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Sample GSM402426 Query DataSets for GSM402426
Status Public on May 12, 2009
Title Rpl16a-ZZ Gradient (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 Gradient RNA Rpl16a-ZZ
Organism Saccharomyces cerevisiae
Characteristics test: Gradient RNA 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/2009-01/82653.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 1177 1523 52 97 1125 1426 1101 1564 53 99 1049 1467 0 0 301 347 13 25 100 100 100 100 2551 2516 .789 1.268 1.398 1.269 1.291 1.207 32 176 1.257 .97 60 2200 6680 41 47 41 47 0 1685 107 1578 1.403 1731 1623 .713 1.548 .488 .63
2 179 179 51 97 128 82 183 178 52 97 132 81 0 0 28 35 14 20 100 93 100 84 210 213 1.561 .641 .614 .574 .662 1.829 32 176 .709 .78 60 2430 6670 40 46 64 70 0 198 107 91 .709 197 90 1.411 .679 -.496 -.558
3 700 695 51 100 649 595 699 714 52 101 648 614 0 0 151 150 14 26 100 100 100 100 1244 1262 1.091 .917 .948 .91 .959 1.25 32 236 .897 .96 70 2650 6670 39 46 85 92 0 769 111 658 1.015 790 679 .986 1.049 .021 .068
4 68 110 51 99 17 11 66 107 53 101 15 8 0 0 23 28 15 25 48 22 20 7 28 23 1.545 .647 .533 .895 .794 3.613 80 560 3.053 .2 100 2870 6670 38 48 106 116 -50 122 110 12 .716 118 9 1.397 .59 -.482 -.761
5 60 103 52 99 8 4 59 101 54 102 7 2 0 0 17 26 15 27 28 13 11 2 12 9 2 .5 .286 1.279 1.272 3.084 80 560 18.113 .07 100 3090 6670 38 48 128 138 -50 114 110 4 .553 112 2 1.807 .316 -.854 -1.661
6 69 106 51 103 18 3 58 103 52 106 7 0 0 0 52 35 13 26 32 15 17 3 21 7 6 .167 null 1.198 1.132 2.924 80 560 .939 .38 100 3310 6670 38 48 150 160 -50 117 114 3 .184 114 0 5.422 null -2.439 null
7 354 471 50 106 304 365 370 467 52 107 320 361 0 0 71 117 13 27 100 100 100 100 669 681 .833 1.201 1.128 1.171 1.113 1.29 32 236 1.26 .94 70 3540 6670 39 46 174 181 0 521 117 404 1.329 517 400 .753 1.248 .41 .32
8 266 277 51 106 215 171 265 270 52 107 214 164 0 0 65 78 12 27 100 93 100 93 386 378 1.257 .795 .766 .763 .783 1.498 32 236 .864 .87 70 3760 6660 38 45 196 203 0 307 117 189 .88 299 181 1.136 .848 -.184 -.238
9 211 245 50 105 161 140 216 246 52 107 166 141 0 0 46 56 14 25 100 100 100 96 301 307 1.15 .87 .849 .829 .908 1.618 32 176 .961 .84 60 3980 6660 39 45 219 225 0 271 116 155 .962 272 156 1.039 .94 -.055 -.089
10 215 213 51 100 164 113 225 218 52 103 174 118 0 0 60 44 13 25 100 96 100 93 277 292 1.451 .689 .678 .711 .669 1.463 32 176 .669 .87 60 4200 6670 40 46 241 247 0 236 111 125 .763 241 131 1.311 .75 -.391 -.414
11 1405 1997 52 100 1353 1897 1389 2095 54 103 1337 1995 0 0 328 425 13 27 100 100 100 100 3250 3332 .713 1.402 1.492 1.406 1.419 1.114 32 236 1.395 .99 70 4420 6670 39 46 262 269 0 2210 111 2099 1.552 2318 2208 .644 1.651 .634 .724
12 91 124 52 101 39 23 88 131 54 102 36 30 0 0 20 24 14 24 91 58 58 8 62 66 1.696 .59 .833 .811 .893 1.692 12 104 1.419 .26 50 4650 6650 38 43 286 291 0 137 112 25 .653 145 33 1.532 .922 -.616 -.117
13 105 138 51 99 54 39 106 137 52 100 55 38 0 0 26 31 12 24 94 65 86 38 93 93 1.385 .722 .691 .667 .797 2.226 52 340 1.078 .54 80 4850 6670 39 47 305 313 0 153 110 43 .799 152 42 1.251 .765 -.323 -.387
14 224 239 51 102 173 137 221 239 53 103 170 137 0 0 52 60 13 25 100 98 100 88 310 307 1.263 .792 .806 .729 .797 1.603 52 340 .881 .89 80 5080 6670 39 47 328 336 0 264 113 152 .876 264 152 1.141 .892 -.19 -.165
15 144 202 52 100 92 102 136 191 53 101 84 91 0 0 62 70 14 24 90 92 81 72 194 175 .902 1.109 1.083 1.112 1.109 1.89 80 560 1.2 .84 100 5290 6660 37 47 348 358 0 224 111 113 1.227 211 101 .815 1.199 .295 .262
16 517 602 50 98 467 504 551 643 52 100 501 545 0 0 221 220 12 22 100 98 100 98 971 1046 .927 1.079 1.088 1.131 1.093 1.303 52 340 1.061 .97 80 5510 6660 38 46 371 379 0 666 108 558 1.194 712 603 .837 1.204 .256 .268
17 221 307 49 97 172 210 227 309 50 99 178 212 0 0 67 79 13 24 100 100 98 100 382 390 .819 1.221 1.191 1.239 1.291 1.466 52 340 1.246 .91 80 5730 6660 38 46 393 401 0 340 107 232 1.351 342 235 .74 1.318 .434 .398
18 133 170 50 99 83 71 128 166 51 100 78 67 0 0 27 38 12 23 100 90 100 73 154 145 1.169 .855 .859 .814 .827 1.871 52 340 1.069 .68 80 5950 6660 38 46 415 423 0 188 110 79 .947 184 74 1.056 .951 -.079 -.073
19 217 257 53 98 164 159 215 250 55 101 162 152 0 0 53 55 15 25 100 100 100 100 323 314 1.031 .97 .938 .964 .893 1.414 32 236 1.024 .89 70 6170 6650 37 44 437 444 0 284 108 176 1.073 277 168 .932 1.038 .102 .054
20 63 110 51 101 12 9 61 113 52 102 10 12 0 0 18 27 14 27 43 23 17 5 21 22 1.333 .75 1.2 1.312 1.146 3.096 80 560 4.301 .25 100 2210 6890 60 70 40 50 -50 122 112 10 .83 125 13 1.205 1.328 -.269 .409

Total number of rows: 10944

Table truncated, full table size 2337 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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