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Sample GSM343554 Query DataSets for GSM343554
Status Public on May 12, 2009
Title CFW100 RPL16a-ZZ IP poly 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 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 = 2720, 19720; 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 = 370; Parameter Laser on time = 15045; Parameter Laser Power = 2.95; Parameter Scan Time = 13:37:34; 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 = 2006-09-20; 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 = 15044; Parameter Laser Power = 3.63; Parameter Scan Time = 13:37:34; 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/2006-10/70537.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 1443 3135 131 65 1312 3070 1321 2976 135 67 1190 2911 0 0 434 936 28 14 100 100 100 100 4382 4101 .427 2.34 2.446 2.365 2.336 1.124 52 406 2.328 .99 90 3350 19900 13 22 58 67 0 3470 72 3398 2.59 3294 3222 .386 2.708 1.373 1.437
2 20930 29721 131 66 20799 29655 27774 40168 137 69 27643 40102 0 0 13978 20203 38 19 100 100 100 100 50454 67745 .701 1.426 1.451 1.36 1.43 1.194 80 554 1.437 1 110 3550 19900 12 23 77 88 0 32899 73 32826 1.578 44463 44390 .634 1.606 .658 .683
3 21984 30823 131 67 21853 30756 23735 32345 133 68 23604 32278 0 0 9143 13331 27 12 100 100 100 100 52609 55882 .711 1.407 1.367 1.411 1.405 1.103 52 384 1.42 1 90 3720 19900 13 22 95 104 0 34119 74 34045 1.558 35804 35730 .642 1.514 .64 .598
4 2983 3581 130 67 2853 3514 2858 3537 144 68 2728 3470 0 0 1008 1427 136 14 100 100 100 100 6367 6198 .812 1.232 1.272 1.179 1.213 1.21 52 327 1.267 .99 80 3910 19910 15 23 115 123 0 3964 74 3890 1.363 3915 3841 .733 1.408 .447 .494
5 821 1039 128 67 693 972 770 951 130 67 642 884 0 0 306 419 29 12 100 100 100 100 1665 1526 .713 1.403 1.377 1.425 1.407 1.318 52 334 1.4 .97 80 4090 19910 15 23 133 141 0 1150 74 1076 1.553 1053 979 .644 1.524 .635 .608
6 6686 21143 129 68 6557 21075 7115 21773 134 69 6986 21705 0 0 1928 6247 30 13 100 100 100 100 27632 28691 .311 3.214 3.107 3.253 3.247 1.128 52 408 3.223 1 90 4270 19900 13 22 150 159 0 23404 75 23329 3.558 24101 24026 .281 3.439 1.831 1.782
7 1844 2183 126 67 1718 2116 1773 2224 131 67 1647 2157 0 0 429 507 32 12 100 100 100 100 3834 3804 .812 1.232 1.31 1.227 1.256 1.183 52 396 1.238 .98 90 4460 19910 14 23 169 178 0 2416 74 2342 1.363 2462 2388 .733 1.45 .447 .536
8 1412 1359 131 73 1281 1286 1634 1523 157 86 1503 1450 0 0 603 604 105 73 100 100 100 100 2567 2953 .996 1.004 .965 .986 1.016 1.304 12 104 1.015 .98 50 4610 19910 16 21 186 191 0 1504 81 1424 1.111 1686 1605 .9 1.068 .152 .095
9 1039 410 131 72 908 338 1231 444 167 88 1100 372 0 0 415 150 151 62 100 100 83 83 1246 1472 2.686 .372 .338 .38 .366 1.224 12 104 .388 .97 50 4840 19930 18 23 209 214 0 454 80 374 .412 491 412 2.427 .374 -1.279 -1.418
10 750 636 127 69 623 567 739 658 167 81 612 589 0 0 379 336 223 53 83 91 75 83 1190 1201 1.099 .91 .962 .923 .985 1.272 12 104 .865 .97 50 4980 19930 18 23 223 228 0 704 76 628 1.007 728 652 .993 1.065 .011 .091
11 1561 1333 127 66 1434 1267 1795 1504 128 70 1668 1438 0 0 849 718 24 17 96 100 94 94 2701 3106 1.132 .884 .862 .925 .868 1.29 52 318 .862 .99 80 5180 19920 16 24 242 250 0 1476 73 1402 .978 1665 1592 1.022 .954 -.032 -.067
12 556 694 126 65 430 629 526 629 130 67 400 564 0 0 182 296 26 11 100 100 100 100 1059 964 .684 1.463 1.41 1.438 1.469 1.23 52 318 1.523 .97 80 5360 19910 15 23 260 268 0 768 72 696 1.619 696 624 .618 1.561 .695 .642
13 995 1353 126 65 869 1288 961 1308 131 66 835 1243 0 0 346 521 25 10 100 100 100 100 2157 2078 .675 1.482 1.489 1.459 1.473 1.2 52 334 1.502 .98 80 5550 19920 16 24 279 287 0 1498 72 1426 1.641 1448 1376 .61 1.648 .714 .721
14 14255 10266 130 65 14125 10201 14142 10595 134 68 14012 10530 0 0 6533 5046 26 37 100 100 100 100 24326 24542 1.385 .722 .751 .694 .733 1.264 52 394 .731 .99 90 5730 19910 14 23 296 305 0 11364 72 11292 .799 11728 11656 1.251 .832 -.323 -.266
15 2139 1787 132 66 2007 1721 2575 2127 160 88 2443 2061 0 0 903 720 90 70 100 100 96 100 3728 4504 1.166 .857 .844 .891 .88 1.243 52 334 .844 .99 80 5900 19910 15 23 314 322 0 1978 73 1905 .949 2354 2281 1.054 .934 -.075 -.099
16 1304 1024 134 65 1170 959 1346 1047 437 88 1212 982 0 0 309 310 1744 89 0 100 0 100 2129 2194 1.22 .82 .81 .806 .819 1.227 52 407 .097 .36 90 6100 19910 14 23 333 342 0 1133 72 1062 .907 1159 1087 1.102 .897 -.14 -.157
17 1222 783 139 68 1083 715 1301 823 682 105 1162 755 0 0 422 296 2127 112 0 96 0 88 1798 1917 1.515 .66 .65 .65 .645 1.172 52 334 .19 .51 80 6290 19910 15 23 353 361 0 867 75 791 .731 911 836 1.368 .719 -.452 -.475
18 3269 3088 129 65 3140 3023 3661 3426 156 90 3532 3361 0 0 948 917 107 85 100 100 100 100 6163 6893 1.039 .963 .952 .959 .958 1.159 52 340 .967 .99 80 6470 19910 15 23 371 379 0 3418 72 3346 1.066 3792 3720 .938 1.053 .092 .075
19 1240 1073 123 62 1117 1011 1198 1025 126 63 1075 963 0 0 512 401 29 10 100 100 100 100 2128 2038 1.105 .905 .896 .922 .903 1.198 52 334 .879 .98 80 6660 19920 16 24 390 398 0 1188 69 1119 1.002 1135 1066 .998 .992 .003 -.012
20 697 484 117 63 580 421 609 481 121 63 492 418 0 0 292 203 23 11 100 100 100 100 1001 910 1.378 .726 .85 .721 .725 1.292 52 334 .716 .97 80 6840 19920 16 24 408 416 0 536 70 466 .803 532 463 1.245 .94 -.316 -.089

Total number of rows: 9216

Table truncated, full table size 2038 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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