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Sample GSM82435 Query DataSets for GSM82435
Status Public on Feb 28, 2006
Title dPum-TAP IP, adults (3b)
Sample type RNA
 
Channel 1
Source name Extract tot. RNA, adults (3)
Organism Drosophila melanogaster
Characteristics Extract tot. RNA, adults (3)
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name IP RNA, adults (3)
Organism Drosophila melanogaster
Characteristics IP RNA, adults (3)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/54596.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 3865 734 272 287 3593 447 3645 746 276 292 3373 459 0 0 1192 145 50 44 100 100 100 100 4040 3832 8.038 .124 .136 .124 .125 1.29 80 484 .118 .92 100 950 18780 53 63 38 48 0 4921 1924 2997 .834 5002 3077 1.199 .912 -.262 -.132
2 1009 111 249 281 760 -170 1025 110 257 291 776 -171 0 0 134 23 66 82 100 0 100 0 590 605 null null null 0 0 1 80 475 4.878 .79 100 1130 18780 53 63 56 66 0 744 1884 -1140 null 738 -1146 null null null null
3 351 117 236 266 115 -149 371 76 246 276 135 -190 0 0 71 84 90 102 71 1 11 0 -34 -55 null null null .614 .808 6.191 80 494 .719 .63 100 1320 18760 51 61 75 85 -50 784 1783 -999 null 510 -1274 null null null null
4 753 222 237 278 516 -56 744 217 251 286 507 -61 0 0 77 48 135 73 100 1 100 1 460 446 null null null .066 .061 2.317 80 506 12.981 .3 100 1500 18780 53 63 93 103 0 1488 1864 -375 null 1455 -409 null null null null
5 857 221 230 274 627 -53 860 215 236 277 630 -59 0 0 139 53 70 50 100 3 98 1 574 571 null null null .057 .046 2.655 80 462 17.598 .3 100 1690 18780 53 63 112 122 0 1482 1837 -355 null 1441 -396 null null null null
6 1481 281 224 261 1257 20 1492 250 226 264 1268 -11 0 0 346 118 36 40 100 23 100 17 1277 1257 62.85 .016 null .034 .032 3.457 80 548 .034 .28 110 1870 18770 51 62 129 140 0 1884 1750 134 .107 1676 -74 9.374 null -3.229 null
7 744 152 210 247 534 -95 754 141 212 249 544 -106 0 0 129 59 35 44 100 3 98 0 439 438 null null null .058 .053 1.773 80 484 6.553 .58 100 2060 18770 52 62 149 159 0 1019 1656 -637 null 945 -711 null null null null
8 1066 140 200 231 866 -91 1024 131 204 223 824 -100 0 0 182 50 35 49 100 3 100 2 775 724 null null null .044 .052 2.905 80 472 12.067 .57 100 2250 18780 53 63 168 178 0 939 1549 -610 null 878 -670 null null null null
9 1371 574 198 223 1173 351 1372 572 201 223 1174 349 0 0 229 107 33 39 100 100 100 100 1524 1523 3.342 .299 .297 .289 .289 1.376 80 474 .29 .9 100 2440 18780 53 63 187 197 0 3848 1495 2353 2.006 3835 2340 .498 1.993 1.004 .995
10 466 118 188 205 278 -87 473 117 191 207 285 -88 0 0 63 32 31 33 100 0 98 0 191 197 null null null .06 .06 1 80 464 3.619 .62 100 2620 18770 52 62 205 215 0 791 1374 -583 null 784 -590 null null null null
11 2165 299 185 195 1980 104 2162 299 188 193 1977 104 0 0 357 52 31 35 100 90 100 73 2084 2081 19.038 .053 .053 .047 .051 2.013 80 480 .053 .77 100 2800 18780 53 63 223 233 0 2005 1307 697 .352 2005 697 2.84 .353 -1.506 -1.504
12 445 127 181 170 264 -43 452 116 188 169 271 -54 0 0 81 48 43 42 100 6 100 3 221 217 null null null .04 .045 5.278 32 176 .017 .03 60 2990 18780 55 61 244 250 0 851 1140 -288 null 778 -362 null null null null
13 932 477 176 165 756 312 868 474 181 163 692 309 0 0 559 257 36 44 96 84 90 75 1068 1001 2.423 .413 .447 .496 .481 2.817 32 176 .414 .83 60 3150 18780 55 61 260 266 0 3198 1106 2092 2.767 3178 2072 .361 2.994 1.468 1.582
14 524 349 175 157 349 192 457 235 179 154 282 78 0 0 238 293 34 39 96 59 90 50 541 360 1.818 .55 .277 .342 .401 3.244 32 176 .979 .8 60 3340 18790 56 62 279 285 0 2340 1053 1287 3.689 1576 523 .271 1.854 1.883 .891
15 587 91 184 168 403 -77 586 77 188 171 402 -91 0 0 91 57 37 37 98 8 98 6 326 311 null null null .158 .156 1.436 80 490 6.332 .53 100 3530 18780 53 63 296 306 0 610 1126 -516 null 516 -610 null null null null
16 793 103 180 169 613 -66 798 102 183 170 618 -67 0 0 112 21 31 28 100 0 100 0 547 551 null null null 0 0 1 80 552 11.078 .62 110 3720 18780 52 63 314 325 0 691 1133 -443 null 684 -449 null null null null
17 1001 132 177 163 824 -31 1007 121 180 166 830 -42 0 0 191 43 29 39 98 6 98 3 793 788 null null null .055 .072 4.65 80 524 42.963 .23 110 3900 18770 51 62 332 343 0 885 1093 -208 null 811 -282 null null null null
18 4123 432 174 153 3949 279 4136 419 179 155 3962 266 0 0 691 71 33 33 100 100 100 100 4228 4228 14.154 .071 .067 .069 .07 1.225 80 524 .07 .94 110 4080 18770 51 62 350 361 0 2896 1026 1871 .474 2809 1783 2.111 .45 -1.078 -1.152
19 1587 120 180 159 1407 -39 1610 108 183 160 1430 -51 0 0 300 52 31 27 100 11 100 5 1368 1379 null null null .017 .025 4.897 80 523 41.768 .36 110 4260 18770 51 62 368 379 0 805 1066 -261 null 724 -342 null null null null
20 1124 328 184 173 940 155 1104 331 187 177 920 158 0 0 128 56 39 33 100 98 100 95 1095 1078 6.065 .165 .172 .155 .164 1.468 80 523 .161 .82 110 4450 18770 51 62 387 398 0 2199 1160 1039 1.106 2219 1059 .905 1.151 .145 .203

Total number of rows: 17664

Table truncated, full table size 3846 Kbytes.




Supplementary data files not provided
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