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Sample GSM173031 Query DataSets for GSM173031
Status Public on Sep 28, 2007
Title SM, PA #4, low
Sample type RNA
 
Channel 1
Source name Stratagene
Organism Homo sapiens
Characteristics Stratagene
LabeledExtract: 35912.Channel_1
Extracted molecule total RNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name SM, PA #4, low
Organism Homo sapiens
Characteristics SM, PA #4, low
LabeledExtract: 35912.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/2002-12/35912.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
1 299 240 129 95 170 145 297 236 131 95 168 141 0 0 46 58 23 27 100 100 100 100 315 309 1.172 .853 .839 .815 .8 1.535 32 151 .907 .75 60 1590 8490 174 180 96 102 0 381 151 230 1.354 375 224 .739 1.332 .437 .414
2 2057 628 128 96 1929 532 2113 615 130 98 1985 519 0 0 759 209 22 31 100 98 100 98 2461 2504 3.626 .276 .261 .284 .282 1.582 52 278 .258 .93 80 1730 8480 172 180 109 117 0 997 152 844 .438 976 824 2.284 .415 -1.192 -1.269
3 776 286 128 90 648 196 560 299 129 92 432 209 0 0 416 131 22 29 96 90 96 84 844 641 3.306 .302 .484 .311 .298 2.017 32 223 .252 .75 70 1880 8470 171 178 124 131 0 454 143 311 .48 475 332 2.083 .768 -1.059 -.381
4 487 171 127 95 360 76 493 174 127 97 366 79 0 0 102 36 23 30 100 90 100 68 436 445 4.737 .211 .216 .198 .227 1.807 32 165 .18 .63 60 2020 8480 173 179 139 145 0 271 151 121 .335 276 125 2.984 .343 -1.577 -1.545
5 774 2039 127 97 647 1942 743 1991 129 102 616 1894 0 0 261 629 22 39 100 100 100 100 2589 2510 .333 3.002 3.075 3.094 2.87 1.819 52 329 3.206 .88 90 2160 8480 171 180 151 160 0 3237 154 3083 4.764 3160 3006 .21 4.88 2.252 2.287
6 400 182 129 96 271 86 390 162 130 102 261 66 0 0 84 62 20 35 100 81 100 50 357 327 3.151 .317 .253 .238 .26 2.68 32 212 .301 .61 70 2310 8480 172 179 167 174 0 289 152 137 .504 257 105 1.985 .401 -.989 -1.317
7 1131 461 129 96 1002 365 1141 480 130 108 1012 384 0 0 490 171 22 77 100 98 100 96 1367 1396 2.745 .364 .379 .361 .346 2.22 52 284 .309 .78 80 2460 8480 172 180 182 190 0 732 152 579 .578 762 610 1.729 .602 -.79 -.731
8 310 278 125 92 185 186 307 279 127 101 182 187 0 0 53 69 24 54 100 96 100 90 371 369 .995 1.005 1.027 .975 1.019 1.747 32 206 .895 .74 70 2610 8480 172 179 197 204 0 441 146 295 1.596 443 297 .627 1.631 .674 .706
9 336 254 121 88 215 166 333 246 123 95 212 158 0 0 87 62 22 35 100 98 98 98 381 370 1.295 .772 .745 .818 .746 1.636 52 264 .743 .8 80 2750 8480 172 180 211 219 0 403 140 263 1.226 390 251 .816 1.183 .293 .242
10 253 138 119 92 134 46 253 135 120 95 134 43 0 0 44 32 20 28 100 68 100 37 180 177 2.913 .343 .321 .303 .313 2.539 32 158 .241 .3 60 2900 8480 173 179 227 233 0 219 146 73 .545 214 68 1.835 .509 -.876 -.973
11 798 3800 129 98 669 3702 783 3740 132 100 654 3642 0 0 184 1015 24 34 100 100 100 100 4371 4296 .181 5.534 5.569 5.525 5.612 1.381 52 304 6.15 .91 90 3040 8480 171 180 239 248 0 6032 156 5876 8.784 5937 5781 .114 8.839 3.135 3.144
12 1714 1508 133 101 1581 1407 1632 1546 139 108 1499 1445 0 0 1211 953 47 50 90 94 84 90 2988 2944 1.124 .89 .964 .958 .866 2.876 52 301 .829 .88 90 3180 8480 171 180 253 262 0 2394 160 2233 1.413 2454 2294 .708 1.53 .498 .614
13 392 895 126 96 266 799 402 959 132 102 276 863 0 0 115 288 44 44 97 100 92 100 1065 1139 .333 3.004 3.127 3.085 2.955 1.639 80 382 3.146 .87 100 3340 8480 171 181 269 279 0 1421 152 1268 4.768 1522 1370 .21 4.963 2.253 2.311
14 305 219 124 98 181 121 302 155 126 101 178 57 0 0 85 307 30 42 96 63 94 30 302 235 1.496 .669 .32 .393 .368 2.691 52 302 1.131 .85 90 3490 8470 170 179 284 293 0 348 156 192 1.061 246 90 .942 .508 .086 -.976
15 319 173 124 99 195 74 328 169 127 103 204 70 0 0 51 44 29 40 98 75 98 36 269 274 2.635 .379 .343 .341 .347 1.869 52 291 2.305 .74 90 3630 8480 171 180 298 307 0 275 157 117 .602 268 111 1.66 .545 -.731 -.877
16 3309 2278 128 98 3181 2180 3226 2209 131 102 3098 2111 0 0 850 644 25 39 100 100 100 100 5361 5209 1.459 .685 .681 .683 .701 1.278 52 339 .675 .93 90 3770 8470 170 179 312 321 0 3616 156 3460 1.088 3506 3351 .919 1.082 .121 .113
17 1140 610 139 103 1001 507 1089 581 149 113 950 478 0 0 331 237 45 53 100 100 100 96 1508 1428 1.974 .506 .503 .47 .502 1.488 32 206 .54 .9 70 3910 8470 171 178 327 334 0 968 163 805 .804 922 759 1.244 .799 -.315 -.324
18 176 120 144 102 32 18 162 116 149 109 18 14 0 0 58 40 38 38 26 28 13 11 50 32 1.778 .563 .778 1.193 1.046 3.144 52 274 6.019 .15 80 4060 8470 171 179 342 350 -50 190 162 29 .893 184 22 1.12 1.235 -.163 .304
19 1688 1263 144 102 1544 1161 1907 1353 155 117 1763 1251 0 0 908 584 188 174 90 92 87 86 2705 3014 1.33 .752 .71 .873 .735 2.358 80 350 .696 .92 100 4210 8480 171 181 356 366 0 2005 162 1843 1.194 2148 1986 .838 1.126 .255 .172
20 808 432 136 102 672 330 801 402 155 131 665 300 0 0 244 130 221 225 98 82 84 15 1002 965 2.036 .491 .451 .496 .484 1.561 52 253 .321 .74 80 4350 8470 171 179 371 379 0 686 162 524 .779 638 476 1.283 .716 -.359 -.482

Total number of rows: 43104

Table truncated, full table size 9418 Kbytes.




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

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