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Sample GSM306253 Query DataSets for GSM306253
Status Public on Jul 29, 2008
Title age-1; fer-15 (M) vs. N2 mixed stage ref
Sample type RNA
 
Channel 1
Source name N2 mixed stage ref
Organism Caenorhabditis elegans
Characteristics N2 mixed stage ref
Extracted molecule total RNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name age-1; fer-15
Organism Caenorhabditis elegans
Characteristics age-1; fer-15
Extracted molecule total RNA
Extraction protocol not provided
Label Cy5
Label protocol not provided
 
 
Hybridization protocol not provided
Scan protocol not provided
Description Simple annotation: C. elegans, Aging
Image: http://smd.stanford.edu/MicroArray/gifs/2002-07/30348.gif
Place of growth: Stanford
Genotype: age-1; fer-15
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 Jul 18, 2008
Last update date Jul 29, 2008
Contact name Stuart Kim
E-mail(s) kim@cmgm.stanford.edu
Phone 650-725-7671
Fax 650-725-7739
Organization name Stanford University Medical Center
Department Department of Developmental Biology
Street address -
City Stanford
State/province CA
ZIP/Postal code 94305-5307
Country USA
 
Platform ID GPL7065
Series (2)
GSE12094 Aging study
GSE12166 TJ411(fer-15(b26)II; age-1(hx542)II) vs. BA713(fer-15(b26)II)

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 1469 580 123 134 1346 446 609 430 127 137 486 296 0 0 1515 456 39 40 82 78 71 71 1792 782 3.018 .331 .609 1.325 .377 3.526 52 344 .291 .93 90 2470 18440 95 104 134 143 0 1115 258 858 .637 827 569 1.569 1.171 -.65 .228
2 1562 521 118 136 1444 385 1528 541 121 137 1410 405 0 0 507 154 30 36 100 100 100 100 1829 1815 3.751 .267 .287 .282 .272 .116 52 294 .254 .92 80 2630 18430 95 103 151 159 0 1002 262 740 .513 1040 779 1.95 .552 -.964 -.856
3 442 178 117 129 325 49 458 171 130 134 341 42 0 0 200 41 62 38 90 50 75 28 374 383 6.633 .151 .123 .294 .18 .423 32 176 .106 .42 60 2780 18440 97 103 167 173 0 342 248 94 .29 329 81 3.449 .237 -1.786 -2.078
4 1462 1784 123 134 1339 1650 1509 1798 130 137 1386 1664 0 0 527 619 55 40 100 100 98 100 2989 3050 .812 1.232 1.201 1.346 1.264 .505 52 366 1.152 .95 90 2960 18430 94 103 183 192 0 3431 258 3173 2.37 3458 3200 .422 2.309 1.245 1.207
5 1238 435 118 138 1120 297 1253 431 124 140 1135 293 0 0 326 111 34 41 100 100 100 100 1417 1428 3.771 .265 .258 .282 .265 .12 52 313 .242 .88 80 3120 18430 95 103 200 208 0 837 265 571 .51 829 563 1.961 .496 -.972 -1.01
6 1310 1262 123 139 1187 1123 1457 994 132 140 1334 855 0 0 1003 917 44 40 87 84 75 78 2310 2189 1.057 .946 .641 1.586 .952 3.114 32 226 .912 .97 70 3290 18410 93 100 217 224 0 2427 267 2160 1.819 1912 1644 .55 1.233 .863 .302
7 2529 1175 123 134 2406 1041 2691 1250 128 137 2568 1116 0 0 785 394 38 39 100 100 100 100 3447 3684 2.311 .433 .435 .441 .422 .148 80 457 .425 .96 100 3450 18430 94 104 232 242 0 2260 258 2002 .832 2404 2146 1.202 .836 -.265 -.259
8 690 347 125 138 565 209 718 327 127 141 593 189 0 0 284 166 35 43 96 87 93 75 774 782 2.703 .37 .319 .383 .303 .236 32 165 .347 .77 60 3600 18420 95 101 249 255 0 667 265 402 .711 629 363 1.406 .613 -.491 -.706
9 2468 10130 132 145 2336 9985 2439 9744 142 164 2307 9599 0 0 429 1563 70 131 100 100 100 100 12321 11906 .234 4.274 4.161 4.359 4.256 .761 52 373 4.05 .97 90 3770 18430 94 103 264 273 0 19481 279 19202 8.22 18738 18460 .122 8.002 3.039 3
10 997 434 131 147 866 287 1043 439 141 149 912 292 0 0 441 180 49 43 93 90 93 84 1153 1204 3.017 .331 .32 .345 .332 .157 32 236 .319 .85 70 3930 18440 96 103 281 288 0 835 283 552 .637 844 562 1.569 .616 -.65 -.7
11 3965 1792 128 142 3837 1650 4163 1964 135 146 4035 1822 0 0 1510 654 45 51 100 100 100 100 5487 5857 2.325 .43 .452 .462 .433 .194 80 427 .413 .96 100 4100 18440 95 105 297 307 0 3446 273 3173 .827 3777 3504 1.209 .868 -.274 -.204
12 871 380 123 139 748 241 868 371 128 142 745 232 0 0 287 116 39 54 100 96 100 86 989 977 3.104 .322 .311 .348 .328 .162 52 354 .294 .85 90 4250 18440 95 104 312 321 0 731 267 463 .62 713 446 1.614 .599 -.691 -.74
13 2043 2141 125 140 1918 2001 880 1578 123 143 755 1438 0 0 2381 2017 32 41 100 100 100 100 3919 2193 .959 1.043 1.905 1.566 1.116 1.007 12 104 .877 .95 50 4420 18430 96 101 331 336 0 4117 269 3848 2.006 3035 2765 .498 3.663 1.005 1.873
14 706 290 119 128 587 162 702 295 122 133 583 167 0 0 140 66 33 40 100 96 100 86 749 750 3.623 .276 .286 .282 .266 .116 52 367 .261 .78 90 4590 18450 96 105 346 355 0 558 246 312 .531 567 321 1.884 .551 -.914 -.86
15 678 241 120 139 558 102 669 233 126 141 549 94 0 0 174 62 42 39 100 88 100 61 660 643 5.471 .183 .171 .219 .2 .134 52 356 .158 .59 90 4740 18440 95 104 361 370 0 463 267 196 .352 448 181 2.845 .329 -1.508 -1.603
16 780 484 122 141 658 343 789 482 131 143 667 341 0 0 156 107 64 38 100 100 100 100 1001 1008 1.918 .521 .511 .552 .527 .214 52 362 .477 .85 90 4900 18440 95 104 377 386 0 931 271 660 1.002 927 656 .998 .983 .004 -.024
17 4156 3902 118 135 4038 3767 4329 3958 126 138 4211 3823 0 0 1266 975 65 37 100 100 100 100 7805 8034 1.072 .933 .908 1.009 .884 .397 52 354 .862 .96 90 5060 18440 95 104 393 402 0 7504 260 7244 1.794 7612 7352 .557 1.746 .843 .804
18 1148 1068 121 141 1027 927 1128 1046 125 143 1007 905 0 0 253 236 38 40 100 100 100 100 1954 1912 1.108 .903 .899 .934 .874 .265 52 293 .854 .93 80 5220 18440 96 104 410 418 0 2054 271 1783 1.736 2012 1740 .576 1.728 .796 .789
19 1374 758 122 143 1252 615 1342 778 130 146 1220 635 0 0 301 120 41 40 100 100 100 100 1867 1855 2.036 .491 .52 .514 .507 .145 52 352 .46 .93 90 5380 18440 95 104 425 434 0 1458 275 1183 .945 1496 1221 1.059 1.001 -.082 .001
20 1681 5018 121 137 1560 4881 1755 5312 127 142 1634 5175 0 0 631 1689 38 38 100 100 98 100 6441 6809 .32 3.129 3.167 3.638 3.158 2.414 80 440 2.927 .96 100 5540 18450 96 106 441 451 0 9650 263 9387 6.017 10215 9952 .166 6.091 2.589 2.607

Total number of rows: 21504

Table truncated, full table size 4776 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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