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Sample GSM173026 Query DataSets for GSM173026
Status Public on Sep 28, 2007
Title SM, Coronary artery #1
Sample type RNA
 
Channel 1
Source name Stratagene
Organism Homo sapiens
Characteristics Stratagene
LabeledExtract: 34751.Channel_1
Extracted molecule total RNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name Coronary artery SM
Organism Homo sapiens
Characteristics Coronary artery SM
LabeledExtract: 34751.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/2002-11/34751.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 GPL3322
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
1 925 1310 179 185 746 1125 923 1247 181 198 744 1062 0 0 335 394 33 97 96 100 94 100 1871 1806 .663 1.508 1.427 1.753 1.598 1.982 52 300 2.229 .69 90 1460 9210 38 47 73 82 0 1819 257 1563 2.095 1732 1475 .477 1.983 1.067 .987
2 7211 1579 173 186 7038 1393 7744 1673 218 214 7571 1487 0 0 2258 609 307 137 100 92 100 92 8431 9058 5.052 .198 .196 .197 .209 1.599 52 296 .194 .91 90 1590 9200 37 46 86 95 0 2193 258 1935 .275 2324 2065 3.638 .273 -1.863 -1.874
3 3076 1955 162 174 2914 1781 2948 1712 201 255 2786 1538 0 0 1288 747 239 681 100 100 100 59 4695 4324 1.636 .611 .552 .619 .641 1.592 32 212 .575 .85 70 1750 9210 39 46 103 110 0 2715 242 2474 .849 2378 2136 1.178 .767 -.236 -.383
4 1456 869 165 188 1291 681 1431 820 170 229 1266 632 0 0 655 354 41 183 100 92 98 82 1972 1898 1.896 .527 .499 .537 .508 2.193 52 304 .476 .74 90 1890 9210 38 47 116 125 0 1207 261 946 .733 1139 878 1.365 .693 -.449 -.528
5 2290 6130 172 219 2118 5911 2121 6037 201 297 1949 5818 0 0 1027 3209 301 579 97 96 95 93 8029 7767 .358 2.791 2.985 2.496 2.938 2.397 80 396 3.206 .89 110 2040 9210 37 48 130 141 0 8514 304 8210 3.876 8385 8081 .258 4.146 1.955 2.052
6 1151 1374 172 210 979 1164 1110 1345 219 380 938 1135 0 0 439 460 391 1168 92 48 63 0 2143 2073 .841 1.189 1.21 1.232 1.177 1.811 52 232 7.905 .3 80 2180 9210 39 47 146 154 0 1908 292 1617 1.651 1868 1576 .606 1.681 .724 .749
7 2471 1570 162 208 2309 1362 2112 1211 178 229 1950 1003 0 0 1694 1075 124 142 96 96 95 85 3671 2953 1.695 .59 .514 .596 .548 2.393 80 335 .561 .82 100 2330 9220 39 49 160 170 0 2181 289 1892 .819 1682 1393 1.221 .714 -.288 -.485
8 1093 2499 163 239 930 2260 1122 2592 176 257 959 2353 0 0 468 1112 126 145 91 97 88 96 3190 3312 .412 2.43 2.454 2.405 2.342 2.072 80 318 2.648 .86 100 2480 9220 39 49 175 185 0 3471 332 3139 3.375 3600 3268 .296 3.408 1.755 1.769
9 1056 1847 173 283 883 1564 1048 1608 176 312 875 1325 0 0 272 2192 40 176 100 100 100 97 2447 2200 .565 1.771 1.514 1.528 1.547 1.689 80 361 6.842 .43 110 2620 9220 38 49 188 199 0 2565 393 2172 2.46 2233 1840 .406 2.103 1.299 1.073
10 1048 3094 187 303 861 2791 1010 1524 202 386 823 1221 0 0 372 7437 71 658 100 87 100 46 3652 2044 .308 3.242 1.484 1.718 1.453 2.348 32 195 27.662 .31 70 2760 9200 38 45 204 211 0 4297 421 3876 4.502 2117 1696 .222 2.061 2.171 1.043
11 1861 12212 171 294 1690 11918 1878 11708 187 701 1707 11414 0 0 393 3042 72 2642 100 100 100 98 13608 13121 .142 7.052 6.687 7.075 6.551 1.292 80 357 8.764 .86 110 2920 9220 38 49 218 229 0 16961 408 16553 9.795 16261 15853 .102 9.287 3.292 3.215
12 7962 8678 166 268 7796 8410 8393 8427 174 613 8227 8159 0 0 4010 6730 59 2430 95 87 95 74 16206 16386 .927 1.079 .992 1.049 .99 2.359 120 439 1.847 .59 130 3060 9220 37 50 231 244 0 12053 372 11681 1.498 11704 11332 .667 1.377 .583 .462
13 1549 2208 162 279 1387 1929 1553 2219 168 549 1391 1940 0 0 337 585 52 2195 100 30 100 0 3316 3331 .719 1.391 1.395 1.361 1.409 1.33 80 343 11.26 .32 110 3200 9210 37 48 246 257 0 3067 388 2679 1.932 3082 2694 .518 1.937 .95 .954
14 848 667 159 302 689 365 840 660 170 904 681 358 0 0 217 211 67 3872 100 0 100 0 1054 1039 1.888 .53 .526 .454 .509 1.804 80 382 52.324 .04 110 3350 9210 37 48 261 272 0 926 419 507 .736 917 497 1.359 .73 -.443 -.454
15 899 939 159 315 740 624 893 729 188 863 734 414 0 0 161 557 112 4061 100 0 100 0 1364 1148 1.186 .843 .564 .642 .58 2.035 52 262 .003 .03 90 3490 9200 37 46 276 285 0 1304 438 867 1.171 1013 575 .854 .783 .228 -.352
16 18664 24336 148 291 18516 24045 20494 26588 164 357 20346 26297 0 0 6588 9814 84 418 100 98 100 96 42561 46643 .77 1.299 1.292 1.19 1.281 2.226 120 438 1.352 .94 120 3640 9210 37 49 290 302 0 33800 404 33396 1.804 36928 36524 .554 1.795 .851 .844
17 6836 7657 140 291 6696 7366 7187 7806 145 433 7047 7515 0 0 2103 2516 36 778 100 98 99 98 14062 14562 .909 1.1 1.066 1.134 1.113 1.987 120 392 1.16 .88 120 3790 9210 37 49 305 317 0 10635 404 10231 1.528 10842 10438 .655 1.481 .612 .567
18 409 518 145 266 264 252 167 218 148 389 22 -48 0 0 493 635 29 512 48 25 40 11 516 -26 1.048 .955 null 2.261 1.706 4.563 52 188 2.776 .53 80 3930 9200 38 46 321 329 -50 719 369 350 1.326 303 null .754 null .407 null
19 7359 5006 144 290 7215 4716 8055 5618 158 797 7911 5328 0 0 3426 2608 121 3782 94 62 94 10 11931 13239 1.53 .654 .673 .744 .661 3.108 120 392 1.221 .5 120 4080 9210 37 49 334 346 0 6953 403 6550 .908 7803 7400 1.102 .935 -.14 -.096
20 3342 2728 137 296 3205 2432 3384 2788 157 769 3247 2492 0 0 643 813 142 3933 100 1 100 0 5637 5739 1.318 .759 .767 .703 .774 1.552 80 309 14.341 .17 110 4220 9200 36 47 348 359 0 3789 411 3378 1.054 3872 3461 .949 1.066 .076 .092

Total number of rows: 43104

Table truncated, full table size 9511 Kbytes.




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