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Sample GSM343533 Query DataSets for GSM343533
Status Public on May 12, 2009
Title Menadione RPL16a-ZZ total vs reference (4)
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 = 1720, 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 = 2006-10-06; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 380; Parameter Laser on time = 15250; Parameter Laser Power = 2.92; Parameter Scan Time = 11:33:24; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 24.00; 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 = 2006-10-06; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 320; Parameter Scan Power = 100; Parameter Laser on time = 15250; Parameter Laser Power = 3.60; Parameter Scan Time = 11:33:24; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 24.00; Performer: Regula,,Halbeisen
Description Simple annotation: RNA coimmunoprecipitation, Condition media
Image: http://smd.stanford.edu/MicroArray/gifs/2006-10/70639.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 2556 3757 107 52 2449 3705 2543 3630 109 63 2436 3578 0 0 859 1302 22 121 100 100 100 100 6154 6014 .661 1.513 1.469 1.493 1.459 1.175 52 340 1.525 .99 80 1920 19990 11 19 16 24 0 4540 63 4477 1.828 4387 4324 .547 1.775 .87 .828
2 22595 41622 108 54 22487 41568 28230 55322 110 57 28122 55268 0 23 14117 25738 24 29 100 100 100 100 64055 83390 .541 1.849 1.965 1.768 1.832 1.277 80 501 1.845 1 100 2110 19990 10 20 34 44 0 50298 65 50233 2.234 66854 66788 .448 2.375 1.16 1.248
3 33789 31151 107 53 33682 31098 33724 30084 109 56 33617 30031 0 3 14203 15679 24 30 100 100 100 100 64780 63648 1.083 .923 .893 .881 .9 1.171 52 392 .957 .99 90 2280 19980 9 18 51 60 0 37644 64 37580 1.116 36355 36291 .896 1.08 .158 .11
4 4064 3791 129 74 3935 3717 4083 4015 242 285 3954 3941 0 0 1511 1397 762 991 100 100 90 84 7652 7895 1.059 .945 .997 .95 .969 1.128 52 420 .94 .98 90 2470 19990 10 19 70 79 0 4581 89 4492 1.141 4852 4762 .876 1.204 .191 .268
5 1261 1581 122 62 1139 1519 1237 1506 274 322 1115 1444 0 0 419 843 889 1216 76 63 9 7 2658 2559 .75 1.334 1.295 1.263 1.253 1.261 52 334 1.497 .93 80 2660 19980 10 18 90 98 0 1911 75 1836 1.612 1820 1745 .62 1.565 .689 .646
6 6683 14805 107 51 6576 14754 8598 19029 109 52 8491 18978 0 0 4230 9533 20 9 100 100 100 100 21330 27469 .446 2.244 2.235 2.147 2.184 1.235 80 493 2.256 .99 100 2840 19990 10 20 107 117 0 17891 62 17829 2.711 22996 22934 .369 2.701 1.439 1.433
7 2426 2589 105 50 2321 2539 2419 2676 107 52 2314 2626 0 0 542 693 19 9 100 100 100 100 4860 4940 .914 1.094 1.135 1.075 1.098 1.178 52 340 1.113 .99 80 3030 19980 10 18 127 135 0 3129 60 3068 1.322 3234 3173 .756 1.371 .403 .456
8 862 590 105 50 757 540 841 503 108 52 736 453 0 0 445 406 20 13 100 100 100 96 1297 1189 1.402 .713 .615 .627 .688 1.368 32 176 .783 .97 60 3200 19990 12 18 145 151 0 713 60 653 .862 608 547 1.16 .744 -.214 -.427
9 1241 434 108 51 1133 383 1163 439 113 52 1055 388 0 0 350 127 24 10 100 100 100 100 1516 1443 2.958 .338 .368 .335 .331 1.151 12 104 .351 .98 50 3390 20000 13 18 164 169 0 524 62 463 .409 531 469 2.448 .444 -1.292 -1.17
10 653 593 119 64 534 529 633 464 853 952 514 400 0 0 357 424 3604 3990 0 0 0 0 1063 914 1.009 .991 .778 .848 .865 1.598 32 236 1.491 .86 70 3550 19990 11 18 179 186 0 717 77 639 1.197 561 483 .835 .94 .26 -.089
11 2208 1843 105 50 2103 1793 2204 1922 107 54 2099 1872 0 0 620 570 34 31 100 100 100 100 3896 3971 1.173 .853 .892 .841 .841 1.142 32 236 .862 .99 70 3740 19970 9 16 198 205 0 2227 60 2167 1.03 2323 2262 .971 1.078 .043 .108
12 621 503 100 49 521 454 591 459 101 50 491 410 0 0 228 225 18 9 100 100 100 100 975 901 1.148 .871 .835 .862 .867 1.289 52 340 .895 .96 80 3920 19980 10 18 216 224 0 608 59 549 1.053 555 495 .95 1.009 .075 .013
13 1192 1416 102 49 1090 1367 1255 1402 104 52 1153 1353 0 0 423 533 19 25 100 100 100 100 2457 2506 .797 1.254 1.173 1.251 1.242 1.165 52 408 1.26 .99 90 4100 19980 9 18 233 242 0 1711 59 1652 1.516 1694 1635 .66 1.418 .6 .504
14 12834 8727 102 49 12732 8678 12663 8440 103 51 12561 8391 0 0 10579 7747 19 11 98 98 97 96 21410 20952 1.467 .682 .668 .609 .646 1.408 80 418 .705 .99 100 4290 19980 9 19 252 262 0 10546 59 10487 .824 10199 10140 1.214 .807 -.28 -.309
15 1557 1503 103 49 1454 1454 622 521 108 54 519 472 0 0 1568 1700 32 24 100 100 99 100 2908 991 1 1 .909 .896 .943 1.371 156 668 1.053 .99 140 4440 19970 6 20 265 279 0 1816 59 1757 1.208 630 570 .828 1.099 .273 .136
16 1440 1167 110 50 1330 1117 1695 1387 124 68 1585 1337 0 0 630 554 47 49 100 98 94 90 2447 2922 1.191 .84 .844 .828 .852 1.158 52 401 .84 .99 90 4650 19960 7 16 288 297 0 1410 60 1350 1.015 1676 1616 .985 1.019 .021 .028
17 1328 944 111 50 1217 894 1242 943 123 59 1131 893 0 0 844 630 53 27 95 98 88 95 2111 2024 1.361 .735 .79 .747 .755 1.445 80 506 .734 .98 100 4840 19980 9 19 307 317 0 1141 60 1080 .888 1140 1079 1.126 .954 -.172 -.068
18 4165 2963 124 54 4041 2909 4752 3306 178 86 4628 3252 0 0 1451 1165 140 82 100 100 100 100 6950 7880 1.389 .72 .703 .693 .727 1.21 52 401 .732 .99 90 5020 19970 8 17 325 334 0 3581 65 3515 .87 3995 3930 1.15 .849 -.201 -.236
19 1317 956 104 50 1213 906 1297 966 132 66 1193 916 0 0 540 483 94 54 100 100 96 94 2119 2109 1.339 .747 .768 .7 .746 1.337 52 414 .771 .98 90 5200 19970 8 17 343 352 0 1155 60 1095 .903 1167 1107 1.108 .928 -.148 -.108
20 817 524 102 48 715 476 793 486 103 49 691 438 0 0 337 243 19 8 100 100 100 100 1191 1129 1.502 .666 .634 .662 .649 1.432 52 340 .672 .97 80 5390 19980 10 18 363 371 0 633 58 575 .805 587 529 1.243 .766 -.314 -.385

Total number of rows: 9216

Table truncated, full table size 2027 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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