NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM173016 Query DataSets for GSM173016
Status Public on Sep 28, 2007
Title SM, bladder #3, low
Sample type RNA
 
Channel 1
Source name Stratagene
Organism Homo sapiens
Characteristics Stratagene
LabeledExtract: 36241.Channel_1
Extracted molecule total RNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name SM, bladder #3, low
Organism Homo sapiens
Characteristics SM, bladder #3, low
LabeledExtract: 36241.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 = 30.90; Parameter Scan Time = 11:53:34; Parameter PMT Volts = 600; Parameter Scan Date = 2002-12-04; Parameter Pixel Size = 10; Parameter Laser on time = 41892; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 3.01; 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 = 30.90; Parameter Scan Time = 11:53:34; Parameter PMT Volts = 640; Parameter Scan Date = 2002-12-04; Parameter Pixel Size = 10; Parameter Laser on time = 260887; 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/2002-12/36241.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
1 500 247 196 82 304 165 350 131 198 84 154 49 0 0 391 249 47 25 67 59 55 50 469 203 1.842 .543 .318 .458 .534 3.016 52 299 .587 .93 80 1770 8700 86 94 73 81 -50 366 121 244 .804 194 73 1.244 .471 -.315 -1.086
2 7174 728 196 89 6978 639 6973 597 208 90 6777 508 0 0 4932 514 127 30 100 93 93 87 7617 7285 10.92 .092 .075 .094 .085 1.473 32 171 .094 .97 60 1920 8710 88 94 89 95 0 1078 132 946 .136 884 752 7.374 .111 -2.882 -3.171
3 784 357 173 82 611 275 213 116 179 85 40 34 0 0 1034 495 43 27 48 53 44 40 886 74 2.222 .45 .85 .5 .445 3.515 52 283 .463 .97 80 2060 8700 86 94 102 110 -50 529 121 407 .667 172 50 1.5 1.259 -.585 .332
4 930 727 172 78 758 649 822 242 175 84 650 164 0 0 728 1675 42 29 81 75 78 68 1407 814 1.168 .856 .252 .428 .283 3.182 32 144 4.502 .62 60 2200 8680 85 91 117 123 0 1077 116 961 1.268 358 243 .789 .374 .343 -1.42
5 1945 3625 177 85 1768 3540 1852 3770 181 103 1675 3685 0 0 1337 2342 43 71 100 100 100 100 5308 5360 .499 2.002 2.2 2.11 2.107 1.28 32 164 1.931 .97 60 2360 8700 87 93 133 139 0 5368 126 5243 2.965 5583 5457 .337 3.258 1.568 1.704
6 497 263 154 85 343 178 220 144 154 89 66 59 0 0 522 244 32 27 76 65 50 55 521 125 1.927 .519 .894 .654 .57 2.118 52 276 .477 .94 80 2500 8700 86 94 146 154 0 389 126 264 .769 213 87 1.301 1.324 -.38 .405
7 1750 589 151 81 1599 508 581 258 153 85 430 177 0 0 2021 640 32 24 98 80 94 65 2107 607 3.148 .318 .412 .266 .316 1.988 52 274 .313 .98 80 2650 8700 86 94 161 169 0 872 120 752 .47 382 262 2.125 .61 -1.088 -.714
8 673 476 152 84 521 392 312 193 155 87 160 109 0 0 643 501 33 28 84 75 67 61 913 269 1.329 .752 .681 .63 .769 2.004 52 268 .767 .97 80 2790 8700 86 94 175 183 0 705 124 581 1.114 286 161 .897 1.009 .156 .013
9 1054 510 151 85 903 425 1091 488 155 89 940 403 0 0 360 193 36 30 100 100 100 100 1328 1343 2.125 .471 .429 .461 .478 1.278 52 264 .473 .96 80 2930 8710 87 95 189 197 0 755 126 629 .697 723 597 1.435 .635 -.521 -.655
10 314 216 147 84 167 132 194 101 149 91 47 17 0 0 273 238 34 47 59 38 42 32 299 64 1.265 .79 .362 .671 .767 3.064 52 282 .822 .94 80 3070 8700 86 94 203 211 -50 320 124 195 1.171 150 25 .854 .536 .227 -.901
11 3131 9390 153 87 2978 9303 3144 9814 174 158 2991 9727 0 0 1117 2792 142 414 100 100 100 100 12281 12718 .32 3.124 3.252 3.245 3.159 1.214 32 231 3.054 .99 70 3230 8700 86 93 219 226 0 13906 129 13777 4.626 14534 14405 .216 4.816 2.21 2.268
12 2937 1780 152 86 2785 1694 1127 731 156 90 975 645 0 0 3460 2069 33 32 96 94 94 90 4479 1620 1.644 .608 .662 .605 .61 1.692 52 263 .594 .98 80 3380 8710 87 95 234 242 0 2636 127 2509 .901 1083 955 1.11 .98 -.151 -.03
13 1498 3414 157 91 1341 3323 1336 3216 156 94 1179 3125 0 0 720 1578 30 28 100 100 100 100 4664 4304 .404 2.478 2.651 2.563 2.594 1.216 52 289 2.43 .98 90 3500 8700 85 94 245 254 0 5056 135 4921 3.67 4763 4628 .272 3.925 1.876 1.973
14 542 342 149 92 393 250 564 350 151 96 415 258 0 0 196 131 30 31 96 96 95 95 643 673 1.572 .636 .622 .615 .632 1.934 80 404 .63 .9 100 3650 8710 86 96 260 270 0 506 136 370 .942 518 382 1.061 .921 -.086 -.119
15 648 318 145 108 503 210 683 307 147 112 538 199 0 0 173 107 31 37 100 100 100 96 713 737 2.395 .417 .37 .395 .409 1.451 52 311 .416 .86 90 3800 8700 85 94 275 284 0 471 160 311 .618 455 295 1.617 .548 -.694 -.868
16 10155 7567 139 102 10016 7465 10407 7786 139 107 10268 7684 0 0 3825 2521 26 35 100 100 100 100 17481 17952 1.342 .745 .748 .759 .755 1.137 52 338 .729 .99 90 3940 8700 85 94 289 298 0 11206 151 11055 1.104 11531 11380 .906 1.108 .142 .148
17 4182 2578 137 85 4045 2493 4189 2689 138 91 4052 2604 0 0 1706 1091 26 30 100 100 100 100 6538 6656 1.623 .616 .643 .607 .611 1.16 32 213 .618 .99 70 4090 8700 86 93 305 312 0 3818 126 3692 .913 3982 3856 1.096 .952 -.132 -.071
18 149 96 126 80 23 16 132 86 131 83 6 6 0 0 54 43 33 25 25 26 15 17 39 12 1.438 .696 1 1.143 1.306 4.639 52 258 .608 .16 80 4230 8700 86 94 319 327 -50 142 118 24 1.03 127 9 .971 1.481 .043 .567
19 5319 2513 118 80 5201 2433 5132 2443 122 82 5014 2363 0 0 1433 629 31 24 100 100 100 100 7634 7377 2.138 .468 .471 .485 .455 1.402 52 301 .459 .98 90 4370 8700 85 94 332 341 0 3722 118 3603 .693 3618 3499 1.443 .698 -.53 -.519
20 2335 1210 117 81 2218 1129 2359 1252 124 88 2242 1171 0 0 834 435 107 67 100 100 100 100 3347 3413 1.965 .509 .522 .505 .513 1.209 52 302 .508 .98 90 4520 8690 84 93 347 356 0 1792 120 1672 .754 1854 1734 1.327 .773 -.408 -.371

Total number of rows: 43104

Table truncated, full table size 9458 Kbytes.




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

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap