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Sample GSM173011 Query DataSets for GSM173011
Status Public on Sep 28, 2007
Title SM, bladder #3
Sample type RNA
 
Channel 1
Source name Stratagene
Organism Homo sapiens
Characteristics Stratagene
LabeledExtract: 34784.Channel_1
Extracted molecule total RNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name SM, bladder #3
Organism Homo sapiens
Characteristics SM, bladder #3
LabeledExtract: 34784.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/2002-11/34784.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
1 327 358 154 137 173 221 352 343 155 143 198 206 0 0 172 161 32 42 67 84 61 78 394 404 .783 1.277 1.04 1.307 1.147 2.524 52 278 1.14 .74 80 1900 8850 77 85 99 107 -50 398 152 246 1.419 381 229 .705 1.156 .505 .209
2 5324 769 152 138 5172 631 5439 837 157 146 5287 699 0 0 3199 427 61 55 100 88 100 86 5803 5986 8.197 .122 .132 .127 .135 2.629 52 288 .105 .82 90 2050 8850 76 85 113 122 0 854 153 701 .136 930 777 7.377 .147 -2.883 -2.767
3 1104 996 150 134 954 862 634 768 157 143 484 634 0 0 1078 904 65 49 73 76 69 73 1816 1118 1.107 .904 1.31 .986 .859 3.519 52 243 .836 .84 80 2180 8850 77 85 127 135 0 1107 149 958 1.004 853 704 .996 1.455 .006 .541
4 774 553 151 140 623 413 786 582 158 148 635 442 0 0 563 348 73 55 73 78 67 73 1036 1077 1.508 .663 .696 .806 .633 2.772 52 272 .59 .84 80 2330 8850 77 85 142 150 0 614 156 459 .737 647 491 1.358 .773 -.441 -.371
5 1572 5176 151 142 1421 5034 1542 5336 157 150 1391 5194 0 0 830 3076 47 54 96 96 94 94 6455 6585 .282 3.543 3.734 2.995 3.542 2.888 52 346 3.988 .9 90 2490 8850 76 85 157 166 0 5751 158 5593 3.936 5929 5771 .254 4.149 1.977 2.053
6 889 574 145 141 744 433 929 621 149 145 784 480 0 0 339 268 37 47 100 90 100 87 1177 1264 1.718 .582 .612 .597 .613 1.837 32 212 .613 .88 70 2640 8850 77 84 173 180 0 638 157 481 .647 690 533 1.546 .68 -.629 -.556
7 1547 1068 147 139 1400 929 1518 1192 150 144 1371 1053 0 0 1100 707 30 42 88 88 86 84 2329 2424 1.507 .664 .768 .709 .651 2.087 52 267 .623 .91 80 2780 8860 78 86 187 195 0 1187 154 1032 .737 1324 1170 1.356 .853 -.44 -.229
8 900 700 148 143 752 557 972 728 153 147 824 585 0 0 500 411 37 45 92 88 90 84 1309 1409 1.35 .741 .71 .733 .791 2.629 52 313 .74 .82 90 2930 8850 76 85 201 210 0 778 159 619 .823 809 650 1.215 .789 -.281 -.342
9 589 396 148 143 441 253 596 414 149 145 448 271 0 0 252 192 33 42 90 85 90 77 694 719 1.743 .574 .605 .595 .615 2.287 80 343 .601 .82 100 3070 8850 76 86 215 225 0 440 159 281 .637 460 301 1.569 .672 -.65 -.573
10 310 219 155 140 155 79 294 237 154 151 139 97 0 0 174 97 32 53 73 61 63 46 234 236 1.962 .51 .698 .562 .555 2.588 52 221 .464 .62 80 3210 8850 77 85 230 238 -50 243 156 88 .566 263 108 1.766 .775 -.82 -.367
11 2036 4566 151 142 1885 4424 2296 4550 155 148 2145 4408 0 0 849 2354 32 48 100 100 100 100 6309 6553 .426 2.347 2.055 2.19 2.384 1.906 80 330 2.642 .92 100 3360 8850 76 86 244 254 0 5073 158 4916 2.608 5056 4898 .383 2.283 1.383 1.191
12 4783 5562 150 147 4633 5415 5125 5855 153 149 4975 5708 0 0 2840 3213 35 38 91 100 91 97 10048 10683 .856 1.169 1.147 1.172 1.227 2.312 120 403 1.169 .92 120 3500 8860 76 88 257 269 0 6180 163 6017 1.299 6506 6342 .77 1.275 .377 .35
13 815 2681 150 147 665 2534 902 2829 150 150 752 2682 0 0 381 1219 36 41 88 98 87 98 3199 3434 .262 3.811 3.566 4.089 3.793 1.961 80 300 4.056 .89 100 3650 8850 76 86 273 283 0 2979 163 2816 4.234 3143 2980 .236 3.963 2.082 1.987
14 551 396 150 149 401 247 580 388 181 241 430 239 0 0 153 117 261 894 84 0 15 0 648 669 1.623 .616 .556 .589 .575 2.045 120 485 .575 .76 130 3800 8860 75 88 286 299 0 440 166 274 .684 431 266 1.461 .618 -.547 -.695
15 491 371 151 138 340 233 518 378 153 148 367 240 0 0 145 132 37 47 96 87 91 81 573 607 1.459 .685 .654 .65 .674 2.395 80 288 .651 .78 110 3950 8860 76 87 302 313 0 412 153 259 .761 420 267 1.313 .727 -.393 -.461
16 5156 7595 145 141 5011 7454 5266 7869 150 182 5121 7728 0 0 2848 3489 39 527 99 98 98 97 12465 12849 .672 1.488 1.509 1.771 1.475 2.434 156 524 1.435 .93 140 4090 8860 75 89 315 329 0 8439 157 8282 1.653 8743 8587 .605 1.677 .725 .746
17 1779 1949 144 147 1635 1802 2101 2237 154 204 1957 2090 0 0 1003 938 67 646 86 82 85 71 3437 4047 .907 1.102 1.068 1.244 1.067 2.77 156 532 1.134 .82 140 4230 8860 75 89 329 343 0 2166 163 2002 1.225 2486 2322 .817 1.187 .292 .247
18 174 167 146 146 28 21 154 150 160 161 8 4 0 0 98 74 92 148 13 7 5 0 49 12 1.333 .75 .5 .922 1.25 4.013 52 215 .247 .33 80 4380 8850 77 85 347 355 -50 186 162 23 .833 167 4 1.2 .556 -.263 -.848
19 5447 6387 146 153 5301 6234 6217 6262 147 158 6071 6109 0 0 2840 3187 33 49 100 100 100 100 11535 12180 .85 1.176 1.006 1.243 1.179 1.949 80 342 1.225 .9 100 4530 8850 76 86 361 371 0 7097 170 6927 1.307 6958 6788 .765 1.118 .386 .161
20 2074 2231 146 151 1928 2080 2209 2259 147 173 2063 2108 0 0 850 720 33 191 100 98 100 98 4008 4171 .927 1.079 1.022 1.169 1.07 1.791 80 356 1.112 .88 110 4670 8850 75 86 374 385 0 2479 168 2311 1.199 2510 2342 .834 1.135 .261 .183

Total number of rows: 43104

Table truncated, full table size 9459 Kbytes.




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