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Sample GSM173062 Query DataSets for GSM173062
Status Public on Sep 28, 2007
Title SM, bronchial #4 , low
Sample type RNA
 
Channel 1
Source name Stratagene
Organism Homo sapiens
Characteristics Stratagene
LabeledExtract: 36012.Channel_1
Extracted molecule total RNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name SM, bronchial #4 , low
Organism Homo sapiens
Characteristics SM, bronchial #4 , low
LabeledExtract: 36012.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/2002-12/36012.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
1 251 202 158 130 93 72 188 158 160 137 30 28 0 0 170 138 52 52 36 38 23 23 165 58 1.292 .774 .933 .894 .673 3.885 52 273 .556 .6 80 1460 8420 141 149 82 90 -50 256 165 91 .98 200 35 1.02 1.181 -.029 .241
2 6570 3909 164 130 6406 3779 6777 4112 186 149 6613 3982 0 0 2111 1176 147 127 100 100 96 100 10185 10595 1.695 .59 .602 .617 .59 1.351 32 212 .591 .99 70 1600 8430 142 149 96 103 0 4948 165 4784 .747 5205 5041 1.339 .762 -.421 -.392
3 2526 1598 163 129 2363 1469 2175 1116 166 140 2012 987 0 0 1661 1764 42 57 96 100 96 96 3832 2999 1.609 .622 .491 .504 .417 1.75 32 172 .741 .67 60 1760 8430 143 149 113 119 0 2023 163 1859 .787 1413 1249 1.271 .621 -.346 -.687
4 1467 436 155 128 1312 308 1378 356 153 149 1223 228 0 0 759 217 47 102 96 93 96 59 1620 1451 4.26 .235 .186 .215 .228 1.845 32 167 .233 .89 60 1890 8430 143 149 126 132 0 552 162 390 .297 451 289 3.365 .236 -1.751 -2.083
5 1864 4851 150 122 1714 4729 1614 4278 150 145 1464 4156 0 0 1186 2650 48 104 100 100 100 100 6443 5620 .362 2.759 2.839 3.057 3.027 1.375 52 337 2.616 .97 90 2050 8440 142 151 140 149 0 6141 154 5986 3.492 5415 5261 .286 3.593 1.804 1.845
6 946 503 164 130 782 373 891 516 164 142 727 386 0 0 291 149 46 62 100 96 100 93 1155 1113 2.097 .477 .531 .444 .497 1.78 32 213 .449 .89 70 2190 8430 142 149 155 162 0 637 165 472 .604 653 489 1.656 .672 -.728 -.573
7 3289 1322 168 133 3121 1189 3157 1253 175 142 2989 1120 0 0 1849 708 37 71 100 98 100 98 4310 4109 2.625 .381 .375 .373 .391 1.325 52 264 .372 .97 80 2340 8430 142 150 170 178 0 1673 168 1505 .482 1586 1418 2.074 .474 -1.052 -1.076
8 1241 1709 169 138 1072 1571 1307 1646 173 143 1138 1508 0 0 505 699 35 65 100 100 94 98 2643 2646 .682 1.465 1.325 1.596 1.465 1.62 52 242 1.468 .95 80 2480 8440 143 151 184 192 0 2163 175 1989 1.855 2084 1909 .539 1.677 .891 .746
9 1251 502 169 132 1082 370 1204 478 172 142 1035 346 0 0 394 164 34 63 100 100 100 96 1452 1381 2.924 .342 .334 .332 .347 1.454 52 324 .334 .91 90 2630 8430 141 150 198 207 0 635 167 468 .433 605 438 2.31 .423 -1.208 -1.241
10 728 454 169 130 559 324 729 365 171 135 560 235 0 0 276 272 32 49 100 96 100 81 883 795 1.725 .58 .42 .465 .5 1.882 32 198 .643 .82 70 2780 8430 142 149 214 221 0 575 165 410 .734 462 297 1.363 .531 -.447 -.913
11 5254 6758 168 137 5086 6621 4827 6408 173 146 4659 6271 0 0 2348 2751 38 67 100 100 100 100 11707 10930 .768 1.302 1.346 1.331 1.273 1.235 52 304 1.276 .98 90 2920 8430 141 150 227 236 0 8554 173 8381 1.648 8111 7938 .607 1.704 .721 .769
12 6263 4755 173 147 6090 4608 5465 4012 186 161 5292 3865 0 0 5131 3502 69 79 96 98 94 98 10698 9157 1.322 .757 .73 .888 .749 1.71 52 254 .716 .98 80 3060 8430 142 150 242 250 0 6019 186 5833 .958 5078 4892 1.044 .924 -.062 -.113
13 1331 2628 175 133 1156 2495 1287 2496 184 147 1112 2363 0 0 601 1151 60 67 100 100 98 100 3651 3475 .463 2.158 2.125 2.264 2.221 1.349 80 382 2.123 .97 100 3220 8430 141 151 257 267 0 3327 168 3158 2.732 3159 2991 .366 2.69 1.45 1.428
14 684 464 176 141 508 323 660 458 181 149 484 317 0 0 177 157 38 59 100 98 100 94 831 801 1.573 .636 .655 .591 .6 1.452 52 289 .875 .96 90 3370 8430 141 150 272 281 0 587 178 409 .805 580 401 1.242 .829 -.313 -.27
15 1023 343 175 142 848 201 1031 344 178 147 856 202 0 0 176 100 35 50 100 92 100 82 1049 1058 4.219 .237 .236 .199 .226 1.971 52 264 .245 .79 90 3510 8430 141 150 286 295 0 434 180 254 .3 435 256 3.333 .299 -1.737 -1.743
16 15265 13627 175 143 15090 13484 16013 14855 211 199 15838 14712 0 0 5696 5015 260 368 100 100 98 100 28574 30550 1.119 .894 .929 .925 .879 1.385 52 283 .886 .99 90 3640 8430 141 150 299 308 0 17249 181 17068 1.131 18804 18623 .884 1.176 .178 .234
17 4083 2839 175 145 3908 2694 4101 2556 228 248 3926 2411 0 0 1606 1342 344 664 100 100 100 94 6602 6337 1.451 .689 .614 .687 .664 1.246 52 250 .71 .96 80 3800 8430 142 150 316 324 0 3594 184 3410 .873 3235 3052 1.146 .777 -.197 -.363
18 252 203 168 137 84 66 185 156 193 196 17 19 0 0 216 146 222 562 11 1 5 0 150 36 1.273 .786 1.118 .901 .847 3.089 52 256 3.357 .92 80 3940 8420 141 149 330 338 -50 257 173 84 .995 197 24 1.005 1.415 -.008 .501
19 10331 6261 168 130 10163 6131 10612 6172 173 138 10444 6042 0 0 3077 1685 33 55 100 100 100 100 16294 16486 1.658 .603 .579 .615 .602 1.198 52 242 .588 .98 80 4090 8430 142 150 345 353 0 7925 165 7761 .764 7813 7648 1.31 .732 -.389 -.45
20 4446 2788 173 129 4273 2659 4185 2597 177 137 4012 2468 0 0 1961 1186 36 50 100 100 100 100 6932 6480 1.607 .622 .615 .625 .627 1.151 52 244 .611 .99 80 4230 8430 142 150 359 367 0 3529 163 3366 .788 3287 3124 1.27 .779 -.344 -.361

Total number of rows: 43104

Table truncated, full table size 9589 Kbytes.




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

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