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Sample GSM95250 Query DataSets for GSM95250
Status Public on Feb 03, 2006
Title N2 (green, channel 1) vs daf-14 (red, channel 2) Trial #2
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-14 (red, channel 2)
Organism Caenorhabditis elegans
Characteristics daf-14 (red, channel 2)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: dauer, C. elegans
Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15550.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 GPL2754
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 7494 5728 92 150 7402 5578 4540 3289 103 158 4448 3139 2 0 11651 8486 52 49 100 100 100 100 12980 7587 1.327 .754 .706 .671 .632 1.722 80 507 .702 .87 110 2220 18330 35 46 64 75 0 6611 173 6437 .87 3796 3623 1.15 .814 -.201 -.296
2 1380 558 93 157 1287 401 1550 539 104 164 1457 382 0 0 564 263 52 53 100 97 100 86 1688 1839 3.209 .312 .262 .279 .302 1.748 80 429 .319 .88 100 2400 18330 36 46 83 93 0 644 181 463 .36 622 441 2.781 .303 -1.476 -1.725
3 1331 974 99 159 1232 815 350 341 106 161 251 182 0 0 2408 1145 51 44 96 92 92 80 2047 433 1.512 .662 .725 .825 .641 3.177 52 287 .413 .7 80 2570 18320 36 44 101 109 -100 1124 183 941 .763 394 210 1.31 .837 -.389 -.257
4 1314 683 96 154 1218 529 1416 682 109 163 1320 528 0 0 396 176 71 57 100 96 100 96 1747 1848 2.302 .434 .4 .417 .403 1.75 52 382 .393 .9 90 2740 18330 36 45 117 126 0 788 178 611 .501 787 609 1.995 .462 -.996 -1.115
5 7884 12365 95 158 7789 12207 9119 13461 109 166 9024 13303 0 0 2964 3519 88 64 100 100 100 100 19996 22327 .638 1.567 1.474 1.738 1.518 1.516 52 380 1.491 .97 90 2910 18330 36 45 134 143 0 14270 182 14088 1.809 15535 15353 .553 1.701 .855 .767
6 634 758 95 158 539 600 633 686 96 167 538 528 0 0 120 208 24 68 100 100 100 100 1139 1066 .898 1.113 .981 1.084 .934 1.492 12 104 1.202 .86 50 3070 18330 38 43 152 157 0 875 182 692 1.285 792 609 .778 1.133 .361 .18
7 3485 4669 95 167 3390 4502 4421 6122 104 177 4326 5955 0 0 1761 2674 58 64 98 99 96 97 7892 10281 .753 1.328 1.377 1.211 1.37 1.773 120 607 1.4 .96 120 3220 18350 37 49 164 176 0 5388 193 5196 1.533 7065 6873 .652 1.589 .616 .668
8 1582 849 103 174 1479 675 416 543 108 183 313 369 0 0 4062 895 39 59 100 98 100 98 2154 682 2.191 .456 1.179 .878 .927 2.132 52 288 .192 .75 80 3390 18340 38 46 183 191 -100 980 201 779 .527 627 426 1.899 1.361 -.925 .444
9 449 318 104 176 345 142 441 320 120 190 337 144 0 0 113 92 151 110 98 63 65 17 487 481 2.43 .412 .427 .379 .426 2.429 52 354 .559 .83 90 3550 18340 37 46 198 207 0 367 203 164 .475 369 166 2.105 .493 -1.074 -1.02
10 245 245 97 173 148 72 247 234 103 186 150 61 0 0 60 61 42 75 98 38 84 11 220 211 2.056 .486 .407 .488 .467 2.316 52 298 .762 .41 80 3710 18340 38 46 215 223 0 283 200 83 .561 270 70 1.781 .469 -.833 -1.091
11 13047 6679 96 177 12951 6502 13380 7060 100 184 13284 6883 0 0 1679 1285 36 70 100 100 100 100 19453 20167 1.992 .502 .518 .496 .523 1.311 52 362 .5 .97 90 3870 18340 37 46 230 239 0 7708 204 7504 .579 8148 7944 1.726 .598 -.787 -.742
12 344 305 98 178 246 127 339 309 104 183 241 131 0 0 87 62 40 48 100 92 98 71 373 372 1.937 .516 .544 .521 .576 1.818 52 374 .533 .66 90 4040 18340 37 46 247 256 0 352 205 147 .596 357 151 1.678 .627 -.747 -.673
13 197 302 100 193 97 109 179 282 106 206 79 89 0 0 106 98 38 95 71 46 50 18 206 168 .89 1.124 1.127 .947 1.142 4.186 32 176 1.564 .38 60 4190 18340 39 45 264 270 0 349 223 126 1.297 325 103 .771 1.3 .375 .379
14 224 248 102 197 122 51 217 248 111 205 115 51 0 0 52 52 42 64 96 37 84 6 173 166 2.392 .418 .443 .388 .512 3.305 32 230 1.631 .31 70 4360 18330 37 44 280 287 0 286 227 59 .482 286 59 2.073 .512 -1.052 -.966
15 225 275 117 201 108 74 216 257 134 205 99 56 0 0 43 78 72 49 83 66 25 25 182 155 1.459 .685 .566 .562 .519 2.159 12 104 .377 .24 50 4500 18350 40 45 295 300 0 317 232 85 .791 297 65 1.265 .653 -.339 -.615
16 451 401 103 194 348 207 416 389 112 200 313 195 0 0 235 109 44 60 100 96 100 84 555 508 1.681 .595 .623 .572 .607 1.857 52 386 .502 .65 90 4680 18340 37 46 311 320 0 463 224 239 .686 449 225 1.457 .719 -.543 -.476
17 8122 1998 105 196 8017 1802 8474 2053 116 202 8369 1857 0 0 1529 474 52 65 100 100 100 100 9819 10226 4.449 .225 .222 .222 .224 1.42 52 308 .217 .94 80 4840 18340 38 46 328 336 0 2306 226 2080 .259 2369 2143 3.855 .256 -1.947 -1.965
18 291 286 116 211 175 75 288 280 120 225 172 69 0 0 54 86 44 89 100 40 100 12 250 241 2.333 .429 .401 .457 .459 2.353 32 230 .947 .27 70 5000 18340 38 45 344 351 0 330 244 87 .495 323 80 2.022 .463 -1.016 -1.111
19 1816 1399 109 194 1707 1205 1885 1368 117 200 1776 1174 0 0 393 301 45 55 100 100 100 100 2912 2950 1.417 .706 .661 .714 .679 1.348 52 367 .682 .95 90 5160 18340 37 46 359 368 0 1615 224 1391 .815 1579 1355 1.227 .763 -.296 -.39
20 479 327 103 199 376 128 495 324 113 204 392 125 0 0 80 71 52 52 100 84 100 65 504 517 2.938 .34 .319 .3 .31 2.105 52 284 .322 .64 80 5320 18350 39 47 376 384 0 377 230 148 .393 374 144 2.545 .368 -1.348 -1.442

Total number of rows: 21504

Table truncated, full table size 4743 Kbytes.




Supplementary data files not provided
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