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Sample GSM402427 Query DataSets for GSM402427
Status Public on May 12, 2009
Title Rpl16a-ZZ in SC (1)
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/2008-08/80811.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 1229 920 66 259 1163 661 1303 959 66 261 1237 700 0 0 334 269 18 59 100 100 100 96 1824 1937 1.759 .568 .566 .527 .539 1.479 32 236 .584 .91 70 2140 7050 17 24 30 37 0 1515 427 1089 .936 1579 1153 1.068 .932 -.095 -.102
2 215 330 57 249 158 81 213 325 58 259 156 76 0 0 46 59 15 58 100 65 100 21 239 232 1.951 .513 .487 .488 .499 2.02 32 176 .834 .45 60 2360 7060 19 25 53 59 0 544 410 133 .844 535 125 1.184 .802 -.244 -.318
3 1207 1346 62 264 1145 1082 1049 781 65 268 987 517 0 0 1156 1894 21 61 100 92 100 82 2227 1504 1.058 .945 .524 .704 .564 2.528 52 340 1.493 .81 80 2590 7050 17 25 75 83 0 2217 435 1782 1.556 1286 851 .643 .863 .638 -.213
4 76 269 58 260 18 9 73 268 62 263 15 8 0 0 21 60 27 60 28 15 5 5 27 23 2 .5 .533 2.257 2.671 3.725 80 560 6.093 .15 100 2800 7060 17 27 95 105 -50 443 428 15 .823 441 13 1.214 .878 -.28 -.187
5 63 258 58 267 5 -9 63 253 60 270 5 -14 0 0 16 59 16 58 21 11 3 2 -4 -9 null null null 3.316 3.387 3.329 80 560 -78.232 -.04 100 3020 7060 17 27 117 127 -50 425 440 -15 null 417 -23 null null null null
6 69 263 56 260 13 3 68 251 58 266 12 -9 0 0 22 60 16 65 38 16 20 2 16 3 4.333 .231 null 2.612 2.261 3.084 80 554 31.49 .09 100 3240 7060 17 27 139 149 -50 433 428 5 .38 413 -15 2.631 null -1.396 null
7 208 347 55 257 153 90 199 341 57 260 144 84 0 0 45 52 13 59 100 65 100 37 243 228 1.7 .588 .583 .49 .541 2.263 32 236 1.359 .47 70 3480 7060 18 25 164 171 0 572 423 148 .969 562 138 1.032 .961 -.046 -.058
8 428 583 64 274 364 309 426 582 66 271 362 308 0 0 88 115 19 58 100 96 100 90 673 670 1.178 .849 .851 .757 .901 2.04 32 176 .948 .85 60 3690 7070 20 26 186 192 0 960 451 509 1.398 959 507 .715 1.401 .484 .487
9 86 286 58 260 28 26 82 287 60 263 24 27 0 0 29 61 17 57 53 28 37 7 54 51 1.077 .929 1.125 1.998 1.643 2.708 80 560 11.517 .19 100 3910 7070 18 28 206 216 -50 471 428 43 1.529 473 44 .654 1.853 .613 .89
10 118 294 59 264 59 30 114 299 62 262 55 35 0 0 47 64 17 53 84 40 65 12 89 90 1.967 .508 .636 1.295 1.328 3.196 32 236 1.18 .24 70 4110 7060 18 25 227 234 0 484 435 49 .837 492 58 1.194 1.048 -.256 .068
11 500 610 59 266 441 344 513 596 60 267 454 330 0 0 96 88 15 53 100 100 100 100 785 784 1.282 .78 .727 .783 .735 1.38 32 236 .806 .86 70 4360 7070 19 26 252 259 0 1005 438 567 1.285 982 544 .778 1.197 .361 .26
12 81 275 57 265 24 10 75 277 58 265 18 12 0 0 27 61 14 56 61 18 41 6 34 30 2.4 .417 .667 2.145 1.846 4.095 80 560 -46.895 -.04 100 4570 7070 18 28 272 282 -50 453 436 16 .686 456 20 1.457 1.098 -.543 .135
13 182 318 57 261 125 57 187 312 59 266 130 51 0 0 53 72 19 58 98 48 96 17 182 181 2.193 .456 .392 .547 .719 2.969 52 340 1.171 .34 80 4800 7080 20 28 296 304 0 524 430 94 .751 514 84 1.332 .646 -.413 -.63
14 405 484 56 257 349 227 420 480 58 264 364 223 0 0 103 72 14 54 100 100 100 96 576 587 1.537 .65 .613 .65 .636 1.619 32 236 .644 .75 70 5030 7070 19 26 319 326 0 797 423 374 1.071 791 367 .933 1.009 .099 .013
15 246 398 55 264 191 134 248 409 56 267 193 145 0 0 86 71 14 58 96 90 96 65 325 338 1.425 .702 .751 .809 .69 2.424 52 340 .876 .67 80 5240 7070 19 27 340 348 0 656 435 221 1.155 674 239 .865 1.237 .208 .307
16 1483 1491 57 259 1426 1232 1710 1623 60 264 1653 1364 0 0 618 573 16 57 100 100 100 100 2658 3017 1.157 .864 .825 .834 .844 1.624 52 340 .871 .94 80 5460 7080 20 28 362 370 0 2456 427 2029 1.423 2673 2246 .703 1.359 .509 .443
17 424 433 58 255 366 178 417 424 58 261 359 169 0 0 80 100 15 59 100 81 100 71 544 528 2.056 .486 .471 .401 .517 2.157 32 236 .576 .67 70 5680 7080 20 27 384 391 0 713 420 293 .801 698 278 1.248 .775 -.32 -.367
18 193 316 54 263 139 53 194 308 56 270 140 45 0 0 36 54 14 63 100 40 100 12 192 185 2.623 .381 .321 .392 .413 2.193 32 176 .876 .22 60 5900 7080 21 27 407 413 0 520 433 87 .628 507 74 1.592 .529 -.671 -.918
19 277 402 57 258 220 144 287 398 59 260 230 140 0 0 68 90 15 57 100 84 100 62 364 370 1.528 .655 .609 .557 .637 2.349 32 236 .934 .67 70 6120 7080 20 27 428 435 0 662 425 237 1.078 656 231 .928 1.003 .108 .004
20 71 260 61 253 10 7 69 258 65 258 8 5 0 0 21 54 28 63 20 10 1 2 17 13 1.429 .7 .625 2.421 1.733 4.207 80 560 7.14 .32 100 2140 7280 39 49 29 39 -50 428 417 12 1.153 425 8 .867 1.029 .205 .042

Total number of rows: 10944

Table truncated, full table size 2365 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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