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Sample GSM173073 Query DataSets for GSM173073
Status Public on Sep 28, 2007
Title SM, Popliteal Vein
Sample type RNA
 
Channel 1
Source name Stratagene
Organism Homo sapiens
Characteristics Stratagene
LabeledExtract: 34747.Channel_1
Extracted molecule total RNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name Popliteal Vein SM
Organism Homo sapiens
Characteristics Popliteal Vein SM
LabeledExtract: 34747.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/2002-11/34747.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
1 577 262 452 342 125 -80 496 217 517 374 44 -125 0 0 308 147 260 142 21 11 11 1 45 -81 null null null 1.035 1.127 4.135 52 245 .302 .62 80 1560 8150 59 67 68 76 -50 364 475 -111 null 301 null null null null null
2 1793 701 452 314 1341 387 1804 671 509 341 1352 357 0 0 386 239 254 162 100 80 98 57 1728 1709 3.465 .289 .264 .238 .274 1.997 52 268 .337 .77 80 1690 8140 58 66 81 89 0 974 436 538 .401 932 496 2.495 .367 -1.319 -1.447
3 2007 649 463 228 1544 421 2134 638 465 250 1671 410 0 0 553 266 65 101 100 84 100 75 1965 2081 3.667 .273 .245 .254 .296 1.823 32 229 .292 .81 70 1880 8150 59 66 100 107 0 901 317 585 .379 886 569 2.641 .341 -1.401 -1.553
4 1579 463 449 216 1130 247 1541 447 446 228 1092 231 0 0 257 82 67 91 100 100 100 75 1377 1323 4.575 .219 .212 .215 .222 1.444 12 104 .247 .78 50 2020 8150 60 65 115 120 0 643 300 343 .304 621 321 3.294 .294 -1.72 -1.767
5 1481 1516 432 272 1049 1244 1577 1566 439 292 1145 1294 0 0 663 838 74 117 84 87 84 84 2293 2439 .843 1.186 1.13 1.16 1.28 2.06 32 167 1.259 .9 60 2170 8160 61 67 130 136 0 2106 378 1728 1.647 2175 1797 .607 1.57 .72 .65
6 534 860 435 266 99 594 512 496 431 306 77 230 0 0 226 841 64 162 53 62 43 37 693 307 .167 6 2.987 1.47 .929 6.001 32 166 .032 .13 60 2320 8140 59 65 145 151 0 1194 369 825 8.333 689 319 .12 4.149 3.059 2.053
7 2442 1097 435 260 2007 837 2499 1147 435 283 2064 887 0 0 944 488 59 115 100 87 96 87 2844 2951 2.398 .417 .43 .449 .434 2.432 32 172 .412 .84 60 2450 8150 60 66 158 164 0 1524 361 1163 .579 1593 1232 1.726 .597 -.788 -.745
8 964 403 450 227 514 176 956 387 458 240 506 160 0 0 201 137 66 86 100 71 96 40 690 666 2.92 .342 .316 .329 .369 2.439 32 224 .361 .6 70 2600 8150 59 66 172 179 0 560 315 244 .476 538 222 2.103 .439 -1.072 -1.187
9 959 696 461 300 498 396 994 602 475 307 533 302 0 0 380 426 110 119 80 86 78 57 894 835 1.258 .795 .567 .574 .442 3.195 52 336 2.55 .22 90 2740 8150 58 67 185 194 0 967 417 550 1.104 836 419 .905 .787 .143 -.346
10 652 904 451 321 201 583 666 571 461 328 215 250 0 0 268 804 112 101 57 71 48 51 784 465 .345 2.9 1.163 .722 .531 4.782 52 212 .057 .15 80 2890 8150 59 67 201 209 0 1256 446 810 4.028 793 347 .248 1.615 2.01 .692
11 2099 22812 460 316 1639 22496 2248 24952 471 376 1788 24636 0 0 1036 11955 100 304 87 100 83 100 24135 26424 .073 13.725 13.779 13.411 12.812 1.478 80 432 13.592 .94 110 3010 8150 57 68 211 222 0 31683 439 31244 19.063 34656 34217 .052 19.137 4.253 4.258
12 2614 2612 470 296 2144 2316 2280 2265 477 356 1810 1969 0 0 1884 1492 66 284 86 94 82 90 4460 3779 .926 1.08 1.088 1.521 1.068 2.782 52 302 .942 .93 80 3180 8150 59 67 230 238 0 3628 411 3217 1.5 3146 2735 .667 1.511 .585 .595
13 964 1785 468 286 496 1499 1010 1845 471 293 542 1559 0 0 288 531 58 107 87 96 87 96 1995 2101 .331 3.022 2.876 3.058 3.094 1.611 32 190 3.126 .78 70 3330 8150 59 66 245 252 0 2479 397 2082 4.197 2563 2165 .238 3.995 2.07 1.998
14 1335 488 473 294 862 194 1344 446 475 311 871 152 0 0 413 271 61 169 96 48 96 12 1056 1023 4.443 .225 .175 .178 .199 2.233 80 340 .231 .38 100 3460 8140 57 67 257 267 0 678 408 269 .313 619 211 3.199 .242 -1.678 -2.045
15 691 449 468 279 223 170 691 393 473 305 223 114 0 0 195 231 67 157 78 35 75 15 393 337 1.312 .762 .511 .655 .577 3.689 80 327 40.234 .04 100 3580 8140 57 67 269 279 0 624 388 236 1.059 546 158 .944 .71 .082 -.494
16 4272 4683 458 275 3814 4408 4020 4629 460 301 3562 4354 0 0 2844 3341 67 145 97 100 95 97 8222 7916 .865 1.156 1.222 1.132 1.104 1.7 80 372 1.173 .95 100 3750 8140 57 67 286 296 0 6504 382 6122 1.605 6429 6047 .623 1.698 .683 .764
17 3508 3803 441 259 3067 3544 3791 4219 456 290 3350 3960 0 0 1075 1577 137 186 96 93 96 93 6611 7310 .865 1.156 1.182 1.047 1.173 1.708 80 401 1.24 .93 110 3890 8140 56 67 299 310 0 5282 360 4922 1.605 5860 5500 .623 1.642 .682 .715
18 420 665 445 285 -25 380 411 387 466 316 -34 102 0 0 123 710 171 182 7 46 0 36 355 68 null null null 2.99 2.388 4.557 52 234 59.498 .09 80 4040 8140 58 66 316 324 -50 924 396 528 null 538 142 null null null null
19 4982 2713 456 293 4526 2420 5396 2699 467 310 4940 2406 0 0 2061 1123 117 130 100 98 96 98 6946 7346 1.87 .535 .487 .563 .53 1.575 80 417 .521 .95 110 4180 8140 56 67 328 339 0 3768 407 3361 .743 3749 3342 1.347 .676 -.429 -.564
20 3298 2006 465 274 2833 1732 3374 2167 489 302 2909 1893 0 0 868 685 178 147 100 97 100 95 4565 4802 1.636 .611 .651 .557 .603 1.672 80 407 .596 .92 110 4330 8140 56 67 343 354 0 2786 381 2406 .849 3010 2629 1.178 .904 -.236 -.146

Total number of rows: 43008

Table truncated, full table size 9547 Kbytes.




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