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Sample GSM173012 Query DataSets for GSM173012
Status Public on Sep 28, 2007
Title SM, ureter
Sample type RNA
 
Channel 1
Source name Stratagene
Organism Homo sapiens
Characteristics Stratagene
LabeledExtract: 34785.Channel_1
Extracted molecule total RNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name SM, ureter
Organism Homo sapiens
Characteristics SM, ureter
LabeledExtract: 34785.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/2002-11/34785.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
1 494 583 165 200 329 383 479 548 219 256 314 348 0 0 98 213 273 248 75 75 0 41 712 662 .859 1.164 1.108 .937 1.229 2.683 12 98 .839 .33 50 2040 8820 75 80 114 119 0 634 217 416 1.265 596 378 .79 1.205 .34 .269
2 3869 2785 157 207 3712 2578 2248 2378 169 379 2091 2171 0 0 3485 2317 101 1941 93 51 88 33 6290 4262 1.44 .695 1.038 .759 .714 4.132 80 414 .656 .91 100 2200 8820 73 83 128 138 0 3027 225 2802 .755 2585 2360 1.325 1.129 -.406 .174
3 1509 1556 164 182 1345 1374 1805 1546 167 200 1641 1364 0 0 902 720 41 79 87 96 81 90 2719 3005 .979 1.022 .831 1.414 .993 2.945 32 153 .884 .79 60 2340 8830 76 82 144 150 0 1691 198 1493 1.11 1680 1483 .901 .903 .151 -.146
4 1345 935 164 190 1181 745 1469 960 231 259 1305 770 0 0 518 273 221 223 91 91 91 91 1926 2075 1.585 .631 .59 .67 .65 1.713 12 104 .531 .81 50 2470 8820 75 80 157 162 0 1016 207 810 .686 1043 837 1.458 .641 -.544 -.641
5 1401 1932 158 205 1243 1727 1500 1931 186 517 1342 1726 0 0 990 1327 195 2750 77 28 68 0 2970 3068 .72 1.389 1.286 1.179 1.292 2.764 80 437 6.218 .42 100 2640 8820 73 83 172 182 0 2100 223 1877 1.51 2099 1876 .662 1.398 .595 .483
6 950 707 158 211 792 496 882 734 187 754 724 523 0 0 522 257 231 3987 81 0 71 0 1288 1247 1.597 .626 .722 .805 .676 2.727 32 200 2.651 .61 70 2790 8830 75 82 188 195 0 768 229 539 .681 798 568 1.469 .785 -.555 -.349
7 1740 1424 166 203 1574 1221 1845 1390 172 254 1679 1187 0 0 1240 869 50 588 82 73 80 51 2795 2866 1.289 .776 .707 .923 .824 3.366 52 293 .725 .89 90 2930 8820 73 82 201 210 0 1548 221 1327 .843 1511 1290 1.186 .768 -.246 -.38
8 713 1439 174 208 539 1231 588 1024 200 286 414 816 0 0 516 1082 171 583 63 58 56 45 1770 1230 .438 2.284 1.971 2.096 2.09 3.225 80 370 3.237 .72 100 3070 8820 73 83 215 225 0 1564 226 1338 2.482 1113 887 .403 2.142 1.312 1.099
9 647 487 169 201 478 286 667 490 189 382 498 289 0 0 264 190 117 1175 86 0 78 0 764 787 1.671 .598 .58 .677 .64 2.326 80 412 26.057 .21 110 3230 8820 72 83 230 241 0 529 218 311 .65 533 314 1.538 .631 -.621 -.665
10 465 365 174 188 291 177 476 354 182 212 302 166 0 0 123 167 44 100 96 68 93 34 468 468 1.644 .608 .55 .582 .544 2.361 32 146 .771 .53 60 3370 8820 75 81 247 253 0 397 204 192 .661 385 180 1.513 .597 -.597 -.743
11 2482 1101 177 192 2305 909 2459 1143 180 203 2282 951 0 0 1220 595 37 80 100 92 96 88 3214 3233 2.536 .394 .417 .372 .397 2.802 80 341 .384 .88 100 3520 8820 73 83 260 270 0 1197 209 988 .429 1242 1034 2.333 .453 -1.222 -1.142
12 6599 8924 174 194 6425 8730 6191 7892 176 207 6017 7698 0 0 5459 7087 38 85 98 99 97 96 15155 13715 .736 1.359 1.279 1.373 1.303 3.106 120 423 1.358 .84 120 3650 8820 72 84 272 284 0 9700 211 9489 1.477 8578 8367 .677 1.391 .563 .476
13 924 2148 168 188 756 1960 853 1875 172 214 685 1687 0 0 643 1514 37 162 82 88 76 80 2716 2372 .386 2.593 2.463 2.581 2.293 3.12 80 332 2.82 .84 110 3800 8820 72 83 287 298 0 2335 204 2130 2.818 2038 1834 .355 2.677 1.495 1.421
14 552 539 164 189 388 350 554 498 170 213 390 309 0 0 150 206 36 144 98 84 97 54 738 699 1.109 .902 .792 .82 .815 2.065 120 468 1.167 .66 130 3940 8820 71 84 300 313 0 586 205 380 .981 541 336 1.02 .861 -.028 -.216
15 468 398 165 193 303 205 477 404 170 212 312 211 0 0 147 142 37 105 95 73 90 50 508 523 1.478 .677 .676 .66 .673 2.188 120 370 .789 .58 120 4100 8820 72 84 317 329 0 433 210 223 .735 439 229 1.36 .735 -.443 -.444
16 5736 9105 162 195 5574 8910 6121 9744 171 279 5959 9549 0 0 2664 3963 96 641 100 96 100 94 14484 15508 .626 1.598 1.602 1.615 1.666 2.03 156 488 1.628 .92 140 4240 8830 72 86 330 344 0 9897 212 9685 1.737 10591 10379 .576 1.742 .797 .801
17 2027 2604 155 196 1872 2408 2273 2796 163 274 2118 2600 0 0 1094 1206 52 578 90 87 87 80 4280 4718 .777 1.286 1.228 1.436 1.272 2.547 156 532 1.263 .87 140 4380 8830 72 86 344 358 0 2830 213 2617 1.398 3039 2826 .715 1.334 .484 .416
18 229 269 157 185 72 84 202 226 159 225 45 41 0 0 112 130 30 211 55 13 44 1 156 86 .857 1.167 .911 .92 1.037 3.421 52 215 4.536 .31 80 4530 8820 74 82 362 370 -50 292 201 91 1.268 246 45 .789 .99 .343 -.014
19 4273 4775 156 183 4117 4592 4770 5102 171 260 4614 4919 0 0 2242 2469 108 836 100 88 100 82 8709 9533 .897 1.115 1.066 1.046 1.116 2.223 80 324 1.237 .84 100 4680 8820 73 83 376 386 0 5190 199 4991 1.212 5546 5347 .825 1.159 .278 .213
20 1663 1612 159 185 1504 1427 1850 1759 185 432 1691 1574 0 0 912 715 163 1966 90 23 86 0 2931 3265 1.054 .949 .931 1.06 .947 2.668 120 380 1.4 .64 120 4820 8830 73 85 389 401 0 1752 201 1551 1.031 1912 1711 .97 1.012 .044 .017

Total number of rows: 43104

Table truncated, full table size 9436 Kbytes.




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