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Sample GSM173015 Query DataSets for GSM173015
Status Public on Sep 28, 2007
Title SM, bladder #2, low
Sample type RNA
 
Channel 1
Source name Stratagene
Organism Homo sapiens
Characteristics Stratagene
LabeledExtract: 36240.Channel_1
Extracted molecule total RNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name SM, bladder #2, low
Organism Homo sapiens
Characteristics SM, bladder #2, low
LabeledExtract: 36240.Channel_2
Extracted molecule total RNA
Extraction protocol not provided
Label Cy5
Label protocol not provided
 
 
Hybridization protocol not provided
Scan protocol not provided
Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1000, 7800; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Jen-Tsan Ashley,,Chi
Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.66; Parameter Scan Time = 11:31:33; Parameter PMT Volts = 600; Parameter Scan Date = 2002-12-04; Parameter Pixel Size = 10; Parameter Laser on time = 41870; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 4.79; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Jen-Tsan Ashley,,Chi
Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.66; Parameter Scan Time = 11:31:33; Parameter PMT Volts = 650; Parameter Scan Date = 2002-12-04; Parameter Pixel Size = 10; Parameter Laser on time = 260865; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 3.36; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Jen-Tsan Ashley,,Chi
Description Simple annotation: Smooth muscle cells, Anatomical comparisons
Image: http://smd.stanford.edu/MicroArray/gifs/2002-12/36240.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
1 547 364 290 208 257 156 548 352 290 213 258 144 0 0 102 101 48 62 98 84 88 57 413 402 1.647 .607 .558 .558 .642 1.858 52 244 .667 .65 80 1490 9070 123 131 45 53 0 515 294 221 .859 498 204 1.164 .79 -.219 -.34
2 4903 500 281 208 4622 292 5100 524 285 211 4819 316 0 0 2076 154 50 60 100 90 100 86 4914 5135 15.829 .063 .066 .066 .065 1.411 52 265 .062 .88 80 1630 9060 122 130 59 67 0 708 294 413 .089 742 447 11.183 .093 -3.483 -3.429
3 2076 933 262 182 1814 751 1986 962 271 189 1724 780 0 0 767 409 59 59 100 96 100 90 2565 2504 2.415 .414 .452 .383 .365 1.521 32 225 .422 .91 70 1780 9050 121 128 74 81 0 1321 258 1063 .586 1362 1104 1.707 .64 -.771 -.643
4 1207 409 261 199 946 210 1247 413 267 206 986 214 0 0 255 85 50 64 100 93 100 84 1156 1200 4.505 .222 .217 .207 .236 1.572 32 204 .188 .71 70 1930 9060 122 129 89 96 0 579 282 297 .314 585 303 3.183 .307 -1.67 -1.703
5 1749 4290 245 174 1504 4116 1713 4207 248 178 1468 4033 0 0 527 1449 45 48 100 100 100 100 5620 5501 .365 2.737 2.747 2.721 2.597 1.328 52 329 2.848 .95 90 2070 9060 121 130 102 111 0 6072 246 5826 3.874 5955 5708 .258 3.889 1.954 1.959
6 927 515 229 171 698 344 946 501 233 177 717 330 0 0 129 97 41 61 100 100 100 96 1042 1047 2.029 .493 .46 .48 .499 1.467 32 206 .459 .79 70 2220 9060 122 129 118 125 0 729 242 487 .698 709 467 1.434 .651 -.52 -.618
7 2660 907 224 153 2436 754 2863 935 228 164 2639 782 0 0 1093 350 42 58 100 98 100 98 3190 3421 3.231 .31 .296 .3 .301 1.621 52 266 .289 .92 80 2360 9060 122 130 132 140 0 1284 217 1067 .438 1323 1107 2.283 .419 -1.191 -1.254
8 847 612 214 149 633 463 846 605 221 159 632 456 0 0 190 168 43 65 100 98 100 98 1096 1088 1.367 .731 .722 .729 .713 1.434 52 300 .736 .87 90 2510 9060 121 130 146 155 0 866 211 655 1.035 856 645 .966 1.021 .05 .03
9 710 351 199 145 511 206 703 360 207 155 504 215 0 0 149 90 74 70 100 90 100 78 717 719 2.481 .403 .427 .376 .433 1.782 52 316 .405 .79 90 2660 9060 121 130 161 170 0 497 205 292 .571 510 304 1.753 .604 -.809 -.728
10 440 300 194 168 246 132 449 309 199 175 255 141 0 0 93 75 38 58 100 84 96 53 378 396 1.864 .537 .553 .491 .553 2.019 32 166 .535 .62 60 2800 9050 122 128 177 183 0 425 238 187 .76 437 200 1.317 .783 -.397 -.354
11 1803 5258 175 143 1628 5115 1872 5452 177 151 1697 5309 0 0 416 1140 38 54 100 100 100 100 6743 7006 .318 3.142 3.128 3.17 3.089 1.3 52 313 3.259 .95 90 2950 9060 121 130 190 199 0 7442 202 7240 4.447 7717 7515 .225 4.428 2.153 2.147
12 4315 2968 157 138 4158 2830 3938 2716 172 156 3781 2578 0 0 2727 1696 92 82 96 100 94 100 6988 6359 1.469 .681 .682 .835 .715 2.441 52 254 .634 .92 80 3090 9060 122 130 205 213 0 4201 195 4006 .963 3844 3649 1.038 .965 -.054 -.051
13 845 2334 154 134 691 2200 841 2409 165 145 687 2275 0 0 262 751 81 72 100 100 97 100 2891 2962 .314 3.184 3.311 3.272 3.215 1.303 80 352 3.231 .94 100 3250 9060 121 131 220 230 0 3304 190 3114 4.506 3410 3220 .222 4.687 2.172 2.229
14 454 304 162 136 292 168 457 299 163 141 295 163 0 0 144 89 31 48 98 91 95 76 460 458 1.738 .575 .553 .579 .585 2.167 80 351 .56 .8 100 3390 9060 121 131 234 244 0 430 192 238 .814 423 231 1.228 .782 -.296 -.355
15 607 324 158 139 449 185 608 317 161 144 450 178 0 0 106 77 27 49 100 98 100 88 634 628 2.427 .412 .396 .383 .415 1.599 52 258 .41 .8 90 3550 9060 121 130 250 259 0 459 197 262 .583 449 252 1.715 .56 -.778 -.837
16 8731 7617 158 143 8573 7474 9140 7753 180 314 8982 7610 0 0 4159 3722 167 1211 100 95 100 85 16047 16592 1.147 .872 .847 .853 .831 1.553 80 322 .874 .95 100 3680 9060 121 131 263 273 0 10781 202 10579 1.234 10974 10771 .81 1.199 .303 .262
17 2489 1630 162 140 2327 1490 2442 1622 181 289 2280 1482 0 0 750 483 167 1156 100 75 100 3 3817 3762 1.562 .64 .65 .643 .636 1.37 52 277 .621 .94 90 3830 9060 121 130 278 287 0 2307 198 2109 .906 2296 2098 1.103 .92 -.142 -.12
18 212 172 151 129 61 43 185 160 155 138 34 31 0 0 99 73 31 47 51 38 32 21 104 65 1.419 .705 .912 1.05 .907 4.363 52 254 .861 .54 80 3970 9050 121 129 293 301 -50 243 183 61 .998 226 44 1.002 1.291 -.003 .368
19 6273 3149 152 134 6121 3015 6180 3165 154 141 6028 3031 0 0 2613 1517 28 51 100 100 100 100 9136 9059 2.03 .493 .503 .463 .497 1.518 80 345 .497 .95 100 4120 9060 121 131 307 317 0 4457 190 4268 .697 4480 4290 1.434 .712 -.52 -.491
20 2806 1551 158 133 2648 1418 2607 1504 161 140 2449 1371 0 0 1168 640 37 50 100 100 100 100 4066 3820 1.867 .535 .56 .522 .542 1.393 52 289 .525 .95 90 4260 9050 120 129 321 330 0 2195 188 2007 .758 2129 1941 1.319 .792 -.4 -.336

Total number of rows: 43104

Table truncated, full table size 9446 Kbytes.




Supplementary data files not provided
Raw data included within Sample table
Processed data not provided for this record

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