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Sample GSM402428 Query DataSets for GSM402428
Status Public on May 12, 2009
Title Rpl16b-ZZ in SC (2)
Sample type RNA
 
Channel 1
Source name Total RNA Rpl16b-ZZ
Organism Saccharomyces cerevisiae
Characteristics reference: Total RNA Rpl16b-ZZ
Extracted molecule total RNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name IP RNA (RA) Rpl16b-ZZ
Organism Saccharomyces cerevisiae
Characteristics test: IP RNA (RA) Rpl16b-ZZ
Extracted molecule total RNA
Extraction protocol not provided
Label Cy5
Label protocol not provided
 
 
Hybridization protocol not provided
Scan protocol GenePix 4200A
Description Simple annotation: RNA coimmunoprecipitation, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/80814.gif
Media: SC
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 May 12, 2009
Last update date May 12, 2009
Contact name Andre Gerber
E-mail(s) [email protected]
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 GPL8546
Series (2)
GSE13654 Affinity purification of ribosomes and associated RNAs using tagged Rpl16a and Rpl16b
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 3079 3179 38 102 3041 3077 3476 3387 39 103 3438 3285 0 0 996 906 11 25 100 100 100 100 6118 6723 .988 1.012 .955 1.031 1.02 1.106 32 236 .991 .99 70 2110 7080 40 47 43 50 0 4968 159 4808 1.581 5293 5133 .632 1.493 .661 .578
2 432 319 39 104 393 215 458 328 41 107 419 224 0 0 88 60 14 25 100 100 100 100 608 643 1.828 .547 .535 .543 .531 1.321 32 176 .557 .94 60 2340 7070 40 46 67 73 0 498 163 336 .855 513 350 1.17 .835 -.226 -.259
3 2996 2648 39 104 2957 2544 3547 3075 40 105 3508 2971 0 0 1204 1096 10 24 100 100 100 100 5501 6479 1.162 .86 .847 .824 .86 1.225 52 340 .869 .99 80 2560 7070 39 47 88 96 0 4138 163 3975 1.344 4805 4643 .744 1.323 .427 .404
4 136 164 42 96 94 68 135 174 42 96 93 78 0 0 22 36 8 21 100 83 100 66 162 171 1.382 .723 .839 .605 .679 2.101 12 104 .758 .62 50 2780 7060 39 44 111 116 0 256 150 106 1.13 272 122 .885 1.311 .177 .39
5 49 109 39 101 10 8 44 105 43 106 5 4 0 0 28 36 29 67 3 3 2 1 18 9 1.25 .8 .8 1.676 1.955 4.008 80 560 3.295 .39 100 2990 7070 38 48 130 140 -50 170 158 13 1.25 164 6 .8 1.25 .322 .322
6 41 104 39 103 2 1 41 101 41 105 2 -2 0 0 7 25 20 25 0 16 0 1 3 0 2 .5 null 2.925 3.25 3.454 80 560 1.004 .21 100 3210 7070 38 48 152 162 -50 163 161 2 .781 158 -3 1.28 null -.356 null
7 686 636 39 106 647 530 719 678 40 106 680 572 0 0 277 247 12 23 100 100 100 100 1177 1252 1.221 .819 .841 .811 .794 1.292 52 340 .84 .98 80 3440 7080 40 48 176 184 0 994 166 828 1.28 1059 894 .781 1.314 .356 .394
8 701 604 36 97 665 507 688 599 36 100 652 502 0 0 174 106 7 23 100 100 100 100 1172 1154 1.312 .762 .77 .774 .775 1.244 32 236 .742 .97 70 3660 7080 40 47 198 205 0 944 152 792 1.191 936 784 .839 1.203 .253 .267
9 366 269 36 100 330 169 360 265 36 102 324 165 0 0 74 49 9 22 100 100 100 100 499 489 1.953 .512 .509 .501 .517 1.371 32 236 .502 .9 70 3890 7070 39 46 221 228 0 420 156 264 .8 414 258 1.25 .796 -.321 -.33
10 591 405 35 99 556 306 630 410 36 102 595 311 0 0 129 86 7 25 100 100 100 100 862 906 1.817 .55 .523 .54 .542 1.237 32 176 .552 .97 60 4110 7080 41 47 244 250 0 633 155 478 .86 641 486 1.163 .817 -.218 -.292
11 3110 3234 36 101 3074 3133 3581 3608 37 102 3545 3507 0 0 2018 2122 8 23 100 100 100 100 6207 7052 .981 1.019 .989 .909 1.008 1.394 52 340 1.031 1 80 4330 7070 39 47 265 273 0 5054 158 4896 1.593 5638 5480 .628 1.546 .671 .628
12 150 131 36 101 114 30 150 129 40 105 114 28 0 0 30 27 36 33 96 40 90 6 144 142 3.8 .263 .246 .263 .281 1.94 32 236 .546 .7 70 4550 7070 39 46 287 294 0 205 158 47 .411 202 44 2.432 .384 -1.282 -1.382
13 275 171 35 98 240 73 281 169 35 102 246 71 0 0 94 39 9 23 100 86 100 73 313 317 3.288 .304 .289 .268 .273 1.891 52 340 .303 .81 80 4770 7070 39 47 309 317 0 267 153 114 .475 264 111 2.104 .451 -1.073 -1.149
14 1003 869 36 101 967 768 1056 835 38 103 1020 734 0 0 286 225 13 24 100 100 100 100 1735 1754 1.259 .794 .72 .804 .787 1.184 32 236 .776 .98 70 4980 7070 39 46 330 337 0 1358 158 1200 1.241 1305 1147 .806 1.125 .312 .169
15 605 648 36 100 569 548 651 660 37 104 615 560 0 0 257 273 16 32 100 98 100 96 1117 1175 1.038 .963 .911 .901 .901 1.388 52 340 .99 .98 80 5210 7070 39 47 353 361 0 1013 156 856 1.505 1031 875 .664 1.423 .59 .509
16 2536 3055 36 99 2500 2956 2678 3216 36 101 2642 3117 0 0 1220 1476 7 23 100 100 100 100 5456 5759 .846 1.182 1.18 1.143 1.2 1.225 52 340 1.19 .99 80 5430 7080 40 48 375 383 0 4774 155 4619 1.848 5026 4871 .541 1.844 .886 .883
17 983 682 35 102 948 580 1008 687 36 103 973 585 0 0 435 271 8 23 100 100 100 100 1528 1558 1.634 .612 .601 .588 .611 1.325 52 340 .613 .98 80 5650 7060 38 46 397 405 0 1066 159 906 .956 1074 914 1.046 .94 -.065 -.09
18 315 240 34 99 281 141 317 252 35 103 283 153 0 0 128 70 7 26 100 92 100 88 422 436 1.993 .502 .541 .477 .487 1.657 52 340 .507 .92 80 5870 7070 39 47 419 427 0 375 155 220 .784 394 239 1.275 .845 -.351 -.243
19 599 530 35 99 564 431 628 523 35 100 593 424 0 0 104 107 7 23 100 100 100 100 995 1017 1.309 .764 .715 .755 .801 1.21 32 176 .771 .97 60 6090 7070 40 46 442 448 0 828 155 674 1.194 817 663 .837 1.117 .256 .16
20 64 130 36 104 28 26 66 131 38 106 30 27 0 0 14 25 9 23 91 50 83 33 54 57 1.077 .929 .9 .836 .881 3.749 12 104 3.37 .26 50 2130 7280 61 66 46 51 0 203 163 41 1.451 205 42 .689 1.406 .537 .492

Total number of rows: 10944

Table truncated, full table size 2298 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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