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Sample GSM173039 Query DataSets for GSM173039
Status Public on Sep 28, 2007
Title SM, coronary artery #2, low
Sample type RNA
 
Channel 1
Source name Stratagene
Organism Homo sapiens
Characteristics Stratagene
LabeledExtract: 35889.Channel_1
Extracted molecule total RNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name SM, coronary artery #2, low
Organism Homo sapiens
Characteristics SM, coronary artery #2, low
LabeledExtract: 35889.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/2002-12/35889.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
1 443 364 170 240 273 124 456 330 171 256 286 90 0 0 97 109 36 82 96 56 96 31 397 376 2.202 .454 .315 .328 .333 2.402 32 166 .695 .67 60 1970 8350 80 86 34 40 0 552 364 188 .688 500 136 1.453 .477 -.539 -1.069
2 4018 8912 172 219 3846 8693 4194 9055 174 226 4022 8836 0 0 1748 3886 34 69 100 100 100 100 12539 12858 .442 2.26 2.197 2.265 2.296 1.252 52 332 2.26 .99 90 2110 8350 78 87 46 55 0 13503 332 13171 3.425 13720 13388 .292 3.329 1.776 1.735
3 2139 975 173 213 1966 762 2070 1033 189 225 1897 820 0 0 460 219 87 66 100 100 100 100 2728 2717 2.58 .388 .432 .38 .37 1.312 12 104 .372 .93 50 2250 8340 79 84 62 67 0 1477 323 1155 .587 1565 1242 1.703 .655 -.768 -.611
4 1499 464 179 207 1320 257 1447 480 243 235 1268 273 0 0 223 103 246 97 100 91 100 75 1577 1541 5.136 .195 .215 .177 .186 1.674 12 104 .182 .76 50 2390 8340 79 84 76 81 0 703 314 389 .295 727 414 3.39 .326 -1.761 -1.616
5 2142 5702 136 153 2006 5549 2069 5431 162 163 1933 5278 0 0 1014 2820 154 70 100 100 100 100 7555 7211 .362 2.766 2.73 2.71 2.754 1.262 52 370 2.799 .98 90 2550 8350 78 87 90 99 0 8639 232 8408 4.191 8229 7997 .239 4.137 2.067 2.049
6 1064 969 122 132 942 837 1100 935 130 143 978 803 0 0 281 353 47 57 100 100 100 100 1779 1781 1.125 .889 .821 .84 .909 1.313 32 166 .93 .96 60 2700 8340 79 85 107 113 0 1468 200 1268 1.346 1417 1217 .743 1.244 .429 .315
7 1941 796 141 151 1800 645 1912 800 148 227 1771 649 0 0 897 350 51 308 100 80 100 53 2445 2420 2.791 .358 .366 .349 .354 1.41 52 268 .348 .94 80 2840 8360 80 88 120 128 0 1206 229 977 .543 1212 983 1.842 .555 -.881 -.849
8 861 683 147 150 714 533 857 677 150 162 710 527 0 0 243 186 53 63 100 100 100 100 1247 1237 1.34 .746 .742 .752 .758 1.346 32 190 .726 .93 70 2990 8350 79 86 135 142 0 1035 227 808 1.131 1026 798 .884 1.125 .178 .169
9 703 905 121 130 582 775 690 840 123 135 569 710 0 0 268 355 34 51 100 100 98 100 1357 1279 .751 1.332 1.248 1.362 1.325 1.375 80 394 1.336 .97 100 3120 8350 78 88 147 157 0 1371 197 1174 2.018 1273 1076 .496 1.891 1.013 .919
10 413 221 150 165 263 56 412 209 178 168 262 44 0 0 94 53 87 58 100 33 83 8 319 306 4.696 .213 .168 .179 .162 2.016 12 99 .285 .56 50 3250 8340 79 84 162 167 0 335 250 85 .323 317 67 3.1 .254 -1.632 -1.975
11 2341 12047 120 135 2221 11912 2402 12385 144 147 2282 12250 0 0 846 4385 93 69 100 100 100 100 14133 14532 .186 5.363 5.368 5.465 5.293 1.223 80 409 5.373 .99 100 3410 8350 78 88 176 186 0 18253 205 18048 8.126 18765 18561 .123 8.133 3.023 3.024
12 5420 3783 123 139 5297 3644 6128 3998 124 146 6005 3859 0 0 2097 1404 32 54 100 100 100 100 8941 9864 1.454 .688 .643 .709 .694 1.34 120 433 .678 .98 120 3570 8350 77 89 191 203 0 5732 211 5521 1.042 6058 5847 .959 .974 .06 -.038
13 943 1831 139 153 804 1678 988 1866 143 159 849 1713 0 0 321 586 30 50 100 100 100 100 2482 2562 .479 2.087 2.018 2.167 2.153 1.271 80 302 2.053 .97 100 3700 8350 78 88 205 215 0 2774 232 2542 3.162 2827 2595 .316 3.057 1.661 1.612
14 470 308 144 158 326 150 486 305 148 162 342 147 0 0 101 81 29 43 99 94 99 78 476 489 2.173 .46 .43 .439 .438 1.81 120 415 .47 .73 120 3860 8350 77 89 220 232 0 467 239 227 .697 462 223 1.434 .651 -.52 -.619
15 472 264 147 163 325 101 493 259 158 172 346 96 0 0 126 71 66 76 96 63 87 23 426 442 3.218 .311 .277 .272 .299 2.155 80 304 .357 .7 110 3990 8350 77 88 233 244 0 400 247 153 .471 392 145 2.124 .42 -1.087 -1.25
16 6995 5322 147 165 6848 5157 7521 5704 157 175 7374 5539 0 0 2010 1567 62 75 100 100 100 100 12005 12913 1.328 .753 .751 .753 .756 1.136 120 391 .757 .99 120 4150 8340 76 88 249 261 0 8064 250 7814 1.141 8642 8392 .876 1.138 .19 .187
17 2276 1543 147 173 2129 1370 2320 1534 154 184 2173 1361 0 0 498 369 54 81 100 100 100 100 3499 3534 1.554 .643 .626 .636 .646 1.192 120 476 .637 .97 130 4290 8340 75 88 262 275 0 2338 262 2076 .975 2324 2062 1.026 .949 -.037 -.076
18 256 199 143 168 113 31 219 190 145 181 76 22 0 0 135 66 33 79 69 23 51 3 144 98 3.645 .274 .289 .574 .536 3.81 52 206 .464 .21 80 4430 8340 78 86 279 287 -50 302 255 47 .416 288 33 2.406 .439 -1.267 -1.189
19 5817 3492 139 160 5678 3332 5571 3170 148 167 5432 3010 0 0 2603 1550 56 65 100 100 100 100 9010 8442 1.704 .587 .554 .589 .599 1.215 80 339 .584 .99 100 4580 8350 78 88 293 303 0 5291 242 5048 .889 4803 4561 1.125 .84 -.17 -.252
20 2328 1299 145 165 2183 1134 2353 1318 148 170 2208 1153 0 0 694 386 40 50 100 100 100 98 3317 3361 1.925 .519 .522 .512 .522 1.192 80 389 .523 .98 110 4730 8340 76 87 307 318 0 1968 250 1718 .787 1997 1747 1.271 .791 -.345 -.338

Total number of rows: 43104

Table truncated, full table size 9528 Kbytes.




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