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Sample GSM343547 Query DataSets for GSM343547
Status Public on May 12, 2009
Title CFW 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 = 800, 19320; 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 = 2006-02-10; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 560; Parameter Laser on time = 9431; Parameter Laser Power = 3.12; Parameter Scan Time = 12:31:24; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 24.50; 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 = 2006-02-10; 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 = 9431; Parameter Laser Power = 3.58; Parameter Scan Time = 12:31:24; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 24.50; Performer: Regula,,Halbeisen
Description Simple annotation: RNA coimmunoprecipitation, Condition media
Image: http://smd.stanford.edu/MicroArray/gifs/2006-02/67018.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 4638 661 2029 93 2609 568 4594 645 2052 97 2565 552 0 0 536 209 370 22 100 100 100 100 3177 3117 4.593 .218 .215 .207 .209 1.486 32 236 .202 .88 70 1080 19580 22 29 24 31 0 2861 403 2459 .942 2792 2389 1.061 .932 -.086 -.102
2 19406 29036 2028 95 17378 28941 19228 27898 2029 101 17200 27803 0 0 4520 8287 321 31 100 100 100 100 46319 45003 .6 1.665 1.616 1.653 1.659 1.113 52 336 1.684 .99 80 1270 19580 22 30 43 51 0 125690 411 125279 7.209 120764 120353 .139 6.997 2.85 2.807
3 18099 9313 1969 89 16130 9224 17191 9371 1993 94 15222 9282 0 0 9339 5287 548 22 100 100 98 100 25354 24504 1.749 .572 .61 .586 .582 1.367 52 335 .564 .98 80 1460 19580 22 30 62 70 0 40314 385 39928 2.475 40565 40180 .404 2.64 1.308 1.4
4 4654 1024 1899 82 2755 942 4775 961 1921 84 2876 879 0 0 1197 403 556 16 98 100 94 100 3697 3755 2.925 .342 .306 .35 .339 1.431 52 336 .311 .93 80 1640 19580 22 30 80 88 0 4433 355 4078 1.48 4160 3805 .676 1.323 .566 .404
5 4277 400 1894 87 2383 313 4326 388 1935 91 2432 301 0 0 579 109 381 24 100 100 100 100 2696 2733 7.613 .131 .124 .128 .135 1.444 32 236 .11 .89 70 1830 19560 20 27 99 106 0 1732 377 1355 .569 1680 1303 1.759 .536 -.815 -.9
6 5864 4055 1878 85 3986 3970 5908 4053 1900 117 4030 3968 0 0 962 989 353 89 100 100 100 100 7956 7998 1.004 .996 .985 1.002 .969 1.239 52 340 .976 .95 80 2010 19570 21 29 117 125 0 17553 368 17185 4.311 17544 17177 .232 4.262 2.108 2.092
7 4595 361 1895 87 2700 274 4615 352 1913 89 2720 265 0 0 831 104 360 15 100 100 98 100 2974 2985 9.854 .101 .097 .099 .096 1.405 52 340 .091 .9 80 2200 19570 21 29 136 144 0 1563 377 1186 .439 1524 1147 2.276 .422 -1.187 -1.246
8 2914 248 1868 83 1046 165 2441 121 1918 83 573 38 0 0 1168 223 317 13 62 56 46 53 1211 611 6.339 .158 .066 .078 .104 3.414 32 176 .143 .8 60 2370 19580 23 29 154 160 0 1074 359 714 .683 524 164 1.464 .287 -.55 -1.801
9 4664 273 1908 83 2756 190 4656 273 1895 83 2748 190 0 0 855 52 317 16 100 100 100 100 2946 2938 14.505 .069 .069 .07 .065 1.486 32 236 .06 .88 70 2560 19560 20 27 172 179 0 1182 359 822 .298 1182 822 3.351 .299 -1.745 -1.74
10 4954 527 1978 86 2976 441 5081 529 2106 105 3103 443 0 0 884 114 968 64 100 100 83 100 3417 3546 6.748 .148 .143 .151 .141 1.346 12 104 .128 .89 50 2740 19550 20 25 191 196 0 2281 372 1909 .641 2290 1918 1.559 .618 -.641 -.694
11 3635 295 1764 83 1871 212 3624 281 1799 83 1860 198 0 0 860 110 297 17 96 100 96 100 2083 2058 8.825 .113 .106 .113 .106 1.676 32 236 .103 .89 70 2940 19580 22 29 210 217 0 1277 359 918 .49 1216 857 2.039 .461 -1.028 -1.118
12 3573 229 1748 76 1825 153 3509 228 1755 77 1761 152 0 0 679 59 304 12 100 100 96 100 1978 1913 11.928 .084 .086 .085 .085 1.49 32 236 .065 .85 70 3120 19570 21 28 228 235 0 991 329 662 .363 987 658 2.756 .374 -1.462 -1.42
13 4842 576 1799 80 3043 496 4914 549 1816 80 3115 469 0 0 798 140 336 13 100 100 100 100 3539 3584 6.135 .163 .151 .163 .169 1.352 52 340 .148 .92 80 3300 19570 21 29 246 254 0 2493 346 2147 .706 2376 2030 1.417 .652 -.503 -.618
14 15892 2464 1847 80 14045 2384 9258 1168 1864 82 7411 1088 0 0 16862 2924 319 18 75 92 65 90 16429 8499 5.891 .17 .147 .161 .169 2.032 52 340 .171 .99 80 3490 19570 21 29 265 273 0 10666 346 10320 .735 5056 4710 1.361 .636 -.445 -.654
15 5922 885 1823 83 4099 802 6183 928 1858 86 4360 845 0 0 1541 302 326 19 100 100 100 100 4901 5205 5.111 .196 .194 .196 .195 1.376 52 340 .181 .92 80 3670 19570 21 29 283 291 0 3831 359 3472 .847 4017 3658 1.181 .839 -.24 -.253
16 5260 308 1937 87 3323 221 5262 305 1963 89 3325 218 0 0 625 48 356 21 100 100 100 100 3544 3543 15.036 .067 .066 .066 .066 1.389 32 236 .061 .86 70 3850 19560 20 27 301 308 0 1333 377 957 .288 1320 944 3.474 .284 -1.796 -1.817
17 5436 427 1870 85 3566 342 5494 418 1916 87 3624 333 0 0 1066 93 350 14 100 100 100 100 3908 3957 10.427 .096 .092 .097 .095 1.335 52 337 .09 .92 80 4030 19570 21 29 319 327 0 1848 368 1480 .415 1809 1441 2.409 .398 -1.268 -1.33
18 7309 1055 1838 94 5471 961 7614 1063 1884 96 5776 969 0 0 1537 227 341 21 100 100 100 100 6432 6745 5.693 .176 .168 .179 .184 1.236 52 340 .167 .96 80 4220 19560 20 28 338 346 0 4567 407 4160 .76 4601 4195 1.315 .726 -.395 -.462
19 5111 557 1772 89 3339 468 4820 519 1764 89 3048 430 0 0 1407 183 319 14 100 100 100 100 3807 3478 7.135 .14 .141 .144 .137 1.481 32 236 .124 .94 70 4400 19560 20 27 356 363 0 2411 385 2026 .607 2247 1861 1.648 .611 -.721 -.712
20 3397 236 1699 86 1698 150 2634 158 1709 88 935 72 0 0 2018 173 318 16 67 78 53 69 1848 1007 11.32 .088 .077 .078 .077 2.786 52 335 .079 .89 80 4570 19570 21 29 373 381 0 1022 372 649 .382 684 312 2.615 .333 -1.387 -1.585

Total number of rows: 9216

Table truncated, full table size 2087 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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