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Sample GSM173043 Query DataSets for GSM173043
Status Public on Sep 28, 2007
Title SM, Brochial #3
Sample type RNA
 
Channel 1
Source name Stratagene
Organism Homo sapiens
Characteristics Stratagene
LabeledExtract: 34767.Channel_1
Extracted molecule total RNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name SM, Bronchial #3
Organism Homo sapiens
Characteristics SM, Bronchial #3
LabeledExtract: 34767.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/2002-11/34767.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
1 808 1130 220 144 588 986 820 1185 225 158 600 1041 0 0 195 499 58 88 96 100 96 96 1574 1641 .596 1.677 1.735 1.578 1.536 2.369 32 194 2.068 .74 70 1500 9200 96 103 54 61 0 1507 192 1315 2.236 1580 1388 .447 2.313 1.161 1.21
2 5954 6255 221 140 5733 6115 5297 5515 225 153 5076 5375 0 0 4409 4740 54 63 95 93 93 91 11848 10451 .938 1.067 1.059 1.036 1.073 3.613 120 475 1.077 .91 120 1640 9220 96 108 66 78 0 8340 187 8153 1.422 7353 7167 .703 1.412 .508 .498
3 4624 3488 233 142 4391 3346 4773 3345 236 153 4540 3203 0 0 2279 1658 46 57 100 100 100 100 7737 7743 1.312 .762 .706 .815 .786 1.663 32 189 .737 .93 70 1790 9220 98 105 83 90 0 4651 189 4461 1.016 4460 4271 .984 .941 .023 -.088
4 2027 1302 235 149 1792 1153 2126 1345 237 152 1891 1196 0 0 832 617 48 51 100 98 100 98 2945 3087 1.554 .643 .632 .618 .631 2.316 52 267 .672 .7 80 1940 9210 97 105 98 106 0 1736 199 1537 .858 1793 1595 1.166 .843 -.221 -.246
5 3515 8215 228 157 3287 8058 3385 8091 235 170 3157 7934 0 0 2013 4561 70 85 97 98 97 98 11345 11091 .408 2.451 2.513 2.336 2.389 2.14 80 388 2.591 .89 110 2090 9220 96 107 111 122 0 10953 209 10744 3.269 10788 10579 .306 3.351 1.709 1.745
6 2310 1788 226 156 2084 1632 2352 1643 231 163 2126 1487 0 0 931 962 47 67 100 100 100 100 3716 3613 1.277 .783 .699 .741 .741 1.979 52 276 .826 .88 90 2230 9210 96 105 126 135 0 2384 208 2176 1.044 2191 1983 .958 .933 .062 -.101
7 3059 2231 235 163 2824 2068 2519 2018 249 300 2284 1855 0 0 2085 1583 78 1061 96 65 96 45 4892 4139 1.366 .732 .812 .662 .673 2.489 80 384 .719 .89 110 2370 9220 96 107 139 150 0 2975 217 2757 .976 2691 2473 1.024 1.083 -.034 .115
8 1599 2690 241 162 1358 2528 1448 2737 251 266 1207 2575 0 0 812 1620 73 982 95 78 92 60 3886 3782 .537 1.862 2.133 1.79 1.894 2.293 80 364 3.029 .72 110 2520 9220 96 107 154 165 0 3587 216 3371 2.482 3649 3433 .403 2.845 1.312 1.508
9 1808 1622 228 149 1580 1473 1898 1634 234 159 1670 1485 0 0 719 857 54 69 100 96 98 96 3053 3155 1.073 .932 .889 .937 .921 1.743 80 367 .995 .85 110 2670 9210 95 106 169 180 0 2163 199 1964 1.243 2179 1980 .804 1.186 .314 .246
10 1107 1228 231 160 876 1068 953 936 234 167 722 776 0 0 502 978 43 64 98 100 98 94 1944 1498 .82 1.219 1.075 1.093 1.095 2.177 52 192 1.632 .81 80 2810 9210 97 105 185 193 0 1637 213 1424 1.626 1248 1035 .615 1.433 .701 .519
11 4950 15528 239 162 4711 15366 5191 15396 243 174 4952 15234 0 0 2640 8981 66 77 99 100 98 96 20077 20186 .307 3.262 3.076 2.684 3.295 3.303 120 355 3.53 .93 120 2960 9220 96 108 198 210 0 20704 216 20488 4.349 20528 20312 .23 4.102 2.121 2.036
12 15681 18832 247 157 15434 18675 15571 18350 254 246 15324 18193 0 0 8365 11552 82 1019 99 92 99 92 34109 33517 .826 1.21 1.187 1.056 1.22 3.3 120 342 1.322 .9 120 3100 9220 96 108 212 224 0 25109 209 24900 1.613 24467 24257 .62 1.583 .69 .663
13 2802 7052 234 151 2568 6901 2752 6623 246 256 2518 6472 0 0 900 2536 83 1113 100 100 100 97 9469 8990 .372 2.687 2.57 2.676 2.774 1.339 80 299 2.841 .93 110 3240 9220 96 107 226 237 0 9403 201 9201 3.583 8831 8629 .279 3.427 1.841 1.777
14 1087 925 238 160 849 765 940 652 246 215 702 492 0 0 508 944 69 374 98 70 94 29 1614 1194 1.11 .901 .701 .753 .737 2.261 120 403 1.732 .56 120 3390 9220 96 108 241 253 0 1233 213 1020 1.201 869 656 .832 .934 .265 -.098
15 1473 1345 267 181 1206 1164 1457 1285 1810 1798 1190 1104 0 0 565 687 6859 6054 0 0 0 0 2370 2294 1.036 .965 .928 .913 .874 1.536 52 191 1.029 .87 80 3530 9210 97 105 257 265 -50 1793 241 1552 1.287 1713 1472 .777 1.237 .364 .307
16 16806 16725 251 167 16555 16558 17796 17455 1151 929 17545 17288 0 0 7386 8143 5108 4169 91 90 80 79 33113 34833 1 1 .985 .975 1.043 2.214 120 427 .975 .89 120 3680 9220 96 108 270 282 0 22300 223 22077 1.334 23273 23051 .75 1.314 .415 .394
17 7411 8523 236 141 7175 8382 7760 8843 241 154 7524 8702 0 0 3446 3796 49 75 98 100 96 100 15557 16226 .856 1.168 1.157 1.351 1.215 2.085 120 355 1.166 .94 120 3830 9220 96 108 285 297 0 11364 188 11176 1.558 11791 11603 .642 1.542 .639 .625
18 369 232 235 138 134 94 260 170 240 158 25 32 0 0 264 209 50 114 40 23 32 13 228 57 1.426 .701 1.28 .646 .547 3.404 52 200 .687 .54 80 3970 9210 97 105 301 309 -50 309 184 125 .935 227 43 1.069 1.707 -.096 .771
19 11926 8758 232 148 11694 8610 13078 9749 239 165 12846 9601 0 0 4604 3342 60 96 100 100 100 100 20304 22447 1.358 .736 .747 .724 .75 1.701 80 365 .703 .92 110 4130 9220 96 107 315 326 0 11677 197 11480 .982 12999 12801 1.019 .997 -.027 -.005
20 5981 6133 225 153 5756 5980 6268 6427 244 176 6043 6274 0 0 2245 2366 152 217 100 100 100 100 11736 12317 .963 1.039 1.038 1.018 1.052 1.482 80 341 1.048 .93 110 4260 9210 95 106 328 339 0 8177 204 7973 1.385 8569 8365 .722 1.384 .47 .469

Total number of rows: 43104

Table truncated, full table size 9658 Kbytes.




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