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Sample GSM93694 Query DataSets for GSM93694
Status Public on Jan 25, 2006
Title sir2.1(1.8.1.2) (prep.4) vs. unc-119 (prep.4)
Sample type RNA
 
Channel 1
Source name unc-119
Organism Caenorhabditis elegans
Characteristics unc-119
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name sir2.1(1.8.1.2)
Organism Caenorhabditis elegans
Characteristics sir2.1(1.8.1.2)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: C. elegans, Aging
Image: http://smd.stanford.edu/MicroArray/gifs/2003-10/46082.gif
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 GPL3390
Series (2)
GSE4095 Sir-2.1 low copy transgenic
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 2916 2075 41 53 2875 2022 3116 1986 80 96 3075 1933 0 0 1378 809 333 340 100 100 92 96 4897 5008 1.422 .703 .629 .852 .701 .565 52 367 .658 .885 90 1970 18920 79 88 98 107 0 3713 95 3618 1.258 3554 3459 .795 1.125 .332 .17
2 555 336 38 47 517 289 521 357 66 66 483 310 0 0 258 137 260 207 78 66 48 22 806 793 1.789 .559 .642 .635 .559 .349 80 416 .535 .911 100 2140 18910 78 88 115 125 0 601 84 517 1 639 555 1 1.148 0 .2
3 182 97 38 50 144 47 180 98 41 53 142 48 0 0 53 22 12 27 100 78 100 42 191 190 3.064 .326 .338 .342 .322 .161 52 312 .32 .685 90 2290 18920 79 88 130 139 0 174 89 84 .584 175 86 1.712 .605 -.776 -.725
4 2245 2012 40 53 2205 1959 2643 2214 43 53 2603 2161 0 0 1332 1058 11 13 100 100 100 100 4164 4764 1.126 .888 .83 1.009 .906 .452 80 386 .834 .945 100 2460 18920 79 89 147 157 0 3600 95 3505 1.59 3962 3867 .629 1.486 .669 .571
5 5059 1075 41 52 5018 1023 5363 1083 43 54 5322 1031 0 0 2166 353 12 16 100 100 100 100 6041 6353 4.905 .204 .194 .279 .202 .441 80 420 .187 .921 100 2620 18900 77 87 163 173 0 1924 93 1831 .365 1938 1845 2.741 .347 -1.455 -1.528
6 1878 1555 42 57 1836 1498 2033 1630 46 58 1991 1573 0 0 1147 870 26 15 100 100 98 100 3334 3564 1.226 .816 .79 1.04 .795 .726 52 292 .778 .954 80 2790 18900 78 86 181 189 0 2783 102 2681 1.46 2917 2815 .685 1.414 .546 .5
7 716 447 43 57 673 390 742 463 52 61 699 406 0 0 203 92 40 19 100 100 100 100 1063 1105 1.726 .579 .581 .622 .582 .252 52 349 .537 .881 90 2940 18890 76 85 195 204 0 800 102 698 1.037 828 727 .964 1.039 .052 .056
8 337 232 47 56 290 176 356 230 60 61 309 174 0 0 106 72 43 25 100 96 96 96 466 483 1.648 .607 .563 .617 .613 .178 32 220 .59 .885 70 3090 18910 79 86 211 218 0 415 100 315 1.086 412 311 .921 1.008 .119 .011
9 23836 26137 43 58 23793 26079 29739 28354 53 61 29696 28296 0 0 10958 11092 73 20 100 100 100 100 49872 57992 .912 1.096 .953 1.236 1.109 .584 80 477 1.058 .96 100 3270 18900 77 87 228 238 0 46770 104 46666 1.961 50737 50633 .51 1.705 .972 .77
10 666 522 45 60 621 462 748 538 49 62 703 478 0 0 299 220 18 15 100 100 100 100 1083 1181 1.344 .744 .68 .848 .755 .412 52 334 .716 .913 90 3430 18890 76 85 244 253 0 934 107 827 1.331 963 855 .751 1.217 .413 .283
11 13501 8180 45 63 13456 8117 16058 9544 49 65 16013 9481 0 0 5771 3005 17 17 100 100 100 100 21573 25494 1.658 .603 .592 .672 .607 .253 80 500 .562 .947 110 3590 18890 75 86 259 270 0 14637 113 14525 1.079 17078 16965 .926 1.059 .11 .083
12 462 256 41 59 421 197 465 256 44 61 424 197 0 0 154 53 13 18 100 100 100 100 618 621 2.137 .468 .465 .536 .435 .274 52 374 .455 .854 90 3750 18880 75 84 276 285 0 458 106 353 .837 458 353 1.194 .831 -.256 -.266
13 1221 1109 41 68 1180 1041 745 694 45 73 704 626 0 0 1448 1173 16 24 93 87 84 81 2221 1330 1.134 .882 .889 1.401 .837 1.785 32 197 .716 .739 70 3930 18860 74 81 295 302 0 1984 122 1863 1.579 1242 1120 .633 1.591 .659 .67
14 271 175 41 64 230 111 270 172 45 79 229 108 0 0 49 30 21 211 100 0 100 0 341 337 2.072 .483 .472 .494 .477 .14 52 360 .466 .793 90 4070 18890 76 85 308 317 0 313 115 199 .864 308 193 1.158 .844 -.212 -.245
15 372 253 42 63 330 190 335 233 45 66 293 170 0 0 132 81 13 18 100 100 100 100 520 463 1.737 .576 .58 .594 .558 .163 52 353 .589 .869 90 4240 18880 75 84 325 334 0 453 113 340 1.03 417 304 .971 1.038 .043 .054
16 931 780 42 65 889 715 989 817 45 68 947 752 0 0 311 207 13 18 100 100 100 100 1604 1699 1.243 .804 .794 .866 .808 .293 80 400 .753 .922 100 4400 18890 76 86 341 351 0 1396 116 1279 1.439 1462 1346 .695 1.421 .525 .507
17 7936 7158 41 65 7895 7093 9593 8080 44 66 9552 8015 0 0 3410 2529 10 18 100 100 100 100 14988 17567 1.113 .898 .839 1.007 .883 .379 80 400 .838 .951 100 4560 18890 76 86 357 367 0 12809 116 12692 1.608 14458 14342 .622 1.501 .685 .586
18 1267 1168 40 58 1227 1110 1344 1229 42 60 1304 1171 0 0 326 217 10 16 100 100 100 100 2337 2475 1.105 .905 .898 1.03 .909 .668 52 340 .847 .924 90 4720 18880 75 84 373 382 0 2090 104 1986 1.619 2199 2095 .618 1.607 .695 .684
19 1085 888 40 59 1045 829 1239 965 43 62 1199 906 0 0 364 256 10 17 100 100 100 100 1874 2105 1.261 .793 .756 .865 .769 .366 80 407 .746 .918 100 4880 18880 75 85 389 399 0 1589 106 1483 1.42 1727 1621 .704 1.352 .505 .435
20 5936 6574 42 64 5894 6510 7230 7380 44 66 7188 7316 0 0 2498 2466 10 18 100 100 100 100 12404 14504 .905 1.105 1.018 1.18 1.093 .34 80 436 1.048 .946 110 5040 18890 75 86 404 415 0 11764 115 11649 1.976 13206 13091 .506 1.821 .983 .865

Total number of rows: 21504

Table truncated, full table size 4623 Kbytes.




Supplementary data files not provided
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