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Sample GSM94888 Query DataSets for GSM94888
Status Public on Feb 03, 2006
Title intestine mRNAtagging exp. 2
Sample type RNA
 
Channel 1
Source name L4/YA lysate 230 ug amplified no IP
Organism Caenorhabditis elegans
Characteristics L4/YA lysate 230 ug amplified no IP
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name L4/YA lysate 500 ug amplified IP
Organism Caenorhabditis elegans
Characteristics L4/YA lysate 500 ug amplified IP
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: C. elegans, C. elegans
Image: http://smd.stanford.edu/MicroArray/gifs/2003-02/38262.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 Feb 01, 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 GPL3411
Series (1)
GSE4150 mRNA tagging (intestine)

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
1 315 300 71 236 244 64 107 270 73 244 36 34 0 0 462 169 17 93 67 26 51 16 308 70 3.813 .262 .944 .718 .532 4.939 80 454 .278 .52 100 1550 18990 64 74 96 106 -50 1041 819 222 .91 937 118 1.099 3.276 -.136 1.712
2 1636 799 73 238 1563 561 1738 823 75 243 1665 585 0 0 551 290 22 88 100 94 100 86 2124 2250 2.786 .359 .351 .295 .375 2.315 52 333 .374 .84 90 1720 18980 63 72 113 122 0 2772 826 1946 1.245 2855 2029 .803 1.219 .316 .286
3 1231 360 70 230 1161 130 1300 361 73 240 1230 131 0 0 362 105 21 88 100 65 100 34 1291 1361 8.931 .112 .107 .106 .131 2.302 52 284 .132 .31 80 1870 18990 65 73 129 137 0 1249 798 451 .388 1252 454 2.574 .369 -1.364 -1.436
4 1000 470 69 238 931 232 1019 474 70 244 950 236 0 0 223 141 17 91 100 84 100 65 1163 1186 4.013 .249 .248 .229 .241 1.759 52 293 .248 .67 80 2050 18990 65 73 147 155 0 1631 826 805 .864 1644 819 1.157 .862 -.21 -.215
5 10417 2609 64 226 10353 2383 10978 2869 73 239 10914 2643 0 0 4016 1133 50 95 100 100 100 98 12736 13557 4.345 .23 .242 .211 .227 1.404 52 346 .231 .96 90 2200 18990 64 73 161 170 0 9051 784 8267 .799 9953 9169 1.252 .84 -.325 -.251
6 1356 517 61 224 1295 293 1519 439 62 233 1458 215 0 0 735 232 13 88 100 81 100 59 1588 1673 4.42 .226 .147 .204 .236 2.241 32 160 .204 .72 60 2360 18990 66 72 179 185 0 1794 777 1016 .785 1523 746 1.274 .512 -.349 -.967
7 1869 1478 61 241 1808 1237 1860 1494 68 243 1799 1253 0 0 375 397 45 96 100 100 100 100 3045 3052 1.462 .684 .696 .657 .713 1.408 52 364 .693 .93 90 2520 18990 64 73 193 202 0 5127 836 4291 2.374 5183 4347 .421 2.416 1.247 1.273
8 822 384 62 233 760 151 816 396 64 241 754 163 0 0 246 146 17 97 100 61 100 38 911 917 5.033 .199 .216 .195 .25 2.429 52 301 .195 .5 80 2690 18990 65 73 211 219 0 1332 808 524 .689 1374 565 1.451 .75 -.537 -.415
9 2571 650 61 231 2510 419 2698 641 64 240 2637 410 0 0 594 158 21 98 100 96 100 94 2929 3047 5.99 .167 .155 .16 .161 1.578 52 346 .159 .8 90 2850 19000 65 74 226 235 0 2255 801 1454 .579 2224 1422 1.727 .539 -.788 -.891
10 985 343 57 239 928 104 965 336 60 241 908 97 0 0 441 103 16 89 100 55 100 26 1032 1005 8.923 .112 .107 .105 .123 2.692 52 287 .103 .42 80 3010 19000 66 74 243 251 0 1190 829 361 .389 1166 337 2.572 .371 -1.363 -1.432
11 1622 514 57 224 1565 290 1629 485 58 232 1572 261 0 0 655 196 12 86 100 84 100 69 1855 1833 5.397 .185 .166 .177 .19 1.965 52 341 .177 .71 90 3170 18990 64 73 258 267 0 1783 777 1006 .643 1683 905 1.556 .576 -.637 -.796
12 1754 360 59 222 1695 138 1815 355 62 232 1756 133 0 0 475 109 24 92 100 63 100 32 1833 1889 12.283 .081 .076 .086 .093 2.18 52 353 .078 .48 90 3320 19000 65 74 273 282 0 1249 770 479 .282 1232 461 3.541 .263 -1.824 -1.928
13 1753 589 57 233 1696 356 1737 563 65 238 1680 330 0 0 349 152 42 93 100 96 100 86 2052 2010 4.764 .21 .196 .191 .202 1.755 52 371 .188 .75 90 3490 19000 65 74 290 299 0 2043 808 1235 .728 1953 1145 1.373 .681 -.458 -.553
14 1679 445 55 234 1624 211 1822 437 63 237 1767 203 0 0 413 149 44 87 100 82 100 55 1835 1970 7.697 .13 .115 .119 .132 2.227 52 348 .112 .59 90 3660 19000 65 74 307 316 0 1544 812 732 .451 1516 704 2.219 .399 -1.15 -1.327
15 836 416 54 248 782 168 851 411 55 250 797 163 0 0 178 152 8 95 100 65 100 38 950 960 4.655 .215 .205 .189 .213 2.013 52 278 .22 .56 80 3810 19000 66 74 323 331 0 1443 860 583 .745 1426 565 1.342 .71 -.424 -.495
16 1972 480 54 242 1918 238 1982 478 57 247 1928 236 0 0 246 142 19 85 100 88 100 65 2156 2164 8.059 .124 .122 .106 .13 1.984 52 350 .12 .68 90 3970 19000 65 74 338 347 0 1665 840 826 .43 1658 819 2.323 .425 -1.216 -1.236
17 4248 1532 54 242 4194 1290 4407 1531 56 253 4353 1289 0 0 1008 446 17 88 100 100 100 100 5484 5642 3.251 .308 .296 .296 .318 1.426 52 341 .294 .93 90 4140 19000 65 74 355 364 0 5315 840 4475 1.067 5311 4472 .937 1.027 .094 .039
18 2086 565 51 245 2035 320 2085 544 65 251 2034 299 0 0 420 171 106 93 100 92 100 80 2355 2333 6.359 .157 .147 .145 .143 1.692 52 332 .157 .76 90 4290 19000 65 74 370 379 0 1960 850 1110 .546 1887 1037 1.833 .51 -.874 -.972
19 956 499 52 245 904 254 969 472 63 251 917 227 0 0 196 141 106 98 100 86 100 57 1158 1144 3.559 .281 .248 .25 .271 1.708 52 295 .316 .73 80 4450 19010 67 75 387 395 0 1731 850 881 .975 1637 788 1.026 .859 -.037 -.22
20 1064 479 53 237 1011 242 1146 480 55 252 1093 243 0 0 300 135 15 97 100 84 100 63 1253 1336 4.178 .239 .222 .215 .239 1.931 52 349 .215 .65 90 4620 19010 66 75 403 412 0 1662 822 840 .83 1665 843 1.204 .771 -.268 -.375

Total number of rows: 21504

Table truncated, full table size 4694 Kbytes.




Supplementary data files not provided
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