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Sample GSM173053 Query DataSets for GSM173053
Status Public on Sep 28, 2007
Title SM, bronchial #2 , low
Sample type RNA
 
Channel 1
Source name Stratagene
Organism Homo sapiens
Characteristics Stratagene
LabeledExtract: 36009.Channel_1
Extracted molecule total RNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name SM, bronchial #2 , low
Organism Homo sapiens
Characteristics SM, bronchial #2 , low
LabeledExtract: 36009.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/2002-12/36009.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 GPL3341
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
1 542 288 221 129 321 159 546 279 230 137 325 150 0 0 78 67 51 49 100 96 100 81 480 475 2.019 .495 .462 .465 .465 1.627 32 145 .531 .77 60 1520 8670 192 198 89 95 0 339 152 187 .583 328 176 1.716 .543 -.779 -.881
2 3413 3361 223 128 3190 3233 3719 3617 236 145 3496 3489 0 0 1347 1513 88 106 100 98 98 98 6423 6985 .987 1.013 .998 .953 1.01 1.309 52 321 1.045 .98 90 1650 8650 188 197 100 109 0 3954 151 3804 1.192 4255 4105 .839 1.174 .254 .232
3 2068 797 224 129 1844 668 2179 791 237 150 1955 662 0 0 950 371 100 123 100 93 100 84 2512 2617 2.76 .362 .339 .367 .383 1.42 32 218 .356 .96 70 1800 8650 189 196 116 123 0 938 152 786 .426 931 779 2.346 .398 -1.23 -1.328
4 1155 418 221 130 934 288 1057 402 225 135 836 272 0 0 431 148 40 47 100 96 100 90 1222 1108 3.243 .308 .325 .283 .293 1.655 32 204 .292 .9 70 1950 8660 190 197 131 138 0 492 153 339 .363 473 320 2.757 .383 -1.463 -1.385
5 1532 3476 222 128 1310 3348 1417 3186 375 176 1195 3058 0 0 733 1873 1494 434 35 97 2 91 4658 4253 .391 2.556 2.559 2.54 2.562 1.352 80 412 2.596 .98 100 2100 8650 188 198 145 155 0 4089 151 3939 3.007 3748 3598 .333 3.011 1.588 1.59
6 877 464 228 132 649 332 878 417 226 136 650 285 0 0 147 134 36 44 100 100 100 100 981 935 1.955 .512 .438 .486 .471 1.341 32 198 .52 .9 70 2240 8650 189 196 160 167 0 546 155 391 .602 491 335 1.662 .516 -.733 -.955
7 2362 786 225 129 2137 657 2403 778 227 135 2178 649 0 0 850 255 35 48 100 98 100 98 2794 2827 3.253 .307 .298 .3 .315 1.372 52 330 .3 .96 90 2390 8650 188 197 174 183 0 925 152 773 .362 915 764 2.765 .351 -1.467 -1.512
8 887 506 229 137 658 369 845 477 239 148 616 340 0 0 252 172 62 66 100 100 100 96 1027 956 1.783 .561 .552 .539 .532 1.433 32 206 .576 .9 70 2520 8650 189 196 188 195 0 595 161 434 .66 561 400 1.516 .649 -.6 -.623
9 698 337 225 127 473 210 692 353 232 137 467 226 0 0 182 118 59 57 100 88 95 76 683 693 2.252 .444 .484 .404 .469 1.906 80 410 .441 .83 100 2680 8650 188 198 203 213 0 396 149 247 .522 415 266 1.915 .569 -.937 -.813
10 518 221 217 134 301 87 516 191 218 140 299 57 0 0 106 86 36 86 100 31 100 25 388 356 3.46 .289 .191 .234 .226 2.612 32 198 .336 .56 70 2820 8650 189 196 218 225 0 260 158 102 .34 225 67 2.941 .224 -1.556 -2.157
11 1788 7873 216 135 1572 7738 1652 7714 227 149 1436 7579 0 0 523 2549 79 92 100 100 100 100 9310 9015 .203 4.922 5.278 4.929 4.864 1.181 52 336 5.046 .98 90 2970 8650 188 197 232 241 0 9262 159 9104 5.791 9075 8916 .173 6.209 2.534 2.634
12 5168 4475 215 126 4953 4349 5052 4537 225 147 4837 4411 0 0 3605 3171 57 89 98 100 98 100 9302 9248 1.139 .878 .912 .931 .902 1.432 52 312 .876 .99 90 3120 8650 188 197 247 256 0 5265 148 5116 1.033 5338 5189 .968 1.073 .047 .101
13 1073 1573 214 133 859 1440 1056 1576 222 142 842 1443 0 0 308 529 63 61 100 100 100 100 2299 2285 .597 1.676 1.714 1.634 1.642 1.422 80 389 1.713 .96 100 3270 8650 188 198 262 272 0 1851 156 1694 1.972 1854 1698 .507 2.016 .98 1.012
14 639 341 217 136 422 205 640 330 222 139 423 194 0 0 130 92 43 47 100 100 100 92 627 617 2.059 .486 .459 .461 .458 1.567 52 288 .504 .81 90 3410 8650 188 197 276 285 0 401 160 241 .572 388 228 1.75 .54 -.807 -.89
15 719 312 217 134 502 178 715 316 222 148 498 182 0 0 155 103 42 113 100 67 100 30 680 680 2.82 .355 .365 .307 .34 1.813 80 346 .371 .82 100 3560 8650 188 198 291 301 0 367 158 209 .417 372 214 2.397 .43 -1.261 -1.218
16 9110 8529 213 131 8897 8398 9385 8656 221 141 9172 8525 0 0 3316 3524 83 63 100 100 100 100 17295 17697 1.059 .944 .929 .911 .972 1.287 80 400 .963 .99 110 3700 8650 187 198 304 315 0 10034 154 9880 1.11 10184 10029 .901 1.093 .151 .129
17 2545 2170 204 141 2341 2029 2367 2116 211 146 2163 1975 0 0 820 846 42 53 100 100 100 100 4370 4138 1.154 .867 .913 .845 .861 1.278 52 242 .884 .98 80 3840 8650 189 197 320 328 0 2553 166 2387 1.02 2489 2324 .981 1.074 .028 .103
18 265 168 207 129 58 39 231 152 208 142 24 23 0 0 108 60 35 51 44 28 23 13 97 47 1.487 .672 .958 .741 .588 8.753 52 275 .107 .04 80 3990 8640 188 196 335 343 -50 198 152 46 .791 179 27 1.264 1.127 -.338 .173
19 5304 3233 207 137 5097 3096 5477 3426 210 146 5270 3289 0 0 1984 1258 38 52 100 100 100 100 8193 8559 1.646 .607 .624 .602 .601 1.174 80 359 .605 .99 100 4150 8650 188 198 350 360 0 3804 161 3642 .715 4031 3869 1.399 .734 -.485 -.446
20 2164 1371 202 138 1962 1233 2080 1279 205 143 1878 1141 0 0 857 634 36 48 100 100 100 100 3195 3019 1.591 .628 .608 .601 .617 1.313 80 322 .645 .97 100 4290 8650 188 198 364 374 0 1613 162 1451 .739 1505 1342 1.353 .715 -.436 -.484

Total number of rows: 43104

Table truncated, full table size 9670 Kbytes.




Supplementary data files not provided
Raw data included within Sample table
Processed data not provided for this record

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