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Sample GSM173046 Query DataSets for GSM173046
Status Public on Sep 28, 2007
Title SM, uterus #2, low
Sample type RNA
 
Channel 1
Source name Stratagene
Organism Homo sapiens
Characteristics Stratagene
LabeledExtract: 36004.Channel_1
Extracted molecule total RNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name SM, uterus #2, low
Organism Homo sapiens
Characteristics SM, uterus #2, low
LabeledExtract: 36004.Channel_2
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: Smooth muscle cells, Anatomical comparisons
Image: http://smd.stanford.edu/MicroArray/gifs/2002-12/36004.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 Mar 05, 2007
Last update date Sep 28, 2007
Contact name Jen-Tsan Ashley Chi
E-mail(s) jentsan.chi@duke.edu
Phone 919-668-4759
Fax 919-668-4777
Organization name Duke University
Department Duke Institute for Genome Sciences & Policy
Lab CIEMAS 2177A
Street address 101 Science Drive
City Durham
State/province NC
ZIP/Postal code 27710
Country USA
 
Platform ID GPL3341
Series (1)
GSE7195 Smooth Muscle Cells

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
1 698 465 256 128 442 337 686 469 259 136 430 341 0 0 125 136 50 54 100 100 100 96 779 771 1.312 .762 .793 .72 .696 1.503 32 204 .784 .85 70 1570 8120 136 143 93 100 0 727 200 527 1.191 733 533 .839 1.239 .253 .309
2 2619 14774 245 129 2374 14645 2859 15774 253 151 2614 15645 0 0 1472 8328 110 172 90 98 88 97 17019 18259 .162 6.169 5.985 6.289 6.236 1.516 80 358 6.075 .98 100 1720 8130 136 146 107 117 0 23084 202 22883 9.639 24647 24445 .104 9.352 3.269 3.225
3 2345 843 219 133 2126 710 2265 836 239 156 2046 703 0 0 726 287 143 187 100 93 100 90 2836 2749 2.994 .334 .344 .317 .343 1.38 32 172 .361 .93 60 1870 8110 136 142 124 130 0 1317 208 1109 .522 1306 1098 1.916 .537 -.938 -.897
4 1313 373 204 125 1109 248 1232 365 206 126 1028 240 0 0 461 110 47 40 100 96 100 96 1357 1268 4.472 .224 .233 .207 .251 2.049 32 196 .2 .82 70 2020 8120 136 143 138 145 0 583 195 388 .349 570 375 2.862 .365 -1.517 -1.455
5 1606 3508 200 132 1406 3376 1728 3648 205 133 1528 3516 0 0 764 1743 48 42 98 100 98 100 4782 5044 .416 2.401 2.301 2.481 2.381 1.358 80 392 2.415 .96 100 2160 8120 135 145 151 161 0 5481 206 5275 3.752 5700 5494 .267 3.595 1.908 1.846
6 878 530 180 129 698 401 906 539 186 133 726 410 0 0 158 172 38 43 100 100 100 100 1099 1136 1.741 .574 .565 .531 .538 1.457 32 199 .614 .89 70 2310 8110 135 142 167 174 0 828 202 627 .898 842 641 1.114 .882 -.156 -.18
7 2780 1017 179 129 2601 888 2924 1056 183 131 2745 927 0 0 1034 412 38 38 100 98 100 98 3489 3672 2.929 .341 .338 .32 .328 1.486 52 317 .35 .95 90 2440 8110 134 143 179 188 0 1589 202 1388 .533 1650 1448 1.875 .528 -.907 -.922
8 929 1036 186 128 743 908 971 1021 192 130 785 893 0 0 283 253 44 40 100 100 98 100 1651 1678 .818 1.222 1.138 1.303 1.279 1.452 52 239 1.184 .95 80 2600 8120 136 144 196 204 0 1619 200 1419 1.909 1595 1395 .524 1.777 .933 .83
9 731 1875 182 123 549 1752 763 1976 186 127 581 1853 0 0 229 572 38 38 98 100 97 100 2301 2434 .313 3.191 3.189 3.366 3.104 1.464 80 348 3.215 .95 100 2740 8120 135 145 209 219 0 2930 192 2738 4.986 3088 2895 .201 4.983 2.318 2.317
10 505 270 182 129 323 141 494 258 186 136 312 129 0 0 83 78 38 45 100 87 100 75 464 441 2.291 .437 .413 .368 .382 1.97 32 200 .418 .67 70 2890 8110 135 142 225 232 0 422 202 220 .682 403 202 1.466 .646 -.552 -.63
11 2170 1039 185 124 1985 915 2207 1052 188 128 2022 928 0 0 768 357 38 43 100 100 100 100 2900 2950 2.169 .461 .459 .463 .452 1.278 80 359 .451 .97 100 3040 8120 135 145 239 249 0 1623 194 1430 .72 1644 1450 1.388 .717 -.473 -.48
12 5158 3505 188 123 4970 3382 5410 3847 199 134 5222 3724 0 0 2735 1985 78 59 100 100 100 100 8352 8946 1.47 .68 .713 .648 .646 1.291 52 286 .691 .99 90 3170 8110 134 143 252 261 0 5477 192 5284 1.063 6011 5819 .941 1.114 .088 .156
13 1135 2088 192 122 943 1966 1113 1974 202 133 921 1852 0 0 315 545 68 55 100 100 100 100 2909 2773 .48 2.085 2.011 2.139 2.068 1.236 80 404 2.064 .97 110 3330 8120 134 145 267 278 0 3263 191 3072 3.258 3084 2894 .307 3.142 1.704 1.652
14 635 355 192 127 443 228 639 354 197 133 447 227 0 0 129 87 39 42 100 98 100 98 671 674 1.943 .515 .508 .489 .552 1.562 52 279 .499 .84 90 3470 8110 134 143 282 291 0 555 198 356 .804 553 355 1.244 .793 -.314 -.334
15 816 300 202 127 614 173 856 299 208 136 654 172 0 0 168 71 38 46 100 96 100 90 787 826 3.549 .282 .263 .271 .269 1.464 52 277 .277 .82 90 3610 8110 134 143 296 305 0 469 198 270 .44 467 269 2.271 .411 -1.184 -1.283
16 8572 6497 209 125 8363 6372 8870 6708 214 129 8661 6583 0 0 3677 2967 43 47 100 100 100 100 14735 15244 1.312 .762 .76 .727 .76 1.32 80 451 .768 .99 110 3760 8110 133 144 310 321 0 10152 195 9956 1.191 10481 10286 .84 1.188 .252 .248
17 2714 1154 210 125 2504 1029 2616 1168 212 132 2406 1043 0 0 1029 417 47 54 100 100 100 100 3533 3449 2.433 .411 .433 .404 .42 1.193 52 277 .405 .97 90 3910 8110 134 143 326 335 0 1803 195 1608 .642 1825 1630 1.557 .677 -.639 -.562
18 235 159 209 127 26 32 211 144 212 130 2 17 0 0 82 49 45 41 23 36 17 19 58 19 .813 1.231 8.5 .716 .795 4.016 52 246 .62 .37 80 4050 8100 134 142 341 349 -50 248 198 50 1.923 225 27 .52 13.281 .943 3.731
19 6709 3525 207 126 6502 3399 6649 3568 250 154 6442 3442 0 0 2207 1265 233 151 100 100 100 100 9901 9884 1.913 .523 .534 .514 .526 1.139 52 302 .534 .99 90 4190 8110 134 143 354 363 0 5508 197 5311 .817 5575 5378 1.224 .835 -.292 -.26
20 2811 1546 206 126 2605 1420 2781 1444 246 152 2575 1318 0 0 846 567 225 146 100 100 100 96 4025 3893 1.835 .545 .512 .522 .553 1.257 52 324 .562 .97 90 4340 8110 134 143 369 378 0 2416 197 2219 .852 2256 2059 1.174 .8 -.232 -.322

Total number of rows: 43104

Table truncated, full table size 9498 Kbytes.




Supplementary data files not provided
Raw data included within Sample table
Processed data not provided for this record

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