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Sample GSM93688 Query DataSets for GSM93688
Status Public on Jan 25, 2006
Title C7 vs R7
Sample type RNA
 
Channel 1
Source name C7
Organism Caenorhabditis elegans
Characteristics C7
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name R7
Organism Caenorhabditis elegans
Characteristics R7
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: C. elegans, C. elegans
Image: http://smd.stanford.edu/MicroArray/gifs/2004-06/53246.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)
GSE4094 N2 worms treated with Resveratrol
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 1513 1433 121 108 1392 1325 1601 1487 122 112 1480 1379 0 0 397 380 26 38 100 100 100 100 2717 2859 1.051 .952 .932 .967 .988 1.386 120 394 .947 .96 120 2180 6090 25 37 58 70 0 2102 158 1943 1.396 2181 2022 .716 1.367 .481 .451
2 191 182 116 105 75 77 188 175 119 112 72 70 0 0 46 60 26 40 81 71 65 40 152 142 .974 1.027 .972 1.241 1.252 3.169 120 419 1.523 .45 120 2350 6090 25 37 75 87 0 267 154 113 1.506 257 103 .664 1.426 .59 .512
3 181 142 115 107 66 35 179 131 117 114 64 24 0 0 39 49 26 40 86 41 58 17 101 88 1.886 .53 .375 .605 .779 3.35 80 386 1.89 .2 100 2520 6090 26 36 93 103 0 208 157 51 .778 192 35 1.286 .55 -.363 -.863
4 181 114 115 107 66 7 177 111 117 112 62 4 0 0 39 36 27 39 81 22 56 1 73 66 9.429 .106 .065 .479 .538 4.77 80 356 .499 .17 100 2690 6090 26 36 110 120 -50 167 157 10 .156 163 6 6.429 .095 -2.685 -3.402
5 419 311 120 114 299 197 428 311 141 127 308 197 0 0 98 98 79 61 95 94 92 78 496 505 1.518 .659 .64 .625 .649 1.759 156 457 .67 .78 150 2860 6090 23 38 124 139 0 456 167 289 .966 456 289 1.035 .938 -.049 -.092
6 691 1098 112 113 579 985 685 1043 125 122 573 930 0 0 173 285 61 53 99 100 98 100 1564 1503 .588 1.701 1.623 1.753 1.715 1.484 120 395 1.744 .94 120 3030 6090 25 37 143 155 0 1610 166 1445 2.495 1530 1364 .401 2.38 1.319 1.251
7 132 93 103 108 29 -15 133 88 106 110 30 -20 0 0 21 38 20 39 62 7 27 2 14 10 null null null .571 .638 4.177 80 383 -1 -1 100 3200 6080 25 35 161 171 -50 136 158 -22 null 129 -29 null null null null
8 157 120 101 95 56 25 160 111 104 102 59 16 0 0 35 52 21 39 85 36 68 16 81 75 2.24 .446 .271 .81 .812 3.917 80 391 2.081 .26 100 3370 6080 25 35 178 188 -50 176 139 37 .655 163 23 1.527 .398 -.611 -1.33
9 212 223 104 96 108 127 210 220 106 107 106 124 0 0 48 69 25 55 95 83 88 57 235 230 .85 1.176 1.17 1.148 1.097 2.369 80 436 1.734 .56 110 3540 6100 26 37 194 205 0 327 141 186 1.725 323 182 .58 1.716 .786 .779
10 158 138 102 101 56 37 156 133 105 106 54 32 0 0 39 42 24 41 77 40 53 12 93 86 1.514 .661 .593 .838 .788 4.24 80 357 2.01 .23 100 3710 6080 25 35 212 222 -50 202 148 54 .969 195 47 1.032 .869 -.045 -.202
11 283 202 102 102 181 100 273 193 106 107 171 91 0 0 74 69 24 40 98 77 98 56 281 262 1.81 .552 .532 .482 .567 2.416 120 454 .611 .66 120 3870 6090 25 37 227 239 0 296 150 147 .81 283 133 1.234 .78 -.303 -.358
12 152 135 106 103 46 32 148 131 109 106 42 28 0 0 31 51 25 37 75 38 36 19 78 70 1.438 .696 .667 .802 1.022 4.171 52 332 1.606 .23 90 4050 6070 24 33 246 255 0 198 151 47 1.02 192 41 .98 .978 .029 -.032
13 397 326 103 101 294 225 384 347 105 104 281 246 0 0 91 90 22 35 100 100 100 96 519 527 1.307 .765 .875 .731 .754 1.564 80 393 .765 .83 100 4210 6090 26 36 262 272 0 478 148 330 1.122 509 361 .891 1.284 .167 .361
14 122 108 103 101 19 7 115 98 104 106 12 -3 0 0 27 48 21 36 36 22 17 10 26 9 2.714 .368 null 2.712 2.37 4.822 80 371 22.611 .04 100 4380 6080 25 35 279 289 -50 158 148 10 .54 144 -4 1.851 null -.888 null
15 221 151 104 106 117 45 221 147 106 109 117 41 0 0 44 47 21 38 99 51 96 20 162 158 2.6 .385 .35 .372 .435 2.768 120 444 .479 .37 120 4550 6090 25 37 295 307 0 221 155 66 .564 216 60 1.773 .514 -.826 -.96
16 143 108 104 103 39 5 136 99 105 108 32 -4 0 0 30 46 20 36 72 16 38 5 44 28 7.8 .128 null .879 1.018 3.631 80 371 8.092 .05 100 4720 6080 25 35 313 323 -50 158 151 7 .188 145 -6 5.318 null -2.411 null
17 179 165 103 105 76 60 179 157 106 110 76 52 0 0 67 69 21 37 76 52 62 36 136 128 1.267 .789 .684 .812 .958 3.665 80 389 1.198 .5 100 4890 6080 25 35 330 340 -50 242 154 88 1.158 230 76 .864 1.003 .211 .005
18 208 163 103 104 105 59 205 153 106 107 102 49 0 0 50 63 22 34 96 62 90 36 164 151 1.78 .562 .48 .581 .537 2.692 80 371 .836 .51 100 5050 6090 26 36 346 356 0 239 153 87 .824 224 72 1.213 .705 -.279 -.505
19 122 100 103 105 19 -5 119 98 108 109 16 -7 0 0 24 38 36 42 23 8 3 5 14 9 null null null 1.286 1.246 4.786 80 395 .037 .03 100 5230 6080 25 35 364 374 -50 147 154 -7 null 144 -10 null null null null
20 2732 2174 106 109 2626 2065 2836 2268 138 138 2730 2159 0 0 663 477 147 131 100 100 100 100 4691 4889 1.272 .786 .791 .79 .77 1.24 120 459 .77 .97 130 5400 6090 24 37 379 392 0 3188 160 3029 1.153 3326 3166 .867 1.16 .206 .214

Total number of rows: 20736

Table truncated, full table size 4355 Kbytes.




Supplementary data files not provided
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