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Sample GSM173076 Query DataSets for GSM173076
Status Public on Sep 28, 2007
Title SM, bladder #1
Sample type RNA
 
Channel 1
Source name Stratagene
Organism Homo sapiens
Characteristics Stratagene
LabeledExtract: 34781.Channel_1
Extracted molecule total RNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name SM, bladder #1
Organism Homo sapiens
Characteristics SM, bladder #1
LabeledExtract: 34781.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/2002-11/34781.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
1 258 334 116 163 142 171 258 294 117 168 142 131 0 0 111 191 25 52 78 61 76 55 313 273 .83 1.204 .923 1.049 1.387 3.896 52 276 1.735 .66 80 1870 8930 85 93 96 104 -50 407 199 209 1.469 359 160 .681 1.125 .554 .17
2 3654 688 112 137 3542 551 4323 699 114 146 4211 562 0 0 1954 411 25 45 100 90 100 76 4093 4773 6.428 .156 .133 .162 .179 3.133 52 309 .15 .84 90 2010 8920 83 92 109 118 0 839 167 672 .19 852 685 5.271 .163 -2.398 -2.619
3 1074 1170 111 119 963 1051 970 1152 115 122 859 1033 0 0 817 834 27 37 87 90 87 87 2014 1892 .916 1.091 1.203 1.409 1.204 3.862 32 171 1.047 .59 60 2150 8930 86 92 125 131 0 1427 145 1282 1.331 1405 1260 .751 1.467 .412 .552
4 876 566 107 111 769 455 844 575 109 116 737 464 0 0 353 249 24 42 96 87 96 87 1224 1201 1.69 .592 .63 .634 .704 2.385 32 170 .529 .74 60 2300 8930 86 92 140 146 0 690 135 555 .722 701 566 1.386 .768 -.471 -.381
5 1256 3851 115 130 1141 3721 1413 3336 120 137 1298 3206 0 0 608 2185 40 47 96 96 88 96 4862 4504 .307 3.261 2.47 3.475 2.981 3.576 52 296 3.796 .85 80 2450 8940 86 94 154 162 0 4696 159 4538 3.977 4068 3910 .251 3.012 1.992 1.591
6 629 479 116 124 513 355 642 499 118 127 526 375 0 0 196 203 28 41 100 87 100 87 868 901 1.445 .692 .713 .719 .844 2.427 32 214 .703 .74 70 2600 8930 85 92 169 176 0 584 151 433 .844 609 457 1.185 .869 -.245 -.202
7 1357 1111 114 141 1243 970 1430 1108 119 156 1316 967 0 0 831 751 42 84 90 82 90 78 2213 2283 1.281 .78 .735 .696 .835 2.959 52 287 .801 .85 80 2740 8930 85 93 183 191 0 1355 172 1183 .952 1351 1179 1.051 .896 -.071 -.158
8 763 2308 118 155 645 2153 793 2252 122 192 675 2097 0 0 314 1011 31 112 96 100 96 96 2798 2772 .3 3.338 3.107 3.567 3.468 1.805 32 217 3.87 .8 70 2890 8940 86 93 198 205 0 2815 189 2626 4.071 2746 2557 .246 3.789 2.025 1.922
9 405 353 118 167 287 186 477 388 125 219 359 221 0 0 196 170 45 135 82 63 78 42 473 580 1.543 .648 .616 .767 .728 2.33 52 279 .817 .72 80 3030 8920 84 92 212 220 0 430 204 227 .79 473 270 1.265 .751 -.339 -.414
10 261 250 112 189 149 61 275 243 120 236 163 54 0 0 110 103 43 149 76 19 67 1 210 217 2.443 .409 .331 .425 .459 2.561 52 267 1.203 .37 80 3180 8920 84 92 227 235 0 305 230 74 .499 296 66 2.003 .404 -1.002 -1.308
11 1227 4677 113 164 1114 4513 1395 5640 118 173 1282 5476 0 0 562 2226 35 74 97 100 93 98 5627 6758 .247 4.051 4.271 4.222 3.965 2.439 80 337 4.585 .86 100 3340 8940 85 95 242 252 0 5704 200 5504 4.94 6878 6678 .202 5.209 2.305 2.381
12 3448 3945 120 143 3328 3802 3724 4537 127 159 3604 4394 0 0 1892 2232 47 130 95 95 94 93 7130 7998 .875 1.142 1.219 .988 1.136 3.472 120 486 1.179 .88 120 3480 8930 83 95 255 267 0 4811 174 4637 1.393 5533 5359 .718 1.487 .478 .572
13 673 2063 131 154 542 1909 670 2183 140 183 539 2029 0 0 164 572 55 176 100 98 98 98 2451 2568 .284 3.522 3.764 3.433 3.48 1.706 52 259 3.858 .86 90 3640 8940 85 94 272 281 0 2516 188 2328 4.295 2662 2474 .233 4.591 2.103 2.199
14 404 314 123 137 281 177 401 311 129 144 278 174 0 0 86 79 40 60 100 93 100 80 458 452 1.588 .63 .626 .592 .586 1.806 80 364 .634 .6 110 3770 8940 84 95 284 295 0 383 167 216 .768 379 212 1.302 .763 -.381 -.39
15 333 293 116 121 217 172 347 309 123 127 231 188 0 0 118 93 42 46 89 85 84 80 389 419 1.262 .793 .814 .836 .801 2.639 120 396 .75 .68 120 3920 8930 83 95 299 311 0 357 148 210 .967 377 229 1.035 .993 -.049 -.011
16 5270 8439 118 130 5152 8309 5593 8499 125 135 5475 8369 0 0 1794 3248 41 48 100 100 100 100 13461 13844 .62 1.613 1.529 1.537 1.623 2.005 120 413 1.821 .85 130 4060 8930 82 95 312 325 0 10291 159 10133 1.967 10365 10206 .508 1.864 .976 .899
17 1417 1532 117 122 1300 1410 1514 1676 124 130 1397 1554 0 0 532 522 40 50 98 98 98 97 2710 2951 .922 1.085 1.112 1.084 1.105 1.819 120 403 1.071 .88 120 4210 8930 83 95 328 340 0 1868 149 1720 1.323 2044 1895 .756 1.357 .403 .44
18 153 149 104 117 49 32 116 138 108 120 12 21 0 0 104 61 26 37 34 40 23 15 81 33 1.531 .653 1.75 1.133 1.098 3.799 52 217 .347 .23 80 4350 8920 84 92 344 352 -50 182 143 39 .796 168 26 1.256 2.134 -.328 1.094
19 3095 3355 105 117 2990 3238 3383 3809 109 121 3278 3692 0 0 1422 1857 27 35 100 100 100 96 6228 6970 .923 1.083 1.126 .87 .999 2.652 80 370 1.162 .9 110 4510 8930 83 94 358 369 0 4091 143 3949 1.321 4645 4502 .757 1.374 .401 .458
20 1030 1132 107 107 923 1025 1106 1269 112 111 999 1162 0 0 449 498 28 35 99 97 98 97 1948 2161 .9 1.111 1.163 1.1 1.096 2.621 120 383 1.127 .87 120 4650 8930 83 95 372 384 0 1380 130 1250 1.354 1548 1417 .738 1.418 .438 .504

Total number of rows: 43104

Table truncated, full table size 9339 Kbytes.




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