790 3.815 .262 .28 .262 .255 1.363 32 236 .237 .9 70 2860 20010 13 20 214 221 0 646 188 458 .694 646 458 1.44 .743 -.526 -.429
13 1141 399 203 71 938 328 1111 386 208 73 908 315 0 0 357 132 34 17 100 100 100 100 1266 1223 2.86 .35 .347 .348 .354 1.337 52 340 .339 .94 80 3050 20020 14 22 233 241 0 1057 188 869 .926 1023 835 1.079 .919 -.11 -.122
14 14013 4476 210 71 13803 4405 13816 4334 211 73 13606 4263 0 0 7367 2381 36 16 100 100 100 100 18208 17869 3.133 .319 .313 .318 .321 1.126 52 340 .319 1 80 3230 20010 13 21 251 259 0 11858 188 11670 .845 11482 11294 1.183 .83 -.242 -.269
15 2547 763 213 78 2334 685 2786 835 242 84 2573 757 0 0 1128 334 92 27 96 98 92 94 3019 3330 3.407 .293 .294 .288 .29 1.326 52 340 .293 .98 80 3410 20020 14 22 269 277 0 2021 207 1815 .778 2212 2005 1.286 .779 -.363 -.36
16 1737 459 219 76 1518 383 1743 452 225 79 1524 376 0 0 400 116 47 18 100 100 100 100 1901 1900 3.963 .252 .247 .251 .249 1.255 52 340 .246 .96 80 3610 20010 13 21 289 297 0 1216 201 1015 .668 1197 996 1.496 .654 -.581 -.613
17 2104 601 215 77 1889 524 2255 612 221 80 2040 535 0 0 665 181 49 19 100 100 100 98 2413 2575 3.605 .277 .262 .279 .274 1.222 52 414 .272 .97 90 3800 20020 13 22 307 316 0 1592 204 1388 .735 1621 1417 1.361 .695 -.444 -.525
18 4381 1108 219 79 4162 1029 4578 1101 258 88 4359 1022 0 0 1322 357 129 43 100 100 100 100 5191 5381 4.045 .247 .234 .246 .251 1.192 52 414 .248 .97 90 3980 20010 12 21 325 334 0 2935 209 2726 .655 2917 2708 1.527 .621 -.61 -.687
19 1389 409 201 74 1188 335 1278 366 218 77 1077 292 0 0 663 186 75 18 100 100 98 100 1523 1369 3.546 .282 .271 .287 .283 1.317 52 340 .276 .97 80 4170 20020 14 22 345 353 0 1084 196 887 .747 970 774 1.339 .718 -.421 -.477
20 823 259 189 73 634 186 773 240 195 77 584 167 0 0 337 104 54 23 100 98 100 96 820 751 3.409 .293 .286 .286 .298 1.514 52 334 .283 .95 80 4360 20020 14 22 364 372 0 686 193 493 .777 636 442 1.287 .758 -.364 -.401

Total number of rows: 9216

Table truncated, full table size 2063 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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