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Sample GSM173071 Query DataSets for GSM173071
Status Public on Sep 28, 2007
Title SM, Hepatic Vein #1
Sample type RNA
 
Channel 1
Source name Stratagene
Organism Homo sapiens
Characteristics Stratagene
LabeledExtract: 34745.Channel_1
Extracted molecule total RNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name HV #1 SM
Organism Homo sapiens
Characteristics HV #1 SM
LabeledExtract: 34745.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/2002-11/34745.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 GPL3268
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
1 604 326 336 240 268 86 625 322 342 285 289 82 0 0 172 119 54 354 86 1 80 0 354 371 3.116 .321 .284 .396 .493 3.228 52 315 60.472 .03 90 2000 8440 87 96 111 120 0 453 333 119 .446 447 114 2.244 .394 -1.166 -1.343
2 1199 575 329 227 870 348 1269 547 334 257 940 320 0 0 366 177 59 170 97 85 97 45 1218 1260 2.5 .4 .34 .364 .387 1.877 80 407 .361 .7 100 2120 8440 87 97 123 133 0 799 315 483 .556 760 444 1.8 .473 -.848 -1.081
3 1215 524 328 199 887 325 1314 467 328 219 986 268 0 0 457 198 48 102 96 87 96 65 1212 1254 2.729 .366 .272 .331 .378 2.176 32 233 .302 .64 70 2290 8440 88 95 141 148 0 728 276 451 .509 649 372 1.965 .378 -.975 -1.405
4 1178 360 346 219 832 141 1180 340 352 230 834 121 0 0 113 82 55 87 100 75 100 33 973 955 5.901 .169 .145 .145 .146 1.921 12 104 .303 .3 50 2430 8440 89 94 156 161 0 500 304 196 .235 472 168 4.249 .202 -2.087 -2.311
5 999 1422 334 238 665 1184 1034 1463 333 276 700 1225 0 0 448 764 48 163 87 90 87 84 1849 1925 .562 1.78 1.75 1.586 1.602 3.04 32 173 2.045 .75 60 2580 8440 89 95 171 177 0 1975 331 1644 2.473 2032 1701 .404 2.431 1.306 1.281
6 438 463 343 246 95 217 386 358 341 276 43 112 0 0 169 366 47 142 43 37 37 25 312 155 .438 2.284 2.605 1.558 1.122 4.364 32 166 .034 .09 60 2730 8440 89 95 186 192 0 643 342 301 3.173 497 156 .315 3.618 1.666 1.855
7 1521 684 325 218 1196 466 1594 709 325 234 1269 491 0 0 640 313 48 91 100 84 100 71 1662 1760 2.567 .39 .387 .374 .387 1.916 32 161 .389 .8 60 2850 8440 89 95 198 204 0 950 303 647 .541 985 682 1.848 .537 -.886 -.896
8 856 316 339 192 517 124 839 306 348 203 500 114 0 0 136 67 97 72 100 75 100 33 641 614 4.169 .24 .228 .207 .212 2.118 12 104 .319 .39 50 2990 8440 89 94 212 217 0 439 267 172 .333 425 158 3.002 .317 -1.586 -1.659
9 685 487 304 204 381 283 754 450 317 227 450 246 0 0 258 136 70 101 84 94 75 73 664 696 1.346 .743 .547 .793 .606 2.673 52 281 .75 .37 80 3150 8450 89 97 227 235 0 676 283 393 1.032 625 342 .969 .759 .045 -.397
10 439 539 301 233 138 306 499 379 308 250 198 146 0 0 185 371 51 106 71 65 59 34 444 344 .451 2.217 .737 .884 .601 5.743 32 138 .169 .31 60 3300 8430 88 94 243 249 0 749 324 425 3.08 526 203 .325 1.024 1.623 .034
11 1369 15358 320 223 1049 15135 1448 18364 323 337 1128 18141 0 0 749 7982 58 742 83 98 81 92 16184 19269 .069 14.428 16.082 13.359 12.768 1.611 80 419 14.024 .92 100 3420 8440 87 97 253 263 0 21331 310 21021 20.039 25506 25196 .05 22.337 4.325 4.481
12 2958 2770 311 227 2647 2543 3412 2937 318 328 3101 2710 0 0 1657 1276 56 481 87 96 87 81 5190 5811 1.041 .961 .874 .947 .895 1.523 32 219 .887 .92 70 3580 8430 87 94 270 277 0 3847 315 3532 1.334 4079 3764 .749 1.214 .416 .279
13 660 1241 313 227 347 1014 704 1303 318 249 391 1076 0 0 185 363 47 102 90 100 84 96 1361 1467 .342 2.922 2.752 3.426 3.007 1.93 32 195 3.08 .8 70 3730 8440 88 95 285 292 0 1724 315 1408 4.059 1810 1494 .246 3.822 2.021 1.934
14 944 461 318 230 626 231 910 458 321 242 592 228 0 0 377 147 50 101 96 77 95 57 857 820 2.71 .369 .385 .362 .38 2.015 80 394 .321 .68 100 3860 8430 86 96 297 307 0 640 319 321 .513 636 317 1.951 .535 -.964 -.903
15 388 448 302 230 86 218 381 316 308 251 79 86 0 0 119 425 50 109 61 42 40 26 304 165 .394 2.535 1.089 .737 .912 5.115 52 299 .044 .13 90 4010 8440 87 96 312 321 0 622 319 303 3.521 439 119 .284 1.512 1.816 .596
16 3299 3517 297 235 3002 3282 2565 2879 300 252 2268 2644 0 0 2058 2613 49 113 98 96 98 90 6284 4912 .915 1.093 1.166 .885 1.011 2.434 80 378 1.209 .9 100 4180 8430 86 96 329 339 0 4885 326 4558 1.518 3999 3672 .659 1.619 .603 .695
17 2583 2647 311 247 2272 2400 2870 2846 315 310 2559 2599 0 0 824 798 53 334 98 96 97 93 4672 5158 .947 1.056 1.016 1.111 1.024 1.733 80 443 1.049 .91 110 4300 8440 86 97 340 351 0 3676 343 3333 1.467 3953 3610 .682 1.411 .553 .496
18 373 1487 314 253 59 1234 366 1055 313 333 52 802 0 0 102 1435 38 319 58 66 33 58 1293 854 .048 20.915 15.423 10.511 8.975 3.241 12 63 51.511 .16 40 4470 8470 93 97 361 365 -100 2065 351 1714 29.049 1465 1114 .034 21.421 4.86 4.421
19 3265 1588 320 256 2945 1332 3655 1645 330 305 3335 1389 0 0 1486 842 115 292 95 92 93 80 4277 4724 2.211 .452 .416 .444 .417 1.702 80 376 .434 .84 100 4590 8430 86 96 370 380 0 2206 356 1850 .628 2285 1929 1.592 .578 -.671 -.79
20 2079 1403 333 260 1746 1143 2180 1452 352 297 1847 1192 0 0 647 481 140 168 96 93 96 91 2889 3039 1.528 .655 .645 .622 .618 1.656 80 391 .634 .88 110 4730 8430 85 96 383 394 0 1949 361 1588 .909 2017 1656 1.1 .896 -.137 -.158

Total number of rows: 43008

Table truncated, full table size 9441 Kbytes.




Supplementary data files not provided
Processed data not provided for this record
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