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Sample GSM173021 Query DataSets for GSM173021
Status Public on Sep 28, 2007
Title SM, colon #3, low
Sample type RNA
 
Channel 1
Source name Stratagene
Organism Homo sapiens
Characteristics Stratagene
LabeledExtract: 36246.Channel_1
Extracted molecule total RNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name SM, colon #3, low
Organism Homo sapiens
Characteristics SM, colon #3, low
LabeledExtract: 36246.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 = 31.45; Parameter Scan Time = 12:46:54; Parameter PMT Volts = 600; Parameter Scan Date = 2002-12-04; Parameter Pixel Size = 10; Parameter Laser on time = 41945; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 4.44; 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 = 31.45; Parameter Scan Time = 12:46:54; Parameter PMT Volts = 660; Parameter Scan Date = 2002-12-04; Parameter Pixel Size = 10; Parameter Laser on time = 260940; 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/2002-12/36246.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
1 519 277 190 112 329 165 458 205 222 116 268 93 0 0 268 166 134 42 71 81 50 56 494 361 1.994 .502 .347 .5 .499 1.867 32 164 .49 .84 60 1740 8650 82 88 71 77 0 428 173 255 .776 317 144 1.289 .537 -.366 -.898
2 7820 824 186 107 7634 717 8399 827 226 112 8213 720 0 0 5605 550 301 37 87 87 84 84 8351 8933 10.647 .094 .088 .097 .093 1.656 32 222 .09 .96 70 1880 8660 82 89 84 91 0 1275 166 1109 .145 1279 1114 6.883 .136 -2.783 -2.883
3 2475 835 187 106 2288 729 807 261 202 116 620 155 0 0 3076 938 99 98 78 56 65 46 3017 775 3.139 .319 .25 .393 .324 2.618 32 200 .302 .95 70 2010 8620 78 85 97 104 0 1292 164 1128 .493 404 240 2.029 .387 -1.021 -1.371
4 800 224 183 105 617 119 371 148 188 112 188 43 0 0 968 198 38 37 78 53 71 36 736 231 5.185 .193 .229 .243 .206 2.914 52 295 .192 .91 80 2170 8660 82 90 113 121 0 346 162 184 .298 229 67 3.352 .354 -1.745 -1.499
5 2144 2319 171 116 1973 2203 1916 2020 183 123 1745 1904 0 0 1639 1830 52 45 100 90 84 87 4176 3649 .896 1.117 1.091 1.079 1.102 1.663 32 170 1.087 .97 60 2320 8650 82 88 129 135 0 3587 179 3408 1.727 3124 2945 .579 1.688 .788 .755
6 718 318 183 104 535 214 523 212 186 113 340 108 0 0 628 260 37 38 80 73 71 57 749 448 2.5 .4 .318 .407 .392 2.388 52 296 .399 .96 80 2470 8650 81 89 143 151 0 492 161 331 .619 328 167 1.616 .491 -.693 -1.025
7 3228 1901 186 108 3042 1793 2714 1374 190 112 2528 1266 0 0 2839 1648 37 37 100 100 100 93 4835 3794 1.697 .589 .501 .639 .604 1.449 32 210 .582 .99 70 2620 8650 81 88 158 165 0 2940 167 2773 .912 2125 1958 1.097 .775 -.133 -.368
8 692 579 170 112 522 467 337 295 175 118 167 183 0 0 653 583 35 40 73 65 67 61 989 350 1.118 .895 1.096 .896 .896 2.359 52 293 .894 .97 80 2750 8650 81 89 171 179 0 896 173 722 1.384 456 283 .723 1.695 .469 .761
9 1060 632 167 112 893 520 1043 586 212 138 876 474 0 0 234 231 347 149 100 100 81 84 1413 1350 1.717 .582 .541 .548 .574 1.381 32 213 .381 .61 70 2900 8640 80 87 186 193 0 978 173 804 .901 906 733 1.11 .837 -.151 -.257
10 323 203 168 121 155 82 204 150 175 130 36 29 0 0 238 164 40 61 48 32 40 19 237 65 1.89 .529 .806 .477 .541 2.61 52 269 .632 .75 80 3040 8650 81 89 200 208 -50 314 187 127 .818 232 45 1.222 1.246 -.289 .317
11 3209 8989 190 117 3019 8872 2967 8114 196 123 2777 7997 0 0 1791 4900 41 42 100 100 100 100 11891 10774 .34 2.939 2.88 3.191 2.975 1.416 52 285 2.89 .99 80 3190 8660 82 90 215 223 0 13904 181 13723 4.546 12551 12370 .22 4.454 2.184 2.155
12 3922 2793 211 124 3711 2669 2160 1484 220 130 1949 1360 0 0 4386 3264 52 45 94 96 94 90 6380 3309 1.39 .719 .698 .725 .684 1.552 52 304 .732 .99 90 3340 8660 81 90 229 238 0 4320 192 4128 1.112 2295 2104 .899 1.079 .154 .11
13 1320 5569 204 132 1116 5437 1270 4637 206 139 1066 4505 0 0 812 3869 48 49 93 100 93 100 6553 5571 .205 4.872 4.226 5.065 4.888 1.554 80 352 4.886 .98 100 3480 8650 80 90 243 253 0 8614 204 8410 7.536 7172 6968 .133 6.537 2.914 2.709
14 883 573 189 155 694 418 866 557 192 165 677 402 0 0 164 143 45 55 100 100 100 100 1112 1079 1.66 .602 .594 .576 .6 1.382 52 242 .626 .91 80 3620 8650 81 89 258 266 0 886 240 647 .932 862 622 1.073 .918 -.102 -.123
15 726 320 212 174 514 146 727 332 214 183 515 158 0 0 158 87 48 58 100 84 98 59 660 673 3.521 .284 .307 .266 .279 1.549 52 264 .323 .79 80 3780 8650 81 89 274 282 0 495 269 226 .439 514 244 2.276 .475 -1.187 -1.075
16 12056 8998 225 181 11831 8817 11637 8937 230 191 11412 8756 0 0 4805 3501 48 58 100 100 100 100 20648 20168 1.342 .745 .767 .747 .747 1.116 52 257 .739 .99 80 3920 8650 81 89 288 296 0 13918 280 13638 1.153 13824 13544 .868 1.187 .205 .247
17 4366 2097 285 187 4081 1910 4313 1945 283 196 4028 1758 0 0 2177 1164 76 69 100 100 100 100 5991 5786 2.137 .468 .436 .436 .455 1.222 32 148 .481 .99 60 4070 8640 81 87 304 310 0 3244 289 2954 .724 3008 2719 1.381 .675 -.466 -.567
18 221 167 225 152 -4 15 203 168 235 156 -22 16 0 0 74 48 78 57 9 15 3 1 11 -6 null null null .867 .796 2.529 52 257 .448 .38 80 4200 8640 80 88 316 324 -50 258 235 23 null 260 25 null null null null
19 7920 3746 193 121 7727 3625 8218 3771 200 125 8025 3650 0 0 2544 1332 50 49 100 100 100 100 11352 11675 2.132 .469 .455 .462 .469 1.119 52 301 .472 .99 90 4350 8650 80 89 330 339 0 5794 187 5607 .726 5833 5646 1.378 .704 -.463 -.507
20 2924 1434 187 105 2737 1329 2893 1455 194 111 2706 1350 0 0 887 540 49 39 100 100 100 100 4066 4056 2.059 .486 .499 .467 .506 1.262 52 301 .499 .97 90 4490 8640 79 88 344 353 0 2218 162 2056 .751 2251 2088 1.331 .772 -.413 -.374

Total number of rows: 43104

Table truncated, full table size 9619 Kbytes.




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

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