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Sample GSM343530 Query DataSets for GSM343530
Status Public on May 12, 2009
Title Menadione RPL16a-ZZ total 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 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 = 720, 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 = 14366; Parameter Laser Power = 2.98; Parameter Scan Time = 14:18:51; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 25.00; 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 = 340; Parameter Scan Power = 100; Parameter Laser on time = 14366; Parameter Laser Power = 3.61; Parameter Scan Time = 14:18:51; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 25.00; Performer: Regula,,Halbeisen
Description Simple annotation: RNA coimmunoprecipitation, Condition media
Image: http://smd.stanford.edu/MicroArray/gifs/2006-09/70010.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 1800 1205 185 60 1615 1145 1684 1136 205 78 1499 1076 0 0 572 387 143 99 100 100 100 100 2760 2575 1.41 .709 .718 .707 .72 1.2 32 236 .698 .97 70 830 19970 9 16 7 14 0 2280 114 2166 1.341 2149 2036 .746 1.358 .424 .441
2 26238 28067 177 58 26061 28009 32989 36098 183 60 32812 36040 0 0 18707 20234 43 20 100 100 97 100 54070 68852 .93 1.075 1.098 1.006 1.068 1.301 80 516 1.08 1 100 1020 19970 8 18 25 35 0 53097 110 52987 2.033 68290 68180 .492 2.078 1.024 1.055
3 22638 11403 180 57 22458 11346 20961 10429 183 58 20781 10372 0 0 10836 5449 33 11 100 100 100 100 33804 31153 1.979 .505 .499 .504 .5 1.095 52 340 .503 1 80 1210 19980 10 18 45 53 0 21572 108 21464 .956 19729 19622 1.046 .944 -.065 -.083
4 3184 1411 174 55 3010 1356 3056 1374 178 56 2882 1319 0 0 1161 490 30 10 100 100 100 100 4366 4201 2.22 .45 .458 .455 .444 1.122 52 340 .444 .99 80 1390 19980 10 18 63 71 0 2669 104 2565 .852 2599 2495 1.173 .866 -.231 -.208
5 1024 411 210 60 814 351 1042 387 221 62 832 327 0 0 204 139 74 16 100 100 100 100 1165 1159 2.319 .431 .393 .413 .416 1.356 32 236 .448 .93 70 1580 19970 9 16 82 89 0 778 114 664 .816 732 619 1.226 .744 -.294 -.428
6 7746 8730 203 60 7543 8670 8377 9604 212 63 8174 9544 0 0 2368 2487 49 17 100 100 100 100 16213 17718 .87 1.149 1.168 1.162 1.156 1.092 52 416 1.145 1 90 1750 19980 9 18 98 107 0 16515 114 16402 2.174 18169 18055 .46 2.209 1.121 1.143
7 1994 893 182 56 1812 837 2064 929 185 58 1882 873 0 0 646 286 35 13 100 100 100 100 2649 2755 2.165 .462 .464 .461 .464 1.197 52 340 .453 .98 80 1940 19970 9 17 118 126 0 1689 106 1583 .874 1757 1652 1.144 .878 -.195 -.188
8 1142 428 180 59 962 369 1152 478 190 62 972 419 0 0 526 173 59 21 100 100 100 100 1331 1391 2.607 .384 .431 .399 .397 1.313 12 104 .39 .94 50 2110 19980 11 16 136 141 0 810 112 698 .726 904 793 1.378 .815 -.463 -.294
9 1116 304 189 64 927 240 1023 307 227 72 834 243 0 0 541 104 167 36 100 100 91 91 1167 1077 3.863 .259 .291 .272 .289 1.4 12 104 .223 .92 50 2280 19990 12 17 153 158 0 575 121 454 .49 581 460 2.042 .551 -1.03 -.859
10 1073 479 175 58 898 421 1168 486 182 60 993 428 0 0 276 118 38 14 100 100 100 100 1319 1421 2.133 .469 .431 .473 .475 1.187 12 104 .451 .97 50 2490 19990 12 17 174 179 0 906 110 796 .887 919 810 1.128 .815 -.173 -.294
11 2492 1323 174 57 2318 1266 2450 1412 189 65 2276 1355 0 0 388 224 95 44 100 100 100 100 3584 3631 1.831 .546 .595 .545 .548 1.148 12 104 .528 .98 50 2660 19990 12 17 191 196 0 2503 108 2395 1.033 2671 2563 .968 1.126 .047 .172
12 743 309 163 57 580 252 641 284 166 57 478 227 0 0 259 102 33 10 100 100 100 100 832 705 2.302 .434 .475 .438 .448 1.327 32 236 .406 .94 70 2840 19970 9 16 208 215 0 585 108 477 .822 537 429 1.217 .898 -.283 -.155
13 1104 605 167 57 937 548 1064 577 172 57 897 520 0 0 289 182 33 10 100 100 100 100 1485 1417 1.71 .585 .58 .579 .565 1.235 52 340 .583 .97 80 3030 19980 10 18 227 235 0 1145 108 1037 1.106 1092 984 .904 1.097 .146 .133
14 14098 4457 169 57 13929 4400 15057 4211 179 60 14888 4154 0 0 9946 3204 59 24 100 100 100 100 18329 19042 3.166 .316 .279 .319 .315 1.182 52 340 .316 .99 80 3210 19970 9 17 245 253 0 8432 108 8324 .598 7966 7858 1.673 .528 -.743 -.922
15 3792 1952 197 61 3595 1891 4320 2342 249 88 4123 2281 0 0 1389 716 146 67 100 100 100 100 5486 6404 1.901 .526 .553 .523 .524 1.15 52 414 .523 .99 90 3400 19970 8 17 263 272 0 3693 115 3577 .995 4431 4315 1.005 1.047 -.007 .066
16 1298 563 178 58 1120 505 1568 697 190 65 1390 639 0 0 707 327 63 27 96 96 91 90 1625 2029 2.218 .451 .46 .44 .45 1.288 80 489 .448 .98 100 3590 19970 8 18 282 292 0 1065 110 955 .853 1319 1209 1.172 .87 -.229 -.201
17 2477 1083 166 58 2311 1025 2773 1149 179 64 2607 1091 0 0 954 403 61 18 100 100 100 100 3336 3698 2.255 .444 .418 .456 .444 1.214 52 398 .439 .98 90 3760 19970 8 17 299 308 0 2049 110 1939 .839 2174 2064 1.192 .792 -.253 -.337
18 5975 1874 148 56 5827 1818 6446 1939 185 65 6298 1883 0 0 1586 531 108 29 100 100 100 100 7645 8181 3.205 .312 .299 .31 .304 1.151 52 414 .311 .98 90 3950 19970 8 17 318 327 0 3545 106 3439 .59 3668 3562 1.694 .566 -.761 -.822
19 1273 549 131 52 1142 497 1182 531 134 53 1051 479 0 0 601 264 27 10 100 100 100 100 1639 1530 2.298 .435 .456 .437 .436 1.333 52 340 .431 .98 80 4130 19970 9 17 337 345 0 1039 98 940 .823 1005 906 1.215 .862 -.28 -.214
20 888 359 134 52 754 307 828 347 139 54 694 295 0 0 370 158 81 29 100 100 98 100 1061 989 2.456 .407 .425 .402 .404 1.293 52 340 .396 .96 80 4320 19970 9 17 356 364 0 679 98 581 .77 656 558 1.298 .804 -.377 -.314

Total number of rows: 9216

Table truncated, full table size 2047 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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