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Sample GSM173018 Query DataSets for GSM173018
Status Public on Sep 28, 2007
Title SM, urethra#2, low
Sample type RNA
 
Channel 1
Source name Stratagene
Organism Homo sapiens
Characteristics Stratagene
LabeledExtract: 36243.Channel_1
Extracted molecule total RNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name SM, urethra#2, low
Organism Homo sapiens
Characteristics SM, urethra#2, low
LabeledExtract: 36243.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 = 31.18; Parameter Scan Time = 12:14:39; Parameter PMT Volts = 600; Parameter Scan Date = 2002-12-04; Parameter Pixel Size = 10; Parameter Laser on time = 41914; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 4.59; 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 = 31.18; Parameter Scan Time = 12:14:39; Parameter PMT Volts = 640; Parameter Scan Date = 2002-12-04; Parameter Pixel Size = 10; Parameter Laser on time = 260909; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 3.38; 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/2002-12/36243.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
1 863 389 267 117 596 272 871 363 279 130 604 246 0 0 300 194 88 61 100 91 91 66 868 850 2.191 .456 .407 .393 .463 1.715 12 98 .509 .87 50 1860 8880 105 110 83 88 0 669 201 468 .785 624 423 1.274 .7 -.35 -.514
2 8771 1316 236 127 8535 1189 9133 1124 246 142 8897 997 0 0 6173 879 67 99 100 90 100 84 9724 9894 7.178 .139 .112 .147 .142 1.346 32 170 .137 .98 60 2010 8860 103 109 98 104 0 2263 218 2045 .24 1933 1714 4.175 .193 -2.062 -2.376
3 7032 2958 247 128 6785 2830 6123 2829 252 132 5876 2701 0 0 5296 2041 64 37 100 100 100 100 9615 8577 2.398 .417 .46 .465 .427 1.271 12 54 .412 .99 40 2160 8850 103 107 114 118 0 5086 220 4866 .717 4865 4644 1.394 .79 -.48 -.339
4 2842 522 243 127 2599 395 2726 552 252 135 2483 425 0 0 1863 274 63 44 100 83 100 83 2994 2908 6.58 .152 .171 .12 .144 2.432 12 104 .147 .94 50 2300 8870 104 109 127 132 0 898 218 679 .261 949 731 3.826 .294 -1.936 -1.765
5 3914 5630 309 155 3605 5475 3768 5630 474 489 3459 5475 0 0 2088 2916 570 1051 91 91 91 91 9080 8934 .658 1.519 1.583 1.531 1.565 1.225 12 90 1.472 .98 50 2440 8840 101 106 141 146 0 9681 267 9414 2.611 9681 9414 .383 2.722 1.385 1.445
6 1551 534 355 150 1196 384 1449 535 369 171 1094 385 0 0 649 181 149 80 100 100 100 91 1580 1479 3.115 .321 .352 .33 .31 1.29 12 104 .325 .94 50 2580 8870 104 109 155 160 0 918 258 660 .552 920 662 1.811 .605 -.857 -.725
7 3576 1337 332 180 3244 1157 3631 1146 427 223 3299 966 0 0 1694 661 469 202 100 100 100 91 4401 4265 2.804 .357 .293 .35 .363 1.279 12 104 .352 .98 50 2740 8880 105 110 171 176 0 2299 310 1989 .613 1971 1661 1.631 .504 -.705 -.99
8 1653 1074 290 194 1363 880 1423 915 344 213 1133 721 0 0 811 517 193 96 100 100 83 91 2243 1854 1.549 .646 .636 .636 .645 1.343 12 54 .666 .98 40 2890 8850 103 107 187 191 0 1847 334 1513 1.11 1573 1240 .901 1.094 .151 .13
9 1350 365 373 215 977 150 1227 338 377 218 854 123 0 0 350 136 122 77 100 68 100 40 1127 977 6.513 .154 .144 .129 .149 2.188 32 170 .172 .7 60 3020 8860 103 109 199 205 0 628 370 258 .264 581 212 3.788 .248 -1.921 -2.014
10 539 247 435 230 104 17 452 187 436 324 17 -43 0 0 297 178 129 1167 25 0 19 0 121 -26 6.118 .163 null .666 .658 3.769 52 284 .497 .7 80 3170 8850 101 109 213 221 -50 425 395 29 .281 322 -74 3.558 null -1.831 null
11 5033 2998 426 242 4607 2756 4430 2715 430 388 4004 2473 0 0 1780 1040 135 1480 100 93 100 37 7363 6477 1.672 .598 .618 .598 .585 1.16 32 176 .581 .95 60 3320 8860 103 109 229 235 0 5155 416 4739 1.029 4669 4252 .972 1.062 .041 .087
12 3806 1814 400 211 3406 1603 2090 868 440 388 1690 657 0 0 3868 1777 418 1623 76 36 61 19 5009 2347 2.125 .471 .389 .534 .494 1.579 52 325 .786 .6 90 3470 8860 101 110 242 251 0 3119 363 2756 .809 1493 1130 1.236 .668 -.305 -.581
13 2267 4804 417 201 1850 4603 2462 5126 458 389 2045 4925 0 0 1002 1973 433 1673 86 86 75 75 6453 6970 .402 2.488 2.408 2.876 2.445 1.88 52 306 3.031 .88 90 3600 8850 100 109 255 264 0 8261 346 7915 4.278 8814 8469 .234 4.141 2.097 2.05
14 899 366 396 220 503 146 903 365 401 232 507 145 0 0 181 94 110 95 100 65 96 28 649 652 3.445 .29 .286 .248 .297 2.037 52 335 .297 .55 90 3750 8860 101 110 270 279 0 629 378 251 .499 628 249 2.004 .492 -1.003 -1.024
15 1013 265 407 229 606 36 1005 255 403 240 598 26 0 0 178 100 94 70 100 31 100 12 642 624 16.833 .059 .043 .098 .12 2.4 32 208 .101 .36 70 3890 8860 102 109 285 292 0 456 394 62 .102 438 45 9.79 .075 -3.291 -3.742
16 11547 6390 383 218 11164 6172 11082 6113 380 225 10699 5895 0 0 4641 2359 85 68 100 100 100 100 17336 16594 1.809 .553 .551 .555 .532 1.164 52 273 .537 .98 80 4040 8860 102 110 300 308 0 10988 375 10613 .951 10511 10137 1.052 .947 -.073 -.078
17 5347 2636 341 205 5006 2431 5546 2684 343 217 5205 2479 0 0 2250 1082 115 83 100 100 100 100 7437 7684 2.059 .486 .476 .488 .485 1.176 32 200 .482 .99 70 4190 8870 103 110 315 322 0 4533 353 4180 .835 4615 4263 1.198 .819 -.26 -.288
18 298 221 304 180 -6 41 275 189 304 187 -29 9 0 0 127 108 86 64 15 32 7 11 35 -20 null null null .423 .482 3.732 52 236 .677 .44 80 4330 8850 101 109 329 337 -50 380 310 71 null 325 15 null null null null
19 8394 3150 284 126 8110 3024 8906 3360 284 133 8622 3234 0 0 3442 1059 78 44 100 100 100 100 11134 11856 2.682 .373 .375 .39 .355 1.32 52 288 .351 .98 90 4450 8850 100 109 340 349 0 5417 217 5200 .641 5778 5561 1.56 .645 -.641 -.633
20 3990 1708 268 123 3722 1585 3870 1616 276 128 3602 1493 0 0 1441 553 82 42 100 100 100 100 5307 5095 2.348 .426 .414 .439 .428 1.296 52 323 .41 .97 90 4610 8850 100 109 356 365 0 2937 212 2725 .732 2779 2567 1.366 .713 -.45 -.489

Total number of rows: 43104

Table truncated, full table size 9469 Kbytes.




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

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