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Sample GSM343553 Query DataSets for GSM343553
Status Public on May 12, 2009
Title CFW100 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 = 680, 20120; 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 = 14351; Parameter Laser Power = 2.97; Parameter Scan Time = 14:03:34; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 24.75; 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 = 330; Parameter Scan Power = 100; Parameter Laser on time = 14351; Parameter Laser Power = 3.60; Parameter Scan Time = 14:03:34; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 24.75; Performer: Regula,,Halbeisen
Description Simple annotation: RNA coimmunoprecipitation, Condition media
Image: http://smd.stanford.edu/MicroArray/gifs/2006-09/70009.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 3374 4084 185 65 3189 4019 3293 4030 189 68 3108 3965 0 0 1219 1348 41 17 100 100 100 100 7208 7073 .793 1.26 1.276 1.292 1.289 1.16 52 334 1.245 .99 80 870 20300 14 22 15 23 0 6495 103 6392 2.004 6409 6306 .499 2.029 1.003 1.021
2 32042 33275 181 61 31861 33214 37078 39141 190 71 36897 39080 1 2 21980 22470 58 78 97 97 96 92 65075 75977 .959 1.042 1.059 1.051 1.039 1.347 80 521 1.035 1 100 1050 20300 13 23 32 42 0 52920 97 52823 1.658 62249 62152 .603 1.684 .729 .752
3 36117 21454 171 58 35946 21396 32620 17898 173 61 32449 17840 7 0 15598 11509 37 15 100 100 100 100 57342 50289 1.68 .595 .55 .574 .564 1.115 52 340 .622 .99 80 1250 20300 14 22 53 61 0 34120 92 34028 .947 28464 28372 1.056 .874 -.079 -.194
4 5689 3600 156 57 5533 3543 5498 3578 158 59 5342 3521 0 0 2188 1239 31 16 100 100 100 100 9076 8863 1.562 .64 .659 .649 .642 1.097 52 340 .627 .99 80 1430 20300 14 22 71 79 0 5725 91 5635 1.018 5690 5600 .982 1.048 .026 .068
5 2073 2464 149 59 1924 2405 2054 2388 155 62 1905 2329 0 0 626 805 34 22 100 100 100 100 4329 4234 .8 1.25 1.223 1.247 1.256 1.156 32 236 1.248 .99 70 1620 20290 13 20 90 97 0 3919 94 3825 1.988 3798 3704 .503 1.944 .991 .959
6 18016 25976 145 59 17871 25917 18620 27110 151 68 18475 27051 0 0 4637 6251 46 40 100 100 100 100 43788 45526 .69 1.45 1.464 1.466 1.457 1.092 52 416 1.441 1 90 1790 20300 13 22 106 115 0 41311 94 41218 2.306 43115 43021 .434 2.329 1.206 1.219
7 4256 3768 136 59 4120 3709 4324 3729 138 63 4188 3670 0 0 1510 1020 32 23 100 100 100 100 7829 7858 1.111 .9 .876 .939 .911 1.211 52 340 .871 .98 80 1980 20290 13 21 126 134 0 5993 94 5899 1.432 5930 5837 .698 1.394 .518 .479
8 1183 536 144 61 1039 475 913 467 205 87 769 406 0 0 662 275 265 121 91 100 66 66 1514 1175 2.187 .457 .528 .467 .471 1.138 12 104 .421 .99 50 2150 20310 16 21 144 149 0 852 97 755 .727 743 646 1.375 .84 -.46 -.252
9 1437 414 148 59 1289 355 1217 441 227 84 1069 382 0 0 842 174 301 82 91 100 75 83 1644 1451 3.631 .275 .357 .307 .304 1.297 12 104 .247 .98 50 2320 20310 16 21 161 166 0 658 94 565 .438 701 608 2.283 .568 -1.191 -.815
10 1273 568 146 61 1127 507 1203 601 196 85 1057 540 0 0 629 311 239 106 91 91 83 75 1634 1597 2.223 .45 .511 .446 .472 1.418 12 104 .45 .98 50 2520 20310 16 21 181 186 0 903 97 806 .715 956 859 1.398 .812 -.483 -.3
11 4053 2947 145 64 3908 2883 4692 3304 155 68 4547 3240 0 0 1518 961 45 25 100 100 100 100 6791 7787 1.356 .738 .713 .77 .726 1.222 12 104 .718 .99 50 2720 20310 16 21 201 206 0 4687 102 4585 1.173 5255 5153 .852 1.133 .231 .18
12 764 493 131 57 633 436 715 438 137 59 584 381 0 0 345 235 30 13 100 100 100 100 1069 965 1.452 .689 .652 .697 .7 1.251 52 337 .68 .97 80 2900 20300 14 22 218 226 0 784 91 693 1.095 697 606 .913 1.038 .131 .053
13 1747 1913 135 60 1612 1853 1704 1612 141 62 1569 1552 0 0 540 689 31 15 100 100 100 100 3465 3121 .87 1.15 .989 1.144 1.134 1.186 52 340 1.175 .98 80 3090 20300 14 22 237 245 0 3042 95 2947 1.828 2564 2468 .547 1.573 .87 .654
14 24116 13212 140 60 23976 13152 23586 12493 146 63 23446 12433 0 0 12261 7666 39 16 100 100 100 100 37128 35879 1.823 .549 .53 .529 .529 1.134 52 352 .565 .99 90 3270 20290 12 21 254 263 0 21012 95 20917 .872 19868 19773 1.146 .843 -.197 -.246
15 2146 1781 138 59 2008 1722 702 599 143 64 564 540 0 0 2429 2079 40 26 100 100 100 100 3730 1104 1.166 .858 .957 .889 .865 1.352 156 844 .855 .99 150 3430 20280 8 23 267 282 0 2832 94 2739 1.364 953 859 .733 1.523 .448 .607
16 2490 1684 137 60 2353 1624 2717 1996 150 77 2580 1936 0 0 1553 1012 59 56 97 97 95 97 3977 4516 1.449 .69 .75 .736 .714 1.281 80 566 .671 .99 110 3640 20290 11 22 290 301 0 2678 95 2583 1.098 3174 3079 .911 1.193 .134 .255
17 2741 1343 142 63 2599 1280 3006 1669 155 75 2864 1606 0 0 1840 855 53 43 98 97 92 87 3879 4470 2.03 .492 .561 .532 .505 1.323 80 496 .477 .99 100 3820 20300 13 23 309 319 0 2136 100 2036 .783 2654 2554 1.277 .892 -.352 -.165
18 3380 2397 136 62 3244 2335 565 397 142 66 429 335 0 0 4138 2963 37 21 100 100 99 100 5579 764 1.389 .72 .781 .718 .725 1.422 156 879 .717 1 150 4030 20270 7 22 327 342 0 3812 99 3714 1.145 631 533 .874 1.242 .195 .313
19 2185 1512 143 62 2042 1450 2288 1542 145 65 2145 1480 0 0 710 537 37 26 100 100 100 100 3492 3625 1.408 .71 .69 .71 .68 1.173 32 205 .692 .98 70 4180 20290 13 20 346 353 0 2405 99 2306 1.129 2452 2354 .886 1.097 .175 .134
20 1234 575 138 62 1096 513 1232 514 141 64 1094 452 0 0 451 205 30 14 100 100 100 100 1609 1546 2.136 .468 .413 .471 .483 1.246 32 236 .446 .97 70 4370 20290 13 20 365 372 0 914 99 816 .744 817 719 1.343 .657 -.426 -.606

Total number of rows: 9216

Table truncated, full table size 2048 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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