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Sample GSM343551 Query DataSets for GSM343551
Status Public on May 12, 2009
Title AAs starvation RPL16a-ZZ total vs reference (6)
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 = 1840, 19680; 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 = 2006-10-17; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 390; Parameter Laser on time = 15579; Parameter Laser Power = 2.95; Parameter Scan Time = 09:16:25; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 23.75; 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 = 2006-10-17; 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 = 15579; Parameter Laser Power = 3.61; Parameter Scan Time = 09:16:25; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 23.75; Performer: Regula,,Halbeisen
Description Simple annotation: RNA coimmunoprecipitation, Condition media
Image: http://smd.stanford.edu/MicroArray/gifs/2006-10/70713.gif
Measurement: time(absolute) 20 m
Growth Condition: Amino acid starvation
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 1454 4437 119 75 1335 4362 1445 4354 121 80 1326 4279 0 0 514 1488 25 30 100 100 100 100 5697 5605 .306 3.267 3.227 3.342 3.373 1.208 52 420 1.111 .96 90 2060 19830 10 19 17 26 0 3822 65 3757 2.814 3750 3686 .355 2.779 1.493 1.475
2 35634 18338 125 78 35509 18260 38498 19938 132 89 38373 19860 0 0 13164 6537 49 49 100 100 100 100 53769 58233 1.945 .514 .518 .519 .519 1.117 52 406 .506 1 90 2250 19830 10 19 36 45 0 15795 67 15728 .443 17173 17106 2.258 .446 -1.175 -1.166
3 24778 11451 171 196 24607 11255 28964 12336 397 866 28793 12140 1 0 18307 7994 554 1582 91 80 86 73 35862 40933 2.186 .457 .422 .537 .439 1.959 80 492 .435 .97 100 2430 19830 10 20 54 64 0 9863 169 9694 .394 10625 10456 2.538 .363 -1.344 -1.461
4 1995 3305 129 106 1866 3199 1957 3304 264 548 1828 3198 0 0 1247 1969 408 1337 81 80 76 61 5065 5026 .583 1.714 1.749 1.85 1.613 1.424 80 508 1.88 .94 100 2610 19830 10 20 72 82 0 2847 91 2755 1.477 2846 2754 .677 1.507 .562 .592
5 964 1810 112 83 852 1727 869 1751 133 166 757 1668 0 0 427 791 255 1003 92 86 80 32 2579 2425 .493 2.027 2.203 2.042 2.05 1.204 52 334 2.16 .96 80 2810 19830 11 19 93 101 0 1559 71 1487 1.746 1508 1437 .573 1.898 .804 .924
6 4304 51234 113 86 4191 51148 4413 54523 116 89 4300 54437 0 7 1334 13637 23 20 100 100 100 100 55339 58737 .082 12.204 12.66 12.536 12.157 1.135 52 407 11.973 .99 90 2980 19820 9 18 109 118 0 44129 74 44055 10.512 46961 46887 .095 10.904 3.394 3.447
7 1572 5463 116 85 1456 5378 1571 5572 119 90 1455 5487 0 0 404 1197 27 48 100 100 100 100 6834 6942 .271 3.694 3.771 3.743 3.772 1.183 52 340 3.703 .98 80 3170 19830 11 19 129 137 0 4705 73 4632 3.181 4799 4726 .314 3.248 1.67 1.7
8 834 1161 112 82 722 1079 715 978 119 105 603 896 0 0 378 607 55 237 100 93 100 84 1801 1499 .669 1.494 1.486 1.438 1.453 1.264 32 176 1.73 .93 60 3340 19840 13 19 147 153 0 1000 71 929 1.287 842 772 .777 1.28 .364 .356
9 735 627 132 92 603 535 681 560 156 114 549 468 0 0 315 316 114 97 91 100 91 91 1138 1017 1.127 .887 .852 .901 .95 1.341 12 68 .879 .97 40 3520 19850 15 19 166 170 0 540 79 461 .764 482 403 1.309 .734 -.388 -.446
10 748 840 120 86 628 754 698 723 127 113 578 637 0 0 272 447 52 175 100 100 100 75 1382 1215 .833 1.201 1.102 1.125 1.277 1.57 12 104 1.298 .95 50 3690 19840 13 18 182 187 0 724 74 649 1.034 623 549 .967 .949 .048 -.075
11 1645 1486 117 89 1528 1397 1665 1524 120 94 1548 1435 0 0 408 462 36 30 100 100 100 100 2925 2983 1.094 .914 .927 .89 .904 1.234 32 236 .917 .98 70 3880 19820 10 17 200 207 0 1280 77 1203 .787 1313 1236 1.27 .798 -.345 -.325
12 557 2474 113 84 444 2390 572 2137 115 87 459 2053 0 0 175 1207 23 23 100 100 100 100 2834 2512 .186 5.383 4.473 5.204 5.212 1.267 52 340 5.822 .97 80 4070 19830 11 19 219 227 0 2131 72 2059 4.636 1841 1768 .216 3.852 2.213 1.946
13 967 1536 114 84 853 1452 934 1528 115 88 820 1444 0 0 465 581 23 32 100 100 100 100 2305 2264 .587 1.702 1.761 1.73 1.799 1.332 52 340 1.621 .9 80 4250 19840 12 20 237 245 0 1323 72 1251 1.466 1316 1244 .682 1.517 .552 .601
14 14183 15904 116 78 14067 15826 12262 13157 120 86 12146 13079 0 0 6092 7479 27 43 100 100 100 100 29893 25225 .889 1.125 1.077 1.106 1.129 1.093 52 335 1.147 1 80 4430 19830 11 19 255 263 0 13698 67 13631 .969 11332 11265 1.032 .927 -.045 -.109
15 1544 2054 112 73 1432 1981 683 956 117 80 571 883 0 0 1287 1617 30 36 100 100 100 100 3413 1454 .723 1.383 1.546 1.596 1.499 1.357 120 553 1.32 .99 120 4620 19810 7 19 272 284 0 1769 63 1706 1.192 823 761 .839 1.332 .253 .414
16 757 998 109 69 648 929 431 568 110 72 322 499 0 0 597 764 22 19 98 100 95 100 1577 821 .698 1.434 1.55 1.823 1.672 1.609 120 586 1.364 .98 130 4790 19810 6 19 288 301 0 860 59 800 1.235 489 430 .81 1.335 .304 .417
17 1152 1443 106 69 1046 1374 1317 1593 110 76 1211 1524 0 0 654 885 27 32 100 98 98 97 2420 2735 .761 1.314 1.258 1.28 1.271 1.341 80 545 1.332 .98 110 4980 19830 9 20 308 319 0 1243 59 1183 1.131 1372 1313 .884 1.084 .178 .116
18 1921 3473 105 70 1816 3403 626 1194 109 77 521 1124 0 0 1810 3211 32 56 100 100 100 100 5219 1645 .534 1.874 2.157 2.121 1.982 1.321 120 648 1.828 .99 130 5180 19810 6 19 327 340 0 2991 60 2931 1.614 1028 968 .62 1.858 .691 .894
19 1300 1649 104 70 1196 1579 1234 1511 109 77 1130 1441 0 0 556 726 37 74 100 100 100 100 2775 2571 .757 1.32 1.275 1.336 1.29 1.173 52 317 1.32 .99 80 5350 19830 11 19 347 355 0 1420 60 1360 1.137 1301 1241 .879 1.098 .185 .135
20 1036 1308 104 73 932 1235 1033 1331 106 76 929 1258 0 0 255 401 22 20 100 100 100 100 2167 2187 .755 1.325 1.354 1.301 1.329 1.249 32 236 1.376 .97 70 5530 19830 11 18 365 372 0 1127 63 1064 1.141 1146 1084 .876 1.166 .191 .222

Total number of rows: 9216

Table truncated, full table size 2049 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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