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Sample GSM173019 Query DataSets for GSM173019
Status Public on Sep 28, 2007
Title SM, colon #1, low
Sample type RNA
 
Channel 1
Source name Stratagene
Organism Homo sapiens
Characteristics Stratagene
LabeledExtract: 36244.Channel_1
Extracted molecule total RNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name SM, colon #1, low
Organism Homo sapiens
Characteristics SM, colon #1, low
LabeledExtract: 36244.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 = 31.27; Parameter Scan Time = 12:25:38; Parameter PMT Volts = 600; Parameter Scan Date = 2002-12-04; Parameter Pixel Size = 10; Parameter Laser on time = 41924; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 4.46; 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 = 31.27; Parameter Scan Time = 12:25:38; Parameter PMT Volts = 660; Parameter Scan Date = 2002-12-04; Parameter Pixel Size = 10; Parameter Laser on time = 260919; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 3.40; 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/2002-12/36244.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
1 468 279 211 86 257 193 451 300 230 100 240 214 0 0 97 73 85 51 100 91 75 91 450 454 1.332 .751 .892 .725 .749 1.749 12 98 .59 .84 50 1910 8820 99 104 88 93 0 506 156 350 1.362 544 388 .734 1.617 .446 .693
2 3707 399 163 85 3544 314 4101 384 181 89 3938 299 0 0 1920 178 152 26 100 96 93 93 3858 4237 11.287 .089 .076 .09 .09 1.333 32 226 .085 .94 70 2060 8800 96 103 102 109 0 724 154 569 .161 696 542 6.224 .138 -2.638 -2.861
3 2341 653 146 94 2195 559 2298 502 152 95 2152 408 0 0 1316 401 37 30 100 100 100 100 2754 2560 3.927 .255 .19 .234 .254 1.257 12 48 .269 .98 40 2210 8770 95 99 119 123 0 1184 170 1014 .462 910 740 2.165 .344 -1.115 -1.54
4 781 177 143 86 638 91 579 129 151 88 436 43 0 0 528 101 48 24 90 68 90 50 729 479 7.011 .143 .099 .116 .138 2.037 32 145 .152 .87 60 2350 8770 94 100 132 138 0 321 156 165 .259 234 78 3.866 .179 -1.951 -2.483
5 945 836 135 84 810 752 684 743 138 86 549 659 0 0 723 651 24 25 96 90 90 88 1562 1208 1.077 .928 1.2 .88 .871 1.802 52 293 .908 .97 80 2490 8800 96 104 145 153 0 1516 152 1364 1.684 1347 1195 .594 2.177 .751 1.122
6 523 221 142 83 381 138 489 209 143 87 347 126 0 0 206 85 28 28 100 90 96 84 519 473 2.761 .362 .363 .357 .355 1.867 32 165 .333 .81 60 2640 8790 96 102 161 167 0 401 151 250 .657 379 228 1.523 .658 -.606 -.603
7 1222 581 146 89 1076 492 845 427 146 90 699 338 0 0 1023 480 26 27 100 92 98 88 1568 1037 2.187 .457 .484 .408 .444 1.82 52 281 .453 .96 80 2780 8800 96 104 174 182 0 1054 161 892 .829 774 613 1.206 .877 -.27 -.19
8 551 416 148 94 403 322 493 339 149 99 345 245 0 0 307 256 26 27 96 96 90 87 725 590 1.252 .799 .71 .767 .798 1.702 32 171 .804 .94 60 2930 8800 97 103 190 196 0 754 170 584 1.449 615 444 .69 1.288 .535 .365
9 544 219 150 88 394 131 546 218 150 92 396 130 0 0 152 69 23 30 100 96 98 82 525 526 3.008 .332 .328 .301 .312 1.762 52 269 .32 .84 80 3070 8790 95 103 203 211 0 397 160 238 .603 395 236 1.659 .595 -.73 -.748
10 249 111 150 90 99 21 214 102 151 93 64 12 0 0 103 45 26 31 69 30 55 15 120 76 4.714 .212 .188 .242 .24 2.638 52 270 .283 .4 80 3220 8790 95 103 218 226 -50 201 163 38 .385 185 22 2.6 .34 -1.378 -1.556
11 1673 4004 153 97 1520 3907 1652 3925 154 120 1499 3828 0 0 364 1017 28 124 100 100 100 100 5427 5327 .389 2.57 2.554 2.556 2.614 1.122 32 220 2.634 .98 70 3360 8790 95 102 232 239 0 7261 176 7085 4.661 7117 6942 .215 4.631 2.221 2.211
12 2093 1244 154 101 1939 1143 1567 912 155 105 1413 811 0 0 1850 1072 27 39 100 98 100 92 3082 2224 1.696 .589 .574 .578 .589 1.614 52 260 .579 .98 80 3520 8790 95 103 248 256 0 2256 183 2073 1.069 1654 1471 .936 1.041 .096 .058
13 806 3218 147 101 659 3117 897 3443 149 104 750 3342 0 0 414 1718 27 35 97 100 96 100 3776 4092 .211 4.73 4.456 5.198 4.687 1.537 80 377 4.648 .97 100 3650 8790 94 104 260 270 0 5835 183 5652 8.577 6243 6060 .117 8.08 3.1 3.014
14 543 250 143 99 400 151 532 253 143 103 389 154 0 0 123 67 25 33 100 96 100 88 551 543 2.649 .378 .396 .363 .377 1.639 52 267 .363 .79 80 3800 8790 95 103 276 284 0 453 180 274 .685 459 279 1.461 .718 -.547 -.478
15 515 173 143 112 372 61 545 170 143 116 402 58 0 0 133 46 24 37 100 65 100 36 433 460 6.098 .164 .144 .151 .172 2.253 52 258 .16 .59 80 3950 8790 95 103 291 299 0 314 203 111 .297 308 105 3.363 .262 -1.75 -1.934
16 6245 4106 132 116 6113 3990 6593 4223 136 122 6461 4107 0 0 1933 1276 28 40 100 100 100 100 10103 10568 1.532 .653 .636 .654 .66 1.112 52 320 .658 .98 90 4090 8790 94 103 304 313 0 7446 210 7235 1.184 7658 7448 .845 1.153 .243 .205
17 2039 1004 126 109 1913 895 2045 1009 131 113 1919 900 0 0 535 270 42 44 100 100 100 100 2808 2819 2.137 .468 .469 .464 .462 1.136 32 156 .466 .98 60 4250 8790 96 102 322 328 0 1821 198 1623 .848 1830 1632 1.179 .85 -.237 -.234
18 130 97 119 89 11 8 130 93 121 96 11 4 0 0 24 33 23 30 26 25 9 9 19 15 1.375 .727 .364 1.57 2.5 4.953 52 249 .58 .31 80 4370 8780 94 102 333 341 -50 176 161 15 1.319 169 7 .758 .659 .399 -.601
19 3876 2171 117 88 3759 2083 4169 2252 119 97 4052 2164 0 0 1219 760 26 56 100 100 100 100 5842 6216 1.805 .554 .534 .542 .563 1.152 52 293 .569 .98 90 4510 8780 93 102 346 355 0 3937 160 3777 1.005 4084 3924 .995 .968 .007 -.046
20 1151 592 113 83 1038 509 1270 630 119 88 1157 547 0 0 512 264 47 36 100 100 100 95 1547 1704 2.039 .49 .473 .474 .483 1.398 80 352 .485 .96 100 4660 8790 94 104 361 371 0 1074 151 923 .889 1142 992 1.125 .857 -.169 -.222

Total number of rows: 43104

Table truncated, full table size 9494 Kbytes.




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

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