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Sample GSM173063 Query DataSets for GSM173063
Status Public on Sep 28, 2007
Title Coronary SM Serum St, 6 hr
Sample type RNA
 
Channel 1
Source name Strategene
Organism Homo sapiens
Characteristics Strategene
LabeledExtract: 45340.Channel_1
Extracted molecule total RNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name Coronary SM Serum St, 6 hr
Organism Homo sapiens
Characteristics Coronary SM Serum St, 6 hr
LabeledExtract: 45340.Channel_2
Extracted molecule total RNA
Extraction protocol not provided
Label Cy5
Label protocol not provided
 
 
Hybridization protocol not provided
Scan protocol not provided
Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 520, 5000; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Jen-Tsan Ashley,,Chi
Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.54; Parameter Scan Time = 11:00:58; Parameter PMT Volts = 600; Parameter Scan Date = 2003-09-27; Parameter Pixel Size = 10; Parameter Laser on time = 125666; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.23; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Jen-Tsan Ashley,,Chi
Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.54; Parameter Scan Time = 11:00:58; Parameter PMT Volts = 600; Parameter Scan Date = 2003-09-27; Parameter Pixel Size = 10; Parameter Laser on time = 490767; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.89; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Jen-Tsan Ashley,,Chi
Description Simple annotation: Smooth muscle cells, Serum stimulation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-10/45340.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 GPL3526
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
1 368 437 106 156 262 281 359 446 114 161 253 290 0 0 99 127 87 44 96 100 82 96 543 543 .932 1.073 1.146 1.043 1.119 1.862 52 355 1.119 .575 90 1440 6080 103 112 87 96 0 821 293 528 2.015 838 545 .496 2.154 1.011 1.107
2 4290 888 107 165 4183 723 3699 776 116 169 3592 611 0 0 2599 503 84 47 100 93 100 91 4906 4203 5.786 .173 .17 .167 .184 1.689 80 374 .167 .842 100 1580 6080 103 113 101 111 0 1669 310 1359 .325 1458 1148 3.079 .32 -1.622 -1.646
3 4330 2193 105 170 4225 2023 4349 2168 111 174 4244 1998 0 0 1052 488 29 48 100 100 100 100 6248 6242 2.088 .479 .471 .481 .476 1.26 80 418 .454 .886 110 1720 6090 103 114 114 125 0 4121 319 3801 .9 4074 3754 1.111 .885 -.152 -.177
4 1012 393 111 167 901 226 923 393 391 293 812 226 0 0 389 158 2413 798 0 0 0 0 1127 1038 3.987 .251 .278 .228 .256 1.874 32 219 .256 .655 70 1870 6070 103 110 131 138 0 738 314 425 .471 738 425 2.122 .523 -1.085 -.935
5 1182 3355 116 193 1066 3162 1238 3395 494 487 1122 3202 0 0 545 1868 2536 1121 0 78 0 71 4228 4324 .337 2.966 2.854 2.434 2.967 2.184 52 339 .489 .347 90 2040 6080 103 112 147 156 0 6304 363 5941 5.574 6379 6017 .179 5.362 2.479 2.423
6 504 800 114 188 390 612 482 825 115 192 368 637 0 0 147 284 25 52 100 100 100 100 1002 1005 .637 1.569 1.731 1.481 1.794 1.565 32 150 1.704 .775 60 2160 6090 106 112 161 167 0 1503 353 1150 2.949 1550 1197 .339 3.253 1.56 1.702
7 2178 1132 109 187 2069 945 2159 1177 114 195 2050 990 0 0 805 478 40 52 100 98 100 96 3014 3040 2.189 .457 .483 .419 .444 1.685 52 313 .459 .811 90 2310 6080 103 112 174 183 0 2127 351 1776 .858 2212 1860 1.165 .907 -.221 -.14
8 972 893 109 208 863 685 936 898 112 215 827 690 0 0 248 202 27 59 100 100 100 100 1548 1517 1.26 .794 .834 .793 .786 1.377 80 342 .767 .821 100 2450 6090 104 114 188 198 0 1678 391 1287 1.491 1687 1297 .67 1.568 .577 .649
9 585 590 111 218 474 372 579 563 113 223 468 345 0 0 178 215 25 54 100 93 100 85 846 813 1.274 .785 .737 .683 .771 1.992 80 315 .871 .711 100 2600 6080 103 113 203 213 0 1109 410 699 1.475 1058 648 .678 1.385 .56 .47
10 666 1428 113 234 553 1194 680 1292 116 240 567 1058 0 0 236 996 38 71 100 93 97 87 1747 1625 .463 2.159 1.866 1.604 1.856 2.687 80 317 3.358 .591 100 2740 6080 103 113 217 227 0 2683 440 2244 4.057 2428 1988 .246 3.506 2.02 1.81
11 880 16933 116 254 764 16679 896 18378 144 284 780 18124 0 0 528 9876 158 229 82 100 72 100 17443 18904 .046 21.831 23.236 20.356 21.531 1.866 80 355 23.572 .521 110 2890 6100 104 115 231 242 0 31817 477 31340 41.021 34533 34055 .024 43.661 5.358 5.448
12 10995 9470 119 255 10876 9215 10446 9343 151 299 10327 9088 0 0 5392 4450 162 262 100 100 100 100 20091 19415 1.18 .847 .88 .846 .892 1.596 80 360 .83 .835 110 3030 6090 103 114 245 256 0 17794 479 17315 1.592 17556 17076 .628 1.654 .671 .726
13 1129 2903 115 233 1014 2670 1195 3030 295 368 1080 2797 0 0 524 1427 1749 1243 7 83 0 60 3684 3877 .38 2.633 2.59 2.521 2.723 2.257 80 324 .953 .577 100 3180 6090 104 114 261 271 0 5455 438 5017 4.948 5693 5256 .202 4.866 2.307 2.283
14 437 666 110 232 327 434 427 662 270 350 317 430 0 0 97 148 1648 1172 0 0 0 0 761 747 .753 1.327 1.356 1.305 1.253 1.414 80 365 .688 .472 100 3320 6090 104 114 275 285 0 1251 436 815 2.494 1244 808 .401 2.549 1.318 1.35
15 503 461 111 233 392 228 477 403 115 236 366 170 0 0 154 194 30 58 100 84 100 67 620 536 1.719 .582 .464 .53 .507 1.803 52 301 .75 .582 90 3460 6080 103 112 289 298 0 866 438 428 1.093 757 319 .915 .873 .128 -.196
16 6554 8682 110 234 6444 8448 6539 8792 115 243 6429 8558 0 0 2823 3869 36 65 100 100 100 100 14892 14987 .763 1.311 1.331 1.284 1.303 1.317 80 379 1.348 .913 110 3620 6090 103 114 304 315 0 16314 440 15874 2.463 16520 16081 .406 2.501 1.301 1.323
17 1742 2276 104 228 1638 2048 1586 2122 114 245 1482 1894 0 0 850 1039 53 91 100 100 100 100 3686 3376 .8 1.25 1.278 1.283 1.309 1.454 80 326 1.248 .882 100 3760 6090 104 114 319 329 0 4277 428 3848 2.349 3987 3559 .426 2.401 1.232 1.264
18 704 471 91 207 613 264 706 446 99 213 615 239 0 0 182 144 39 60 100 96 100 90 877 854 2.322 .431 .389 .381 .411 2.025 80 316 .413 .494 100 3900 6080 103 113 333 343 0 885 389 496 .809 838 449 1.236 .73 -.305 -.454
19 2903 1903 110 243 2793 1660 2617 1745 125 258 2507 1502 0 0 1687 981 82 87 99 98 98 97 4453 4009 1.683 .594 .599 .594 .587 1.777 120 463 .572 .893 120 4050 6090 103 115 347 359 0 3576 457 3119 1.117 3279 2822 .895 1.126 .159 .171
20 2985 2484 117 223 2868 2261 2847 2350 121 232 2730 2127 0 0 1006 750 34 60 100 100 100 100 5129 4857 1.268 .788 .779 .797 .775 1.336 80 376 .77 .888 110 4200 6090 103 114 362 373 0 4667 419 4248 1.481 4416 3997 .675 1.464 .567 .55

Total number of rows: 41472

Table truncated, full table size 9123 Kbytes.




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