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Sample GSM343519 Query DataSets for GSM343519
Status Public on May 12, 2009
Title RPL16a-ZZ total vs reference (3)
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 = 880, 19640; 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 = 2006-04-04; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 420; Parameter Laser on time = 10162; Parameter Laser Power = 3.06; Parameter Scan Time = 11:51:58; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 23.81; 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 = 2006-04-04; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 330; Parameter Scan Power = 100; Parameter Laser on time = 10162; Parameter Laser Power = 3.56; Parameter Scan Time = 11:51:58; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 23.81; Performer: Regula,,Halbeisen
Description Simple annotation: RNA coimmunoprecipitation, Control experiment
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/67969.gif
Measurement: time(absolute) 0 m
Growth Condition: none
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 4052 4763 285 80 3767 4683 3784 4602 324 97 3499 4522 0 0 1384 1174 370 129 100 100 100 100 8450 8021 .804 1.243 1.292 1.276 1.305 1.178 52 328 1.196 .98 80 1150 19890 21 29 23 31 0 5120 86 5034 1.336 4947 4861 .748 1.389 .418 .474
2 18770 42454 278 78 18492 42376 23845 57940 289 91 23567 57862 0 15 12034 26143 71 40 97 100 96 100 60868 81429 .436 2.292 2.455 2.452 2.331 1.544 80 483 2.263 .99 100 1330 19890 20 30 40 50 0 45636 84 45552 2.463 62282 62198 .406 2.639 1.301 1.4
3 16005 25929 282 75 15723 25854 18607 29455 355 104 18325 29380 0 0 11948 19840 551 187 76 88 73 85 41577 47705 .608 1.644 1.603 1.694 1.66 1.469 80 381 1.657 1 100 1520 19880 19 29 59 69 0 27872 81 27792 1.768 31662 31582 .566 1.723 .822 .785
4 5122 3965 275 73 4847 3892 5151 3876 296 82 4876 3803 0 0 1452 1163 178 80 100 100 100 100 8739 8679 1.245 .803 .78 .803 .791 1.096 52 321 .804 .99 80 1700 19890 21 29 78 86 0 4262 78 4184 .863 4166 4088 1.159 .838 -.212 -.254
5 1795 1408 300 70 1495 1338 1618 1362 299 72 1318 1292 0 0 584 629 55 11 100 100 100 100 2833 2610 1.117 .895 .98 .854 .831 1.383 52 314 .935 .96 80 1890 19890 21 29 97 105 0 1514 75 1438 .962 1464 1389 1.039 1.054 -.056 .076
6 4035 5893 297 72 3738 5821 2346 3654 306 75 2049 3582 0 0 3571 4713 93 27 100 100 99 99 9559 5631 .642 1.557 1.748 1.714 1.726 1.342 208 924 1.437 .99 160 2080 19850 13 29 112 128 0 6335 77 6257 1.674 3928 3850 .597 1.879 .743 .91
7 3789 2669 299 73 3490 2596 3858 2607 306 82 3559 2534 0 0 1181 900 70 69 100 100 100 100 6086 6093 1.344 .744 .712 .745 .716 1.179 52 295 .744 .98 90 2250 19870 18 27 132 141 0 2869 78 2791 .8 2802 2724 1.251 .765 -.323 -.386
8 1585 1362 298 74 1287 1288 1637 1460 300 78 1339 1386 0 0 426 425 56 21 100 100 100 100 2575 2725 .999 1.001 1.035 .997 1.034 1.261 12 68 .978 .96 40 2420 19900 24 28 152 156 0 1464 80 1385 1.076 1569 1490 .93 1.113 .105 .154
9 3407 964 288 71 3119 893 3789 1036 304 79 3501 965 0 0 1427 380 174 78 100 98 96 94 4012 4466 3.493 .286 .276 .291 .279 1.156 52 340 .283 .99 80 2610 19880 20 28 169 177 0 1036 76 960 .308 1114 1037 3.249 .296 -1.7 -1.755
10 1305 966 280 70 1025 896 1373 951 297 74 1093 881 0 0 556 530 133 37 93 100 87 96 1921 1974 1.144 .874 .806 .862 .914 1.268 32 176 .877 .96 60 2790 19870 20 26 188 194 0 1038 75 963 .94 1022 947 1.064 .866 -.09 -.207
11 1286 997 278 70 1008 927 1228 919 285 72 950 849 0 0 508 482 56 18 100 100 100 100 1935 1799 1.087 .92 .894 .895 .891 1.229 52 340 .924 .98 80 2980 19880 20 28 206 214 0 1072 75 996 .989 988 913 1.012 .961 -.017 -.058
12 965 624 275 71 690 553 945 596 282 73 670 525 0 0 297 260 56 19 100 100 98 100 1243 1195 1.248 .801 .784 .778 .787 1.255 52 335 .801 .97 80 3170 19870 19 27 225 233 0 671 76 594 .862 641 564 1.161 .842 -.215 -.248
13 1764 1830 270 71 1494 1759 1793 1758 279 73 1523 1687 0 0 376 444 55 16 100 100 100 100 3253 3210 .849 1.177 1.108 1.183 1.196 1.164 52 340 1.184 .98 80 3350 19880 20 28 243 251 0 1967 76 1891 1.266 1890 1813 .79 1.191 .34 .252
14 24058 19352 274 71 23784 19281 26052 20075 284 78 25778 20004 0 0 12156 9756 61 32 100 100 100 100 43065 45782 1.234 .811 .776 .826 .82 1.184 52 353 .809 .99 90 3530 19870 18 27 260 269 0 20802 76 20726 .871 21579 21503 1.148 .834 -.199 -.262
15 2135 1674 280 72 1855 1602 648 545 300 88 368 473 0 0 2413 1880 134 58 91 97 62 95 3457 841 1.158 .864 1.285 1.109 1.078 1.673 156 915 .796 .98 150 3690 19890 17 32 273 288 0 1799 77 1722 .928 586 508 1.077 1.382 -.107 .466
16 2872 1937 293 76 2579 1861 3150 2152 314 105 2857 2076 0 0 726 538 84 65 100 100 100 100 4440 4933 1.386 .722 .727 .727 .721 1.169 52 409 .709 .99 90 3900 19870 18 27 297 306 0 2082 82 2000 .776 2313 2232 1.289 .781 -.366 -.356
17 2854 1876 291 76 2563 1800 3184 2138 314 104 2893 2062 0 0 1132 735 90 55 98 100 96 100 4363 4955 1.424 .702 .713 .753 .711 1.367 52 414 .691 .98 90 4080 19870 18 27 315 324 0 2017 82 1935 .755 2298 2217 1.325 .766 -.406 -.384
18 8431 4252 319 89 8112 4163 9056 4640 367 141 8737 4551 0 0 2700 1263 150 99 100 100 100 100 12275 13288 1.949 .513 .521 .524 .522 1.111 52 411 .503 1 90 4270 19870 18 27 334 343 0 4571 96 4475 .552 4988 4892 1.813 .56 -.858 -.837
19 1851 1366 260 69 1591 1297 1889 1426 270 76 1629 1357 0 0 1005 813 98 29 84 90 84 88 2888 2986 1.227 .815 .833 .814 .812 1.711 52 340 .812 .98 80 4450 19860 18 26 353 361 0 1468 74 1394 .876 1533 1459 1.141 .895 -.19 -.159
20 1148 795 235 69 913 726 1076 749 243 71 841 680 0 0 413 362 59 14 100 100 100 100 1639 1521 1.258 .795 .809 .758 .808 1.318 52 334 .809 .97 80 4640 19870 19 27 372 380 0 855 74 780 .855 805 731 1.17 .869 -.226 -.202

Total number of rows: 9216

Table truncated, full table size 2067 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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