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Sample GSM173030 Query DataSets for GSM173030
Status Public on Sep 28, 2007
Title SM, PA #3, low
Sample type RNA
 
Channel 1
Source name Stratagene
Organism Homo sapiens
Characteristics Stratagene
LabeledExtract: 35911.Channel_1
Extracted molecule total RNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name SM, PA #3, low
Organism Homo sapiens
Characteristics SM, PA #3, low
LabeledExtract: 35911.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/2002-12/35911.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
1 562 336 131 104 431 232 540 362 134 107 409 258 0 0 96 84 30 43 100 100 100 93 663 667 1.858 .538 .631 .505 .529 1.583 32 194 .543 .81 70 1550 8520 176 183 91 98 0 569 176 393 .912 614 437 1.096 1.069 -.132 .096
2 5541 430 127 96 5414 334 5536 430 133 105 5409 334 0 0 1642 138 53 57 100 96 100 94 5748 5743 16.21 .062 .062 .059 .063 1.52 52 258 .056 .86 80 1690 8510 175 183 105 113 0 729 163 566 .105 729 566 9.564 .105 -3.258 -3.256
3 2466 843 118 97 2348 746 2500 719 128 105 2382 622 0 0 1338 501 50 57 100 93 100 90 3094 3004 3.147 .318 .261 .286 .303 2.462 32 212 .302 .84 70 1830 8500 174 181 119 126 0 1429 164 1264 .539 1219 1054 1.857 .443 -.893 -1.176
4 988 279 117 91 871 188 922 279 120 98 805 188 0 0 314 85 25 39 100 93 100 93 1059 993 4.633 .216 .234 .203 .229 1.78 32 204 .178 .75 70 1980 8510 175 182 134 141 0 473 154 319 .366 473 319 2.733 .396 -1.451 -1.337
5 1380 2928 115 86 1265 2842 1425 3127 118 92 1310 3041 0 0 783 1617 24 32 96 100 95 100 4107 4351 .445 2.247 2.321 2.496 2.309 2.35 80 367 2.33 .91 100 2130 8510 174 184 148 158 0 4963 146 4817 3.808 5300 5154 .263 3.935 1.929 1.976
6 705 295 126 90 579 205 681 300 130 98 555 210 0 0 151 68 36 37 100 100 100 93 784 765 2.824 .354 .378 .343 .378 1.511 32 158 .328 .83 60 2270 8500 175 181 164 170 0 500 153 347 .6 508 356 1.666 .641 -.737 -.641
7 2236 677 118 94 2118 583 2323 692 121 101 2205 598 0 0 825 297 27 45 100 98 100 96 2701 2803 3.633 .275 .271 .249 .275 1.725 52 313 .267 .88 90 2420 8500 173 182 177 186 0 1147 159 988 .467 1173 1014 2.143 .46 -1.1 -1.121
8 641 300 111 92 530 208 674 318 115 99 563 226 0 0 224 101 25 49 98 92 98 86 738 789 2.548 .392 .401 .341 .391 1.956 52 254 .365 .77 80 2560 8500 174 182 192 200 0 508 156 353 .665 539 383 1.503 .68 -.588 -.556
9 717 285 109 92 608 193 713 269 112 99 604 177 0 0 173 105 24 44 100 96 100 82 801 781 3.15 .317 .293 .294 .308 1.878 52 274 .303 .74 80 2710 8500 174 182 207 215 0 483 156 327 .538 456 300 1.859 .497 -.894 -1.01
10 411 182 114 91 297 91 409 165 116 102 295 74 0 0 112 60 25 82 100 43 100 15 388 369 3.264 .306 .251 .277 .347 2.033 32 198 .408 .31 70 2860 8500 174 181 222 229 0 308 154 154 .519 280 125 1.926 .425 -.945 -1.234
11 1992 2059 109 91 1883 1968 2144 2275 113 97 2035 2184 0 0 931 864 24 40 96 100 96 100 3851 4219 .957 1.045 1.073 1.229 1.078 2.463 80 337 1.016 .93 100 3010 8510 174 184 236 246 0 3490 154 3336 1.771 3856 3702 .565 1.819 .825 .863
12 3244 2468 111 94 3133 2374 2409 1697 113 103 2298 1603 0 0 3058 2249 26 48 97 93 95 87 5507 3901 1.32 .758 .698 .758 .712 3.118 80 325 .714 .87 100 3150 8500 173 183 250 260 0 4183 159 4024 1.284 2876 2717 .779 1.182 .361 .242
13 980 1827 112 88 868 1739 929 1736 115 94 817 1648 0 0 324 699 26 33 100 100 100 100 2607 2465 .499 2.003 2.017 1.968 1.974 1.619 80 398 2.158 .91 110 3300 8500 172 183 264 275 0 3097 149 2947 3.396 2942 2793 .294 3.419 1.764 1.774
14 486 246 115 88 371 158 482 244 118 94 367 156 0 0 101 84 25 33 100 98 100 80 529 523 2.348 .426 .425 .37 .483 1.939 52 273 .394 .72 90 3450 8500 173 182 280 289 0 417 149 268 .722 414 264 1.385 .72 -.47 -.473
15 665 227 117 92 548 135 666 229 119 97 549 137 0 0 165 58 23 30 100 96 100 92 683 686 4.059 .246 .25 .235 .262 1.681 52 264 .221 .78 90 3580 8500 173 182 293 302 0 385 156 229 .418 388 232 2.395 .423 -1.26 -1.241
16 8452 7039 118 95 8334 6944 8671 7207 128 103 8553 7112 0 0 3573 3137 145 79 100 100 100 100 15278 15665 1.2 .833 .832 .784 .796 1.623 80 399 .837 .94 110 3730 8500 172 183 307 318 0 11931 161 11769 1.412 12215 12054 .708 1.409 .498 .495
17 2888 1640 114 97 2774 1543 2792 1602 139 115 2678 1505 0 0 894 549 217 148 100 100 100 100 4317 4183 1.798 .556 .562 .552 .561 1.525 52 233 .539 .92 80 3880 8500 174 182 324 332 0 2780 164 2615 .943 2715 2551 1.061 .953 -.085 -.07
18 178 116 110 95 68 21 139 105 113 100 29 10 0 0 109 77 27 53 53 9 32 1 89 39 3.238 .309 .345 .61 .676 4.742 52 236 .383 .28 80 4020 8490 173 181 338 346 -50 197 161 36 .523 178 17 1.91 .584 -.934 -.775
19 5976 4410 108 94 5868 4316 6333 4323 113 100 6225 4229 0 0 2823 2170 27 49 100 100 100 100 10184 10454 1.36 .736 .679 .712 .679 1.579 80 357 .732 .95 100 4170 8500 173 183 352 362 0 7475 159 7315 1.247 7327 7168 .802 1.151 .318 .203
20 2615 1729 113 95 2502 1634 2645 1731 117 99 2532 1636 0 0 952 554 27 34 100 100 100 100 4136 4168 1.531 .653 .646 .669 .62 1.704 52 288 .609 .89 90 4320 8500 173 182 367 376 0 2931 161 2769 1.107 2934 2773 .903 1.095 .147 .131

Total number of rows: 43104

Table truncated, full table size 9527 Kbytes.




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

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