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Sample GSM173051 Query DataSets for GSM173051
Status Public on Sep 28, 2007
Title SM, coronary artery #3, low
Sample type RNA
 
Channel 1
Source name Stratagene
Organism Homo sapiens
Characteristics Stratagene
LabeledExtract: 35891.Channel_1
Extracted molecule total RNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name SM, coronary artery #3, low
Organism Homo sapiens
Characteristics SM, coronary artery #3, low
LabeledExtract: 35891.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/2002-12/35891.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
1 422 402 137 172 285 230 425 383 141 175 288 211 0 0 81 118 32 70 100 90 100 81 515 499 1.239 .807 .733 .727 .854 1.857 32 220 1.025 .73 70 1870 8470 91 98 23 30 0 600 257 343 1.205 572 315 .83 1.093 .268 .129
2 5074 887 140 163 4934 724 5313 869 143 180 5173 706 0 0 2515 338 31 77 100 98 100 98 5658 5879 6.815 .147 .136 .158 .137 1.597 52 278 .135 .94 80 2010 8470 91 99 37 45 0 1324 243 1081 .219 1297 1054 4.566 .204 -2.191 -2.295
3 1535 670 136 173 1399 497 1488 667 147 184 1352 494 0 0 589 231 80 68 100 100 100 91 1896 1846 2.815 .355 .365 .342 .406 1.9 12 104 .36 .86 50 2150 8470 92 97 52 57 0 1000 258 742 .53 996 737 1.886 .545 -.915 -.875
4 909 380 139 166 770 214 860 369 144 177 721 203 0 0 357 146 31 65 100 81 100 65 984 924 3.598 .278 .282 .247 .251 2.119 32 212 .247 .65 70 2300 8470 91 98 66 73 0 567 248 319 .415 551 303 2.411 .42 -1.269 -1.251
5 1556 4644 137 178 1419 4466 1500 4465 142 183 1363 4287 0 0 923 2573 32 59 100 100 100 98 5885 5650 .318 3.147 3.145 3.333 3.082 1.877 52 337 3.175 .94 90 2440 8480 91 100 79 88 0 6931 266 6666 4.697 6664 6399 .213 4.694 2.232 2.231
6 887 800 133 174 754 626 888 817 138 183 755 643 0 0 234 226 28 63 100 100 100 100 1380 1398 1.204 .83 .852 .8 .776 1.372 32 221 .868 .91 70 2600 8470 91 98 96 103 0 1194 260 934 1.239 1219 960 .807 1.271 .309 .346
7 1874 816 139 177 1735 639 1813 767 148 201 1674 590 0 0 877 355 53 135 100 90 100 84 2374 2264 2.715 .368 .352 .333 .412 1.909 32 214 .341 .88 70 2730 8480 92 99 109 116 0 1218 264 954 .55 1145 881 1.819 .526 -.863 -.927
8 597 857 138 169 459 688 590 836 143 186 452 667 0 0 216 213 43 111 96 100 96 100 1147 1119 .667 1.499 1.476 1.665 1.46 1.825 32 204 1.541 .89 70 2880 8480 92 99 124 131 0 1279 252 1027 2.237 1248 996 .447 2.202 1.162 1.139
9 586 705 127 159 459 546 589 733 134 172 462 574 0 0 162 203 34 72 100 94 100 94 1005 1036 .841 1.19 1.242 1.117 1.17 1.764 52 345 1.287 .85 90 3020 8480 91 100 137 146 0 1052 237 815 1.775 1094 857 .563 1.854 .828 .891
10 351 233 134 169 217 64 351 192 137 169 217 23 0 0 51 94 34 64 100 41 100 16 281 240 3.391 .295 .106 .263 .371 3.204 12 99 .798 .53 50 3180 8470 92 97 155 160 0 348 252 96 .44 287 34 2.272 .158 -1.184 -2.66
11 1783 12013 128 173 1655 11840 1921 12646 136 190 1793 12473 0 0 881 4424 59 105 93 100 92 100 13495 14266 .14 7.154 6.956 7.369 6.533 1.514 80 376 6.914 .95 100 3310 8480 91 101 166 176 0 17930 258 17672 10.678 18875 18616 .094 10.383 3.417 3.376
12 5789 3597 126 157 5663 3440 6294 3808 129 169 6168 3651 0 0 1885 1094 30 63 100 100 100 100 9103 9819 1.646 .607 .592 .606 .604 1.34 80 424 .601 .93 110 3460 8470 89 100 180 191 0 5369 234 5134 .907 5684 5449 1.103 .883 -.141 -.179
13 1108 2587 126 161 982 2426 1217 2681 129 170 1091 2520 0 0 365 715 28 73 100 100 100 100 3408 3611 .405 2.47 2.31 2.613 2.386 1.48 52 289 2.616 .93 90 3600 8470 90 99 195 204 0 3861 240 3621 3.687 4001 3761 .271 3.447 1.883 1.786
14 458 309 126 158 332 151 455 298 130 168 329 140 0 0 94 94 32 68 100 80 100 52 483 469 2.199 .455 .426 .386 .432 2.277 80 387 .509 .57 110 3750 8480 90 101 209 220 0 461 236 225 .679 445 209 1.473 .635 -.559 -.655
15 382 259 122 148 260 111 395 249 168 188 273 101 0 0 83 81 766 522 0 0 0 0 371 374 2.342 .427 .37 .406 .445 2.269 80 363 .449 .55 110 3900 8470 89 100 224 235 0 387 221 166 .637 372 151 1.569 .552 -.65 -.857
16 5942 4727 120 152 5822 4575 6330 5195 124 163 6210 5043 0 0 2181 1598 29 61 100 100 100 100 10397 11253 1.273 .786 .812 .794 .766 1.311 120 413 .775 .95 120 4050 8470 89 101 239 251 0 7055 227 6828 1.173 7754 7527 .853 1.212 .23 .277
17 2064 1577 124 174 1940 1403 2218 1608 131 181 2094 1434 0 0 721 431 33 63 100 100 99 100 3343 3528 1.383 .723 .685 .784 .701 1.713 120 416 .669 .92 120 4200 8470 89 101 254 266 0 2354 260 2094 1.079 2400 2140 .926 1.022 .11 .032
18 176 193 129 175 47 18 145 178 134 185 16 3 0 0 106 76 37 63 36 23 25 5 65 19 2.611 .383 .188 .852 1.23 3.563 52 224 1.109 .25 80 4340 8470 91 99 270 278 -50 288 261 27 .572 266 4 1.749 .28 -.807 -1.837
19 5133 3362 123 175 5010 3187 5270 3690 130 178 5147 3515 0 0 1336 1079 56 62 100 100 100 100 8197 8662 1.572 .636 .683 .617 .642 1.371 52 278 .633 .92 90 4480 8480 91 100 283 292 0 5018 261 4757 .949 5507 5246 1.053 1.019 -.075 .028
20 1761 1066 125 177 1636 889 1721 1106 135 181 1596 929 0 0 481 295 54 60 100 100 100 100 2525 2525 1.84 .543 .582 .532 .542 1.405 80 348 .536 .89 100 4630 8470 90 100 298 308 0 1591 264 1327 .811 1651 1387 1.233 .869 -.302 -.203

Total number of rows: 43104

Table truncated, full table size 9500 Kbytes.




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