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Sample GSM173052 Query DataSets for GSM173052
Status Public on Sep 28, 2007
Title SM, cervix #2, low
Sample type RNA
 
Channel 1
Source name Stratagene
Organism Homo sapiens
Characteristics Stratagene
LabeledExtract: 36008.Channel_1
Extracted molecule total RNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name SM, cervix #2, low
Organism Homo sapiens
Characteristics SM, cervix #2, low
LabeledExtract: 36008.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/2002-12/36008.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
1 865 661 233 172 632 489 886 654 239 182 653 482 0 0 174 221 50 61 100 100 100 100 1121 1135 1.292 .774 .738 .719 .715 1.504 32 204 .824 .9 70 1660 8340 158 165 102 109 0 674 176 499 .79 667 492 1.267 .753 -.341 -.409
2 8781 21408 234 169 8547 21239 9348 22507 237 175 9114 22338 0 0 3132 7793 44 57 100 100 100 100 29786 31452 .402 2.485 2.451 2.496 2.485 1.093 52 317 2.489 1 90 1800 8340 157 166 115 124 0 21845 172 21672 2.536 22966 22794 .394 2.501 1.342 1.322
3 5238 3415 235 167 5003 3248 5205 3101 236 170 4970 2934 0 0 2962 1914 44 51 100 100 100 100 8251 7904 1.54 .649 .59 .674 .662 1.317 32 222 .647 .99 70 1950 8330 157 164 131 138 0 3485 170 3314 .662 3164 2994 1.51 .602 -.594 -.731
4 2808 1199 229 159 2579 1040 2840 1221 231 166 2611 1062 0 0 1017 474 34 46 100 100 100 100 3619 3673 2.48 .403 .407 .388 .396 1.207 32 200 .407 .98 70 2090 8340 158 165 145 152 0 1223 162 1061 .411 1246 1084 2.43 .415 -1.281 -1.269
5 4966 3678 234 163 4732 3515 3444 3878 238 171 3210 3715 0 0 7528 2254 42 54 98 100 98 100 8247 6925 1.346 .743 1.157 1.083 1.397 3.08 80 396 .096 .24 100 2240 8340 157 167 159 169 0 3753 166 3587 .758 3957 3791 1.319 1.181 -.4 .24
6 1441 794 235 160 1206 634 1499 811 239 174 1264 651 0 0 311 191 44 73 100 100 100 100 1840 1915 1.902 .526 .515 .521 .518 1.306 32 206 .522 .93 70 2380 8330 157 164 174 181 0 810 163 647 .536 828 664 1.864 .526 -.899 -.928
7 5066 3313 231 158 4835 3155 4730 3057 237 165 4499 2899 0 0 2177 1404 51 57 100 100 100 100 7990 7398 1.532 .653 .644 .656 .651 1.178 52 325 .649 .99 90 2530 8340 157 166 188 197 0 3381 161 3219 .666 3119 2958 1.502 .658 -.587 -.605
8 1794 3920 238 158 1556 3762 1863 4137 250 179 1625 3979 0 0 634 1416 135 127 100 100 100 100 5318 5604 .414 2.418 2.449 2.444 2.489 1.193 52 300 2.403 .98 90 2680 8330 156 165 203 212 0 4000 161 3839 2.467 4221 4060 .405 2.499 1.303 1.321
9 1313 3705 227 149 1086 3556 1380 3933 247 165 1153 3784 0 0 541 1661 177 111 93 100 86 100 4642 4937 .305 3.274 3.282 3.544 3.23 1.427 80 358 3.261 .96 100 2820 8340 157 167 217 227 0 3781 152 3629 3.341 4013 3861 .299 3.349 1.74 1.744
10 845 493 229 149 616 344 818 472 228 155 589 323 0 0 206 151 40 48 100 100 100 100 960 912 1.791 .558 .548 .531 .523 1.298 32 160 .576 .9 60 2970 8330 158 164 234 240 0 503 152 351 .57 482 330 1.755 .56 -.811 -.838
11 5352 3919 226 156 5126 3763 5820 4148 228 160 5594 3992 0 0 2599 1907 39 53 100 100 100 100 8889 9586 1.362 .734 .714 .75 .725 1.241 80 371 .732 .99 100 3120 8340 157 167 247 257 0 3999 159 3840 .749 4233 4073 1.335 .728 -.417 -.458
12 9576 12438 232 161 9344 12277 9334 12645 233 167 9102 12484 0 0 5867 7158 45 67 100 100 100 100 21621 21586 .761 1.314 1.372 1.361 1.364 1.135 52 300 1.283 1 90 3260 8330 156 165 261 270 0 12692 164 12528 1.341 12903 12739 .746 1.4 .423 .485
13 1973 6122 217 151 1756 5971 1856 5715 223 161 1639 5564 0 0 896 3018 46 64 100 100 100 100 7727 7203 .294 3.4 3.395 3.439 3.41 1.167 80 421 3.403 .99 110 3420 8340 156 167 276 287 0 6247 154 6093 3.47 5832 5678 .288 3.464 1.795 1.792
14 1037 654 214 156 823 498 1037 655 217 159 823 499 0 0 250 125 38 49 100 100 100 100 1321 1322 1.653 .605 .606 .614 .591 1.299 52 276 .583 .92 90 3560 8330 156 165 291 300 0 667 159 508 .617 668 509 1.62 .619 -.696 -.693
15 1095 622 223 167 872 455 1134 658 229 171 911 491 0 0 257 209 51 57 100 98 100 96 1327 1402 1.916 .522 .539 .473 .512 1.453 52 289 .535 .92 90 3690 8330 156 165 304 313 0 635 170 464 .532 671 501 1.878 .55 -.909 -.863
16 13183 16087 221 155 12962 15932 14316 16821 226 164 14095 16666 0 0 5350 6562 50 54 100 100 100 100 28894 30761 .814 1.229 1.182 1.229 1.22 1.069 80 378 1.226 1 100 3850 8340 157 167 320 330 0 16415 158 16257 1.254 17164 17006 .797 1.207 .327 .271
17 5174 4983 206 135 4968 4848 5011 4785 212 140 4805 4650 0 0 1936 1807 47 41 100 100 100 100 9816 9455 1.025 .976 .968 .985 .974 1.101 52 233 .967 .99 80 3990 8330 157 165 335 343 0 5085 138 4947 .996 4883 4745 1.004 .987 -.006 -.018
18 343 266 214 138 129 128 203 164 219 144 -11 26 0 0 286 251 40 43 36 34 28 26 257 15 1.008 .992 null 1.072 1.03 2.271 52 247 .883 .88 80 4130 8320 156 164 349 357 -50 271 141 131 1.012 167 27 .988 null .018 null
19 9112 7859 210 139 8902 7720 9796 8295 215 141 9586 8156 0 0 4468 3834 40 45 100 100 100 100 16622 17742 1.153 .867 .851 .881 .876 1.168 80 336 .864 1 100 4280 8340 157 167 363 373 0 8019 142 7878 .885 8464 8322 1.13 .868 -.176 -.204
20 4610 3977 203 131 4407 3846 4575 3875 208 134 4372 3744 0 0 1477 1284 45 44 100 100 100 100 8253 8116 1.146 .873 .856 .87 .876 1.112 52 289 .866 .99 90 4420 8330 156 165 377 386 0 4058 134 3924 .891 3954 3820 1.123 .874 -.167 -.195

Total number of rows: 43104

Table truncated, full table size 9738 Kbytes.




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