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Sample GSM82429 Query DataSets for GSM82429
Status Public on Feb 28, 2006
Title dPum-TAP IP, adults (2)
Sample type RNA
 
Channel 1
Source name Extract tot. RNA, adults (2)
Organism Drosophila melanogaster
Characteristics Extract tot. RNA, adults (2)
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name IP RNA, EDTA, adults (2)
Organism Drosophila melanogaster
Characteristics IP RNA, EDTA, adults (2)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2004-07/53530.gif; format: GIF
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 08, 2005
Last update date Feb 28, 2006
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 GPL3058
Series (1)
GSE3582 RNA affinity isolation with TAP-Pum and controls

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 4512 1039 293 92 4219 947 4617 1042 310 96 4324 950 0 0 607 154 97 31 100 100 100 100 5166 5274 4.455 .224 .22 .224 .224 1.18 80 506 .223 .98 100 880 18520 51 61 31 41 0 6053 536 5517 1.308 6070 5534 .765 1.28 .387 .356
2 1243 163 267 81 976 82 1241 160 291 89 974 79 0 0 116 18 95 32 100 100 100 85 1058 1053 11.902 .084 .081 .083 .081 1.265 80 536 .086 .81 110 1070 18510 49 60 49 60 0 950 472 478 .489 932 460 2.043 .473 -1.031 -1.082
3 815 133 235 70 580 63 797 133 246 75 562 63 0 0 143 21 72 24 100 96 100 71 643 625 9.206 .109 .112 .105 .107 1.423 80 537 .11 .75 110 1250 18510 49 60 67 78 0 775 408 367 .633 775 367 1.58 .653 -.66 -.615
4 1276 305 248 77 1028 228 1208 311 259 78 960 234 0 0 240 53 76 25 100 100 100 98 1256 1194 4.509 .222 .244 .218 .231 1.344 80 484 .22 .95 100 1440 18500 49 59 87 97 0 1777 449 1328 1.292 1812 1363 .774 1.42 .37 .506
5 2632 479 247 77 2385 402 2438 478 266 83 2191 401 0 0 803 110 90 39 100 100 100 98 2787 2592 5.933 .169 .183 .169 .18 1.346 80 474 .159 .96 100 1620 18500 49 59 105 115 0 2791 449 2342 .982 2785 2336 1.018 1.066 -.026 .093
6 3055 509 235 69 2820 440 3055 509 483 115 2820 440 0 0 520 77 1979 345 91 85 0 0 3260 3260 6.409 .156 .156 .157 .154 1.149 80 536 .152 .97 110 1810 18510 49 60 123 134 0 2965 402 2563 .909 2965 2563 1.1 .909 -.138 -.138
7 1299 194 243 71 1056 123 1306 188 484 114 1063 117 0 0 225 38 1979 344 0 0 0 0 1179 1180 8.585 .116 .11 .113 .119 1.244 80 536 .148 .97 110 1990 18510 49 60 141 152 0 1130 414 717 .679 1095 682 1.474 .641 -.559 -.641
8 4037 413 231 64 3806 349 4040 417 241 65 3809 353 0 0 785 67 74 23 100 100 100 100 4155 4162 10.905 .092 .093 .092 .09 1.179 80 484 .09 .95 100 2180 18500 49 59 161 171 0 2406 373 2033 .534 2429 2056 1.872 .54 -.905 -.889
9 3034 1442 218 67 2816 1375 3056 1459 229 69 2838 1392 0 0 492 320 65 21 100 100 100 100 4191 4230 2.048 .488 .49 .483 .496 1.177 80 524 .496 .99 110 2360 18500 48 59 178 189 0 8401 390 8010 2.845 8500 8109 .352 2.857 1.508 1.515
10 1202 163 212 59 990 104 1161 160 224 62 949 101 0 0 217 28 75 20 100 100 100 97 1094 1050 9.519 .105 .106 .103 .105 1.254 80 536 .108 .94 110 2540 18500 48 59 196 207 0 950 344 606 .612 932 588 1.634 .62 -.708 -.69
11 3173 547 216 63 2957 484 3259 553 222 64 3043 490 0 0 540 87 77 19 100 100 100 100 3441 3533 6.11 .164 .161 .165 .163 1.153 80 548 .161 .99 110 2730 18510 49 60 215 226 0 3187 367 2820 .954 3222 2855 1.049 .938 -.069 -.092
12 1172 292 176 50 996 242 1195 289 186 54 1019 239 0 0 358 62 54 14 100 100 100 100 1238 1258 4.116 .243 .235 .252 .246 1.229 80 462 .228 .97 100 2920 18500 49 59 235 245 0 1701 291 1410 1.415 1684 1392 .706 1.366 .501 .45
13 2061 406 201 60 1860 346 1247 274 210 63 1046 214 0 0 1583 287 62 17 100 100 98 100 2206 1260 5.376 .186 .205 .198 .196 1.404 52 384 .179 .97 90 3080 18490 48 57 251 260 0 2365 350 2016 1.084 1596 1247 .923 1.192 .116 .253
14 2038 387 202 58 1836 329 1607 318 207 60 1405 260 0 0 1441 225 55 19 100 100 100 100 2165 1665 5.581 .179 .185 .194 .186 1.336 80 506 .164 .98 100 3290 18500 49 59 272 282 0 2255 338 1917 1.044 1853 1515 .958 1.078 .062 .108
15 1151 116 206 56 945 60 1142 114 208 57 936 58 0 0 130 18 51 14 100 100 100 97 1005 994 15.75 .063 .062 .061 .061 1.342 80 462 .067 .9 100 3480 18500 49 59 291 301 0 676 326 350 .37 664 338 2.704 .361 -1.435 -1.47
16 1847 248 215 60 1632 188 1842 247 220 61 1627 187 0 0 212 31 50 14 100 100 100 100 1820 1814 8.681 .115 .115 .115 .115 1.161 80 464 .114 .97 100 3660 18500 49 59 309 319 0 1445 350 1095 .671 1439 1089 1.49 .67 -.575 -.579
17 2099 290 213 57 1886 233 2103 285 221 60 1890 228 0 0 241 49 65 26 100 100 100 100 2119 2118 8.094 .124 .121 .122 .122 1.195 80 523 .12 .94 110 3840 18500 48 59 326 337 0 1689 332 1357 .72 1660 1328 1.389 .703 -.474 -.509
18 8866 1285 234 67 8632 1218 8714 1252 237 68 8480 1185 0 0 1488 201 63 17 100 100 100 100 9850 9665 7.087 .141 .14 .141 .141 1.072 80 536 .139 .99 110 4030 18500 48 59 345 356 0 7486 390 7096 .822 7294 6904 1.217 .814 -.283 -.297
19 3551 203 271 74 3280 129 3565 201 277 76 3294 127 0 0 544 25 76 21 100 100 100 100 3409 3421 25.426 .039 .039 .039 .039 1.204 80 536 .038 .93 110 4210 18490 47 58 363 374 0 1183 431 752 .229 1171 740 4.364 .225 -2.126 -2.154
20 2512 975 270 76 2242 899 2449 980 277 78 2179 904 0 0 324 182 81 22 100 100 100 100 3141 3083 2.494 .401 .415 .396 .407 1.148 80 474 .402 .98 100 4400 18490 48 58 383 393 0 5680 443 5237 2.336 5709 5266 .428 2.417 1.224 1.273

Total number of rows: 17664

Table truncated, full table size 3921 Kbytes.




Supplementary data files not provided
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