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Sample GSM95254 Query DataSets for GSM95254
Status Public on Feb 03, 2006
Title N2 (green, channel 1) vs daf-7 (red, channel 2) Trial #3
Sample type RNA
 
Channel 1
Source name N2 (green, channel 1)
Organism Caenorhabditis elegans
Characteristics N2 (green, channel 1)
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name daf-7 (red, channel 2)
Organism Caenorhabditis elegans
Characteristics daf-7 (red, channel 2)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: dauer, C. elegans
Image: http://smd.stanford.edu/MicroArray/gifs/2001-01/12696.gif
Data processing VALUE is Log (base 2) of the ratio of the mean of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)
 
Submission date Feb 02, 2006
Last update date Sep 22, 2006
Organization Stanford Microarray Database (SMD)
E-mail(s) array@genome.stanford.edu
Phone 650-498-6012
URL http://genome-www5.stanford.edu/
Department Stanford University, School of Medicine
Street address 300 Pasteur Drive
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
 
Platform ID GPL2646
Series (1)
GSE4164 Regulation of signaling genes by TGFbeta during entry into dauer diapause in C. elegans

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
VALUE 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
LOG_RAT2N_MEDIAN 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 VALUE LOG_RAT2N_MEDIAN
1 10698 8484 184 440 10514 8044 11367 8934 206 460 11183 8494 0 0 2909 2360 93 151 100 100 100 100 18558 19677 1.307 .765 .76 1.345 1.278 .252 80 540 .738 .98 110 2380 16490 47 58 68 79 0 10563 548 10016 .953 11124 10576 1.05 .946 -.07 -.081
2 2128 1426 181 421 1947 1005 2137 1368 184 438 1956 947 0 0 418 368 43 136 100 100 100 96 2952 2903 1.937 .516 .484 2.258 1.972 1.115 80 453 .486 .88 100 2550 16500 49 59 86 96 0 1776 524 1251 .643 1703 1179 1.556 .603 -.638 -.73
3 415 558 183 429 232 129 408 548 243 457 225 119 0 0 62 165 487 172 0 43 0 3 361 344 1.798 .556 .529 6.016 1.413 15.092 32 226 .263 .2 70 2720 16490 49 56 104 111 -50 695 534 161 .692 682 148 1.444 .659 -.53 -.603
4 2072 1562 188 441 1884 1121 2123 1581 340 513 1935 1140 0 0 421 334 817 408 98 100 76 76 3005 3075 1.681 .595 .589 1.809 1.638 .629 52 360 .548 .9 90 2870 16510 50 59 118 127 0 1945 549 1396 .741 1969 1419 1.35 .734 -.433 -.447
5 24369 25043 185 438 24184 24605 25898 26481 191 448 25713 26043 0 0 6097 5519 43 130 100 100 100 100 48789 51756 .983 1.017 1.013 1 .966 .312 52 318 .978 .98 80 3040 16510 51 59 136 144 0 31181 545 30636 1.267 32972 32426 .789 1.261 .341 .335
6 480 701 178 424 302 277 284 665 180 439 106 241 0 0 365 305 41 120 68 59 56 53 579 347 1.09 .917 2.274 1.468 1.145 1.517 32 230 .731 .74 70 3200 16490 49 56 152 159 -50 873 528 345 1.142 828 300 .876 2.831 .192 1.501
7 11992 13436 175 414 11817 13022 12759 13672 181 423 12584 13258 0 0 2269 1683 68 121 100 100 100 100 24839 25842 .907 1.102 1.054 .902 .901 .128 52 380 1.016 .97 90 3360 16500 49 58 167 176 0 16729 515 16214 1.372 17023 16508 .729 1.312 .456 .392
8 452 566 174 404 278 162 433 555 177 424 259 151 0 0 110 134 45 132 96 59 96 15 440 410 1.716 .583 .583 2.56 1.554 2.72 32 231 .419 .34 70 3510 16510 51 58 183 190 0 705 503 202 .726 691 188 1.378 .726 -.463 -.462
9 509 631 174 436 335 195 538 639 182 435 364 203 0 0 116 148 49 138 100 59 98 26 530 567 1.718 .582 .558 2.353 1.713 2.84 52 336 .573 .54 80 3680 16510 51 59 200 208 0 786 543 243 .725 796 253 1.38 .694 -.464 -.526
10 460 632 186 437 274 195 434 630 205 446 248 193 0 0 94 184 75 127 100 68 90 37 469 441 1.405 .712 .778 1.181 1.033 .62 32 216 .584 .46 70 3860 16500 50 57 218 225 0 787 544 243 .886 784 240 1.129 .969 -.174 -.045
11 21412 17064 176 430 21236 16634 22257 18002 189 436 22081 17572 0 0 4406 4004 65 132 100 100 100 100 37870 39653 1.277 .783 .796 1.337 1.234 .414 80 441 .767 .97 100 4000 16510 50 60 231 241 0 21246 535 20711 .975 22414 21879 1.025 .991 -.036 -.013
12 336 554 169 428 167 126 366 564 181 441 197 136 0 0 88 140 57 131 81 50 71 15 293 333 1.325 .754 .69 1.394 .843 1.508 32 226 .471 .35 70 4160 16490 49 56 248 255 -50 690 533 157 .939 702 169 1.064 .86 -.09 -.218
13 4830 5260 168 430 4662 4830 4899 5468 173 435 4731 5038 0 0 837 855 43 133 100 100 100 100 9492 9769 .965 1.036 1.065 .989 .983 .225 52 322 .967 .95 80 4320 16510 51 59 264 272 0 6549 535 6014 1.29 6808 6273 .775 1.326 .367 .407
14 442 582 168 413 274 169 438 614 174 421 270 201 0 0 72 160 35 124 100 65 100 34 443 471 1.621 .617 .744 5.719 1.251 16.283 32 176 .496 .44 60 4490 16510 52 58 282 288 0 725 514 210 .768 764 250 1.302 .927 -.381 -.11
15 959 853 178 424 781 429 913 796 181 428 735 372 0 0 301 254 43 127 100 92 100 75 1210 1107 1.821 .549 .506 2.904 1.889 2.89 52 311 .402 .62 80 4640 16510 51 59 296 304 0 1062 528 534 .684 991 463 1.462 .63 -.548 -.666
16 574 655 179 407 395 248 543 616 185 419 364 209 0 0 150 226 44 127 100 73 100 42 643 573 1.593 .628 .574 2.641 1.468 3.712 52 307 .495 .5 80 4810 16510 51 59 313 321 0 816 507 309 .782 767 260 1.279 .715 -.355 -.484
17 14615 7954 183 411 14432 7543 15100 8133 190 427 14917 7722 0 0 2611 1276 51 126 100 100 100 100 21975 22639 1.913 .523 .518 1.929 1.884 .34 52 354 .502 .98 90 4970 16510 50 59 328 337 0 9904 512 9392 .651 10126 9615 1.537 .645 -.62 -.634
18 741 811 178 409 563 402 718 740 181 428 540 331 0 0 180 231 41 124 100 94 100 69 965 871 1.4 .714 .613 1.79 1.459 1.205 52 334 .649 .72 90 5130 16510 50 59 344 353 0 1010 509 501 .889 921 412 1.125 .763 -.17 -.39
19 2130 2609 177 426 1953 2183 2344 2862 179 430 2167 2436 0 0 725 871 44 122 100 100 98 100 4136 4603 .895 1.118 1.124 .979 .93 .467 80 446 1.069 .94 100 5290 16510 50 60 360 370 0 3248 530 2718 1.392 3563 3033 .719 1.4 .477 .485
20 951 845 174 422 777 423 963 794 178 425 789 372 0 0 181 244 43 127 100 88 100 75 1200 1161 1.837 .544 .471 2.727 1.948 2.628 52 347 .497 .71 90 5460 16510 50 59 377 386 0 1052 525 527 .678 989 463 1.475 .587 -.561 -.768

Total number of rows: 21504

Table truncated, full table size 4756 Kbytes.




Supplementary data files not provided
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