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Sample GSM402430 Query DataSets for GSM402430
Status Public on May 12, 2009
Title Rpl16a-ZZ in SC (2)
Sample type RNA
 
Channel 1
Source name Total RNA Rpl16a-ZZ
Organism Saccharomyces cerevisiae
Characteristics reference: Total RNA Rpl16a-ZZ
Extracted molecule total RNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name IP RNA (RA) Rpl16a-ZZ
Organism Saccharomyces cerevisiae
Characteristics test: IP RNA (RA) Rpl16a-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/2008-08/80813.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 1628 948 53 119 1575 829 1664 998 55 119 1611 879 0 0 457 297 19 27 100 100 100 100 2404 2490 1.9 .526 .546 .508 .526 1.261 32 236 .541 .97 70 2110 7010 33 40 43 50 0 2342 294 2048 1.3 2466 2172 .769 1.348 .379 .431
2 327 207 50 114 277 93 359 195 53 116 309 81 0 0 101 55 18 29 100 90 100 71 370 390 2.978 .336 .262 .296 .277 1.819 32 236 .328 .75 70 2330 7010 33 40 65 72 0 511 282 230 .829 482 200 1.206 .648 -.27 -.627
3 1199 605 53 118 1146 487 1453 686 63 122 1400 568 0 0 532 243 98 42 100 98 98 92 1633 1968 2.353 .425 .406 .404 .43 1.323 52 340 .427 .98 80 2560 7010 33 41 88 96 0 1495 292 1203 1.05 1695 1403 .953 1.002 .07 .003
4 76 126 53 117 23 9 68 122 64 121 15 5 0 0 33 30 185 69 0 2 0 0 32 20 2.556 .391 .333 .881 1 3.576 80 560 7.982 .07 100 2770 7010 32 42 108 118 -50 311 289 22 .967 301 12 1.034 .823 -.049 -.28
5 59 117 54 119 5 -2 59 115 59 123 5 -4 0 0 15 31 61 50 0 6 0 0 3 1 null null null 1.88 2.286 4.137 80 560 41.682 .03 100 2990 7010 32 42 130 140 -50 289 294 -5 null 284 -10 null null null null
6 61 124 54 118 7 6 60 126 65 124 6 8 0 0 19 29 86 53 0 5 0 0 13 14 1.167 .857 1.333 1.99 1.906 3.406 80 554 .641 .81 100 3210 7010 32 42 152 162 -50 306 292 15 2.118 311 20 .472 3.294 1.082 1.72
7 520 344 49 118 471 226 533 346 56 119 484 228 0 0 109 81 50 29 100 100 100 96 697 712 2.084 .48 .471 .455 .468 1.375 32 236 .492 .92 70 3440 7000 32 39 176 183 0 850 292 558 1.185 855 563 .844 1.164 .245 .219
8 635 528 50 122 585 406 660 548 51 122 610 426 0 0 154 153 14 28 100 100 100 93 991 1036 1.441 .694 .698 .643 .688 1.425 32 176 .75 .95 60 3660 7010 34 40 199 205 0 1304 301 1003 1.715 1354 1052 .583 1.725 .778 .787
9 347 227 50 115 297 112 340 227 52 117 290 112 0 0 68 42 16 26 100 96 100 93 409 402 2.652 .377 .386 .357 .397 1.606 32 176 .369 .81 60 3880 7010 34 40 221 227 0 561 284 277 .932 561 277 1.073 .954 -.102 -.068
10 407 247 52 115 355 132 410 252 52 118 358 137 0 0 92 63 12 32 100 90 100 84 487 495 2.689 .372 .383 .328 .34 1.737 32 236 .384 .84 70 4100 7010 33 40 242 249 0 610 284 326 .919 623 338 1.089 .945 -.122 -.081
11 3038 2067 53 120 2985 1947 3408 2384 55 120 3355 2264 0 0 844 666 16 29 100 100 100 100 4932 5619 1.533 .652 .675 .63 .654 1.188 32 236 .668 .99 70 4320 7010 33 40 264 271 0 5106 296 4810 1.611 5890 5593 .621 1.667 .688 .737
12 156 138 49 114 107 24 158 140 53 119 109 26 0 0 40 29 37 28 93 46 81 12 131 135 4.458 .224 .239 .336 .276 3.095 32 236 .236 .4 70 4540 7000 32 39 286 293 0 341 282 59 .554 346 64 1.805 .589 -.852 -.763
13 229 171 51 116 178 55 242 171 52 118 191 55 0 0 81 38 14 28 98 80 92 44 233 246 3.236 .309 .288 .285 .356 2.502 52 340 .298 .63 80 4760 7020 34 42 308 316 0 422 287 136 .763 422 136 1.31 .711 -.39 -.491
14 937 559 50 118 887 441 996 569 52 118 946 451 0 0 161 69 15 28 100 100 100 100 1328 1397 2.011 .497 .477 .499 .501 1.197 32 236 .484 .96 70 4980 7010 33 40 330 337 0 1381 292 1089 1.228 1406 1114 .814 1.178 .297 .236
15 636 393 51 121 585 272 645 389 56 122 594 268 0 0 106 75 51 29 100 100 100 100 857 862 2.151 .465 .451 .456 .455 1.307 32 236 .462 .92 70 5200 7010 33 40 352 359 0 971 299 672 1.149 961 662 .871 1.115 .2 .157
16 3337 2083 51 116 3286 1967 3943 2416 53 119 3892 2300 0 0 1654 1014 13 26 100 100 100 100 5253 6192 1.671 .599 .591 .594 .602 1.314 52 340 .6 .99 80 5420 7020 34 42 374 382 0 5146 287 4859 1.479 5969 5682 .676 1.46 .564 .546
17 1193 395 51 118 1142 277 1153 402 53 118 1102 284 0 0 217 87 14 27 100 100 100 100 1419 1386 4.123 .243 .258 .235 .253 1.339 32 236 .232 .91 70 5640 7010 33 40 396 403 0 976 292 684 .599 993 702 1.669 .637 -.739 -.651
18 359 181 51 117 308 64 379 180 52 116 328 63 0 0 80 43 16 26 100 81 100 68 372 391 4.813 .208 .192 .209 .238 2.294 32 236 .206 .64 70 5870 7010 33 40 419 426 0 447 289 158 .513 445 156 1.948 .475 -.962 -1.075
19 640 328 50 113 590 215 645 329 52 114 595 216 0 0 145 59 13 27 100 100 100 100 805 811 2.744 .364 .363 .363 .352 1.27 32 176 .353 .94 60 6080 7010 34 40 441 447 0 810 279 531 .9 813 534 1.111 .897 -.152 -.157
20 71 124 56 122 15 2 66 123 207 139 10 1 0 0 22 29 2325 286 0 0 0 0 17 11 7.5 .133 .1 1.009 .877 4.242 80 560 .055 .89 100 2100 7230 54 64 41 51 -50 306 301 5 .329 304 2 3.036 .247 -1.602 -2.017

Total number of rows: 10944

Table truncated, full table size 2318 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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