NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM173014 Query DataSets for GSM173014
Status Public on Sep 28, 2007
Title SM, urethra #2
Sample type RNA
 
Channel 1
Source name Stratagene
Organism Homo sapiens
Characteristics Stratagene
LabeledExtract: 34788.Channel_1
Extracted molecule total RNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name SM, urethra #2
Organism Homo sapiens
Characteristics SM, urethra #2
LabeledExtract: 34788.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/2002-11/34788.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
1 469 410 146 142 323 268 475 370 152 153 329 228 0 0 71 135 42 92 100 96 100 68 591 557 1.205 .83 .693 .702 .752 2.325 32 219 .995 .8 70 1850 8770 69 76 94 101 0 466 161 305 .943 420 259 1.061 .788 -.085 -.345
2 8524 1425 144 140 8380 1285 9361 1562 149 157 9217 1422 0 0 2611 554 40 151 100 94 100 94 9665 10639 6.521 .153 .154 .145 .159 1.497 52 304 .157 .94 90 2000 8780 69 78 108 117 0 1619 159 1460 .174 1775 1616 5.739 .175 -2.521 -2.512
3 2124 1590 150 136 1974 1454 2361 1581 152 150 2211 1445 0 0 908 463 39 84 100 100 100 100 3428 3656 1.358 .737 .654 .806 .709 1.538 32 152 .633 .91 60 2130 8780 71 77 123 129 0 1807 155 1652 .837 1797 1642 1.195 .743 -.257 -.429
4 1153 554 143 144 1010 410 1054 525 151 163 911 381 0 0 484 195 45 200 100 88 98 48 1420 1292 2.463 .406 .418 .402 .416 1.747 52 264 .453 .54 80 2280 8780 70 78 137 145 0 630 164 466 .461 597 433 2.168 .475 -1.116 -1.073
5 2016 4164 154 157 1862 4007 2007 3966 187 251 1853 3809 0 0 1072 2580 205 613 97 88 95 81 5869 5662 .465 2.152 2.056 1.919 2.187 2.248 80 357 2.333 .94 100 2430 8780 69 79 151 161 0 4732 178 4553 2.445 4507 4328 .409 2.336 1.29 1.224
6 846 673 200 237 646 436 921 582 506 879 721 345 0 0 493 437 810 1485 44 3 0 0 1082 1066 1.482 .675 .479 .805 .539 3.379 52 213 1.239 .89 80 2570 8800 72 80 166 174 0 765 269 495 .767 661 392 1.304 .544 -.383 -.879
7 2666 2290 263 361 2403 1929 2479 1755 403 859 2216 1394 0 0 1289 1381 365 1224 100 65 96 23 4332 3610 1.246 .803 .629 .777 .777 1.484 52 290 1.051 .73 90 2720 8780 69 78 180 189 0 2602 410 2192 .912 1994 1584 1.096 .715 -.133 -.484
8 2639 2822 218 298 2421 2524 2389 2339 453 859 2171 2041 0 0 1351 1536 702 1615 94 73 76 25 4945 4212 .959 1.043 .94 1.073 .973 1.708 52 338 1.615 .74 90 2860 8790 70 79 194 203 0 3207 339 2868 1.185 2658 2319 .844 1.068 .245 .095
9 772 437 156 178 616 259 795 443 223 368 639 265 0 0 237 133 443 912 81 0 11 0 875 904 2.378 .42 .415 .394 .426 1.936 80 369 10.819 .35 100 3020 8780 69 79 210 220 0 497 202 294 .478 503 301 2.093 .471 -1.066 -1.085
10 444 286 143 148 301 138 439 280 155 189 296 132 0 0 101 89 64 239 100 15 100 0 439 428 2.181 .458 .446 .371 .484 2.319 32 174 .696 .41 70 3150 8780 70 77 224 231 0 325 168 157 .521 318 150 1.919 .507 -.941 -.981
11 3078 2257 140 142 2938 2115 3335 2303 150 195 3195 2161 0 0 904 697 65 316 100 100 100 96 5053 5356 1.389 .72 .676 .721 .724 1.508 80 354 .719 .92 100 3300 8780 69 79 238 248 0 2565 161 2403 .818 2617 2456 1.222 .769 -.29 -.38
12 9463 7786 139 148 9324 7638 9427 7840 148 157 9288 7692 0 0 2642 1798 62 61 100 100 100 100 16962 16980 1.221 .819 .828 .845 .82 1.316 80 391 .791 .96 110 3440 8770 67 78 251 262 0 8848 168 8680 .931 8909 8741 1.074 .941 -.103 -.088
13 1281 2599 139 153 1142 2446 1309 2572 152 163 1170 2419 0 0 331 609 67 63 98 100 98 100 3588 3589 .467 2.142 2.068 2.218 2.114 1.484 80 321 2.184 .94 100 3590 8780 69 79 267 277 0 2953 174 2780 2.434 2923 2749 .411 2.349 1.283 1.232
14 575 395 138 145 437 250 563 389 144 155 425 244 0 0 167 143 35 58 99 92 99 85 687 669 1.748 .572 .574 .545 .558 1.851 120 408 .853 .54 120 3740 8780 68 80 281 293 0 449 165 284 .65 442 277 1.538 .652 -.621 -.616
15 618 426 142 157 476 269 621 409 163 171 479 252 0 0 75 91 73 79 100 98 100 93 745 731 1.77 .565 .526 .536 .551 1.481 80 316 .54 .78 110 3880 8770 67 78 295 306 0 484 178 306 .642 465 286 1.557 .598 -.639 -.742
16 9760 8074 139 157 9621 7917 10130 8168 155 174 9991 8011 0 0 2953 2705 68 83 100 100 100 100 17538 18002 1.215 .823 .802 .819 .82 1.29 120 436 .828 .97 130 4030 8770 66 79 309 322 0 9175 178 8997 .935 9282 9103 1.069 .911 -.097 -.134
17 3087 2688 143 160 2944 2528 3304 2829 155 180 3161 2669 0 0 920 895 52 95 100 100 100 100 5472 5830 1.165 .859 .844 .855 .855 1.455 120 395 .87 .95 120 4170 8770 67 79 324 336 0 3055 182 2873 .976 3215 3033 1.025 .959 -.035 -.06
18 314 234 153 168 161 66 229 202 165 196 76 34 0 0 210 110 59 127 55 21 42 7 227 110 2.439 .41 .447 .674 .788 4.541 52 220 .709 .27 80 4320 8770 69 77 341 349 -50 266 191 75 .466 230 39 2.147 .508 -1.102 -.976
19 6567 3831 141 153 6426 3678 6899 3952 144 170 6758 3799 0 0 1866 1250 39 100 100 98 100 98 10104 10557 1.747 .572 .562 .554 .564 1.426 80 323 .566 .95 100 4470 8780 69 79 355 365 0 4353 174 4180 .65 4491 4317 1.537 .639 -.621 -.647
20 2619 1873 146 164 2473 1709 2555 1834 154 176 2409 1670 0 0 536 440 42 78 100 100 100 100 4182 4079 1.447 .691 .693 .684 .671 1.256 80 333 .688 .95 110 4610 8780 68 79 368 379 0 2128 186 1942 .785 2084 1898 1.273 .788 -.349 -.344

Total number of rows: 43104

Table truncated, full table size 9404 Kbytes.




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

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap