NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM173038 Query DataSets for GSM173038
Status Public on Sep 28, 2007
Title SM, coronary artery #2
Sample type RNA
 
Channel 1
Source name Stratagene
Organism Homo sapiens
Characteristics Stratagene
LabeledExtract: 35888.Channel_1
Extracted molecule total RNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name SM, coronary artery #2
Organism Homo sapiens
Characteristics SM, coronary artery #2
LabeledExtract: 35888.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/2002-12/35888.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
1 380 393 143 143 237 250 381 366 146 152 238 223 0 0 107 163 29 51 98 88 94 80 487 461 .948 1.055 .937 .95 1.105 2.658 52 276 1.258 .74 80 1890 8310 75 83 25 33 0 524 191 333 1.406 488 297 .711 1.249 .492 .321
2 4429 9296 143 148 4286 9148 4569 9233 145 159 4426 9085 0 0 1527 3550 27 59 100 100 100 100 13434 13511 .469 2.134 2.053 2.077 2.125 1.464 52 315 2.24 .96 90 2030 8300 73 82 38 47 0 12395 197 12197 2.846 12311 12113 .351 2.737 1.509 1.453
3 1662 1003 141 142 1521 861 1602 937 141 151 1461 795 0 0 654 369 25 56 100 100 100 100 2382 2256 1.767 .566 .544 .573 .59 1.511 32 165 .537 .9 60 2180 8310 76 82 55 61 0 1337 189 1148 .755 1249 1060 1.325 .726 -.406 -.463
4 928 401 147 150 781 251 800 365 149 165 653 215 0 0 486 185 37 65 100 88 100 71 1032 868 3.112 .321 .329 .311 .296 1.879 52 256 .308 .82 80 2320 8310 75 83 68 76 0 535 200 335 .429 487 287 2.334 .439 -1.223 -1.188
5 1887 6391 140 151 1747 6240 1936 6087 145 162 1796 5936 0 0 864 3265 35 63 100 100 100 100 7987 7732 .28 3.572 3.305 3.327 3.716 1.487 52 310 3.773 .95 90 2460 8310 74 83 81 90 0 8521 201 8320 4.762 8116 7915 .21 4.407 2.252 2.14
6 764 777 144 153 620 624 796 797 146 158 652 644 0 0 257 268 27 51 96 100 96 96 1244 1296 .994 1.006 .988 1.015 .987 1.48 52 255 1.023 .93 80 2620 8300 74 82 98 106 0 1036 204 832 1.342 1063 859 .745 1.317 .424 .397
7 1432 1005 138 147 1294 858 1284 971 143 156 1146 824 0 0 635 415 26 55 100 100 100 100 2152 1970 1.508 .663 .719 .657 .708 1.576 52 300 .621 .92 90 2750 8320 75 84 110 119 0 1340 196 1144 .884 1295 1099 1.131 .959 -.178 -.061
8 591 503 134 138 457 365 600 507 136 148 466 369 0 0 131 141 25 53 100 100 100 96 822 835 1.252 .799 .792 .762 .825 1.525 52 299 .824 .87 90 2910 8310 74 83 126 135 0 671 184 487 1.065 676 492 .939 1.056 .091 .078
9 622 1194 138 144 484 1050 654 1225 141 150 516 1081 0 0 152 284 28 50 100 100 100 100 1534 1597 .461 2.169 2.095 2.171 2.179 1.483 52 276 2.291 .92 90 3040 8310 74 83 139 148 0 1592 192 1400 2.893 1633 1441 .346 2.793 1.532 1.482
10 297 216 138 141 159 75 301 197 143 148 163 56 0 0 86 83 37 53 90 50 80 25 234 219 2.12 .472 .344 .497 .546 2.864 52 242 .655 .54 80 3190 8310 75 83 155 163 0 288 188 100 .629 263 75 1.59 .458 -.669 -1.126
11 1648 16263 139 147 1509 16116 1794 17386 142 154 1655 17239 0 0 590 5684 30 57 100 100 100 100 17625 18894 .094 10.68 10.416 10.975 10.306 1.437 80 390 10.834 .96 110 3330 8310 73 84 167 178 0 21684 196 21488 14.24 23181 22985 .07 13.888 3.832 3.796
12 6857 7921 147 167 6710 7754 7129 8554 222 247 6982 8387 0 0 1380 2217 844 586 100 100 100 100 14464 15369 .865 1.156 1.201 1.111 1.164 1.402 80 421 1.206 .96 110 3480 8300 72 83 182 193 0 10561 223 10339 1.541 11405 11183 .649 1.602 .624 .68
13 954 2557 153 197 801 2360 965 2605 230 230 812 2408 0 0 275 656 896 188 37 100 0 97 3161 3220 .339 2.946 2.966 2.994 2.915 1.466 80 359 1.139 .35 100 3630 8310 74 84 198 208 0 3409 263 3147 3.928 3473 3211 .255 3.954 1.974 1.983
14 412 317 148 179 264 138 399 314 152 184 251 135 0 0 90 65 34 70 100 82 98 45 402 386 1.913 .523 .538 .498 .493 1.92 80 384 .577 .61 110 3780 8300 72 83 212 223 0 423 239 184 .697 419 180 1.435 .717 -.521 -.48
15 504 318 147 166 357 152 510 309 236 236 363 143 0 0 91 91 923 805 0 0 0 0 509 506 2.349 .426 .394 .339 .372 2.332 80 296 .473 .7 100 3920 8310 74 84 227 237 0 424 221 203 .568 412 191 1.762 .525 -.817 -.929
16 7400 7993 154 185 7246 7808 7774 8099 221 240 7620 7914 0 0 2364 2674 788 687 100 99 98 99 15054 15534 .928 1.078 1.039 1.069 1.051 1.335 120 407 1.098 .96 120 4070 8300 72 84 241 253 0 10657 247 10411 1.437 10799 10552 .696 1.385 .523 .47
17 2374 2450 147 194 2227 2256 2430 2436 160 210 2283 2242 0 0 558 611 51 89 100 100 100 100 4483 4525 .987 1.013 .982 1.033 1.009 1.448 120 492 1.015 .96 130 4210 8300 71 84 254 267 0 3267 259 3008 1.351 3248 2989 .74 1.309 .434 .389
18 206 202 141 184 65 18 164 193 153 204 23 9 0 0 135 77 52 82 32 21 25 5 83 32 3.611 .277 .391 .822 .85 3.958 52 209 .873 .44 80 4360 8300 74 82 272 280 -50 269 245 24 .369 257 12 2.708 .522 -1.437 -.939
19 4965 3800 140 165 4825 3635 4950 3979 147 175 4810 3814 0 0 1703 1344 41 70 100 100 100 100 8460 8624 1.327 .753 .793 .751 .764 1.369 80 320 .748 .96 100 4500 8310 74 84 285 295 0 5067 220 4847 1.004 5305 5085 .996 1.057 .006 .08
20 1839 1413 149 154 1690 1259 1848 1450 223 208 1699 1296 0 0 474 420 582 435 98 95 86 83 2949 2995 1.342 .745 .763 .719 .742 1.333 80 375 .753 .96 110 4650 8300 72 83 299 310 0 1884 205 1679 .993 1933 1728 1.007 1.017 -.01 .024

Total number of rows: 43104

Table truncated, full table size 9501 Kbytes.




Supplementary data files not provided
Processed data not provided for this record
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap