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Sample GSM93684 Query DataSets for GSM93684
Status Public on Jan 25, 2006
Title dDf-16 D
Sample type RNA
 
Channel 1
Source name CD
Organism Caenorhabditis elegans
Characteristics CD
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name RD
Organism Caenorhabditis elegans
Characteristics RD
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: C. elegans, C. elegans
Image: http://smd.stanford.edu/MicroArray/gifs//54807.gif
Measurement: concentration(absolute) 1000 uM
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 Jan 24, 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 GPL3391
Series (2)
GSE4093 Resveratrol treatment of daf-16 mutant C. elegans
GSE4402 A role for SIR-2.1 regulation of ER stress response genes in determining C. elegans life span

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 5448 2203 115 77 5333 2126 5649 2241 131 87 5534 2164 0 0 1219 503 91 55 100 100 100 100 7459 7698 2.508 .399 .391 .408 .39 1.554 120 411 .382 .94 120 1630 5260 32 44 49 61 0 4204 147 4057 .761 4276 4129 1.315 .746 -.395 -.422
2 304 138 113 72 191 66 301 126 130 83 188 54 0 0 69 68 92 50 92 51 51 23 257 242 2.894 .346 .287 .311 .323 2.864 80 399 .257 .46 110 1790 5260 32 43 65 76 0 263 137 126 .659 240 103 1.517 .548 -.601 -.867
3 253 104 106 72 147 32 253 101 112 78 147 29 0 0 53 48 69 36 93 38 56 16 179 176 4.594 .218 .197 .262 .271 2.443 80 384 .215 .28 100 1970 5260 33 43 84 94 0 198 137 61 .415 193 55 2.407 .376 -1.267 -1.409
4 265 118 99 68 166 50 266 111 105 73 167 43 0 0 72 52 66 35 92 57 65 30 216 210 3.32 .301 .257 .341 .357 2.504 120 397 .178 .33 120 2140 5250 31 43 100 112 0 225 130 95 .575 212 82 1.74 .491 -.799 -1.025
5 762 428 99 67 663 361 778 441 114 78 679 374 0 0 245 162 84 61 96 94 94 90 1024 1053 1.837 .544 .551 .565 .544 2.474 156 364 .529 .86 140 2310 5260 31 45 116 130 0 817 128 689 1.039 842 714 .962 1.051 .055 .072
6 4530 1338 99 70 4431 1268 4567 1275 119 85 4468 1205 0 0 950 363 95 70 100 100 99 100 5699 5673 3.494 .286 .27 .29 .269 1.734 120 323 .258 .88 130 2480 5260 31 44 133 146 0 2553 134 2420 .546 2433 2299 1.831 .515 -.873 -.958
7 152 75 96 66 56 9 145 70 100 73 49 4 0 0 40 39 34 42 66 22 33 5 65 53 6.222 .161 .082 .485 .545 4.087 80 338 11.802 .03 100 2630 5250 32 42 150 160 -50 143 126 17 .307 134 8 3.261 .156 -1.705 -2.682
8 195 94 104 65 91 29 187 82 109 71 83 17 0 0 44 46 40 36 86 36 55 21 120 100 3.138 .319 .205 .444 .535 3.405 52 374 .212 .14 90 2790 5250 32 41 166 175 0 179 124 55 .608 156 32 1.644 .391 -.718 -1.355
9 491 226 104 66 387 160 486 222 111 74 382 156 0 0 100 93 42 38 99 93 99 80 547 538 2.419 .413 .408 .354 .357 2.014 120 430 .398 .7 120 2990 5250 31 43 185 197 0 431 126 305 .789 424 298 1.268 .779 -.342 -.36
10 177 78 101 65 76 13 166 73 106 71 65 8 0 0 61 38 36 35 75 18 40 10 89 73 5.846 .171 .123 .444 .383 3.938 80 334 .052 .06 100 3140 5250 32 42 201 211 -50 149 124 25 .326 139 15 3.064 .235 -1.615 -2.09
11 618 273 102 70 516 203 596 260 111 78 494 190 0 0 152 115 45 41 100 91 100 87 719 684 2.542 .393 .385 .369 .402 1.965 120 458 .378 .72 130 3320 5250 30 43 217 230 0 521 134 387 .751 496 363 1.332 .734 -.414 -.446
12 288 158 100 67 188 91 279 158 106 74 179 91 0 0 80 67 39 40 98 72 90 54 279 270 2.066 .484 .508 .445 .504 2.521 120 359 .491 .61 120 3490 5250 31 43 235 247 0 302 128 174 .924 302 174 1.083 .97 -.115 -.044
13 537 473 99 62 438 411 523 468 102 69 424 406 0 0 148 173 31 33 100 98 99 97 849 830 1.066 .938 .958 .91 .883 1.745 120 389 .956 .84 120 3660 5250 31 43 252 264 0 903 118 784 1.791 893 775 .558 1.827 .84 .87
14 155 100 95 67 60 33 152 93 97 71 57 26 0 0 45 48 28 33 73 38 50 20 93 83 1.818 .55 .456 .678 .621 3.178 80 352 .378 .14 100 3830 5240 31 41 270 280 0 191 128 63 1.05 177 50 .953 .87 .07 -.2
15 441 352 96 68 345 284 435 345 102 74 339 277 0 0 117 106 34 38 98 100 98 98 629 616 1.215 .823 .817 .783 .827 1.772 120 420 .791 .77 120 4000 5250 31 43 286 298 0 672 130 542 1.571 658 529 .637 1.559 .652 .641
16 216 103 97 67 119 36 211 94 101 70 114 27 0 0 57 46 31 33 97 45 86 25 155 141 3.306 .303 .237 .392 .397 2.791 80 336 .26 .29 100 4160 5250 32 42 303 313 0 197 128 69 .577 179 52 1.732 .452 -.793 -1.146
17 161 91 99 65 62 26 149 81 101 72 50 16 0 0 68 44 28 33 67 37 45 16 88 66 2.385 .419 .32 .475 .473 2.881 80 365 .257 .22 100 4320 5240 31 41 319 329 -50 174 124 50 .8 155 31 1.25 .611 -.321 -.712
18 325 158 96 69 229 89 326 157 101 74 230 88 0 0 92 62 31 36 99 78 94 56 318 318 2.573 .389 .383 .348 .378 2.475 120 404 .349 .55 130 4510 5250 30 43 336 349 0 302 132 170 .742 300 168 1.348 .73 -.431 -.454
19 150 72 96 68 54 4 148 65 109 79 52 -3 0 0 38 31 53 49 48 6 7 1 58 49 13.5 .074 null .447 .432 4.036 80 287 -1 -1 100 4660 5240 31 41 353 363 -50 137 130 8 .141 124 -6 7.074 null -2.823 null
20 5838 4454 103 78 5735 4376 5951 4499 141 114 5848 4421 0 0 990 1227 125 123 100 100 100 99 10111 10269 1.311 .763 .756 .724 .784 1.452 120 390 .792 .95 120 4820 5240 30 42 368 380 0 8499 149 8351 1.456 8585 8436 .687 1.443 .542 .529

Total number of rows: 20736

Table truncated, full table size 4333 Kbytes.




Supplementary data files not provided
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