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Sample GSM173041 Query DataSets for GSM173041
Status Public on Sep 28, 2007
Title SM, Cervix #2
Sample type RNA
 
Channel 1
Source name Stratagene
Organism Homo sapiens
Characteristics Stratagene
LabeledExtract: 34764.Channel_1
Extracted molecule total RNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name SM, Cervix #2
Organism Homo sapiens
Characteristics SM, Cervix #2
LabeledExtract: 34764.Channel_2
Extracted molecule total RNA
Extraction protocol not provided
Label Cy5
Label protocol not provided
 
 
Hybridization protocol not provided
Scan protocol not provided
Description Simple annotation: Smooth muscle cells, Anatomical comparisons
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/34764.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 GPL3322
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
1 518 605 143 112 375 493 510 584 143 117 367 472 0 0 192 341 32 44 96 90 94 88 868 839 .761 1.315 1.286 1.348 1.452 2.374 52 281 1.553 .79 90 1530 9060 23 32 80 89 0 672 124 548 1.461 649 524 .685 1.429 .547 .515
2 4728 5793 132 108 4596 5685 4979 6038 147 116 4847 5930 0 0 2562 3697 133 51 100 100 97 98 10281 10777 .808 1.237 1.223 1.04 1.282 2.758 80 386 1.353 .92 110 1660 9060 22 33 92 103 0 6437 120 6317 1.374 6709 6589 .728 1.359 .459 .443
3 3053 1899 134 106 2919 1793 3204 2008 165 117 3070 1902 0 0 1211 810 203 60 100 100 100 100 4712 4972 1.628 .614 .62 .61 .63 1.838 32 159 .566 .85 60 1820 9070 26 32 111 117 0 2110 118 1992 .683 2231 2113 1.465 .688 -.551 -.539
4 1456 735 136 111 1320 624 1639 779 144 121 1503 668 0 0 651 336 49 96 96 94 94 92 1944 2171 2.115 .473 .444 .542 .513 1.924 52 316 .459 .86 90 1960 9060 23 32 123 132 0 817 123 693 .525 866 742 1.904 .494 -.929 -1.018
5 1967 2399 140 110 1827 2289 2040 2544 146 120 1900 2434 0 0 888 1169 51 94 97 100 97 98 4116 4334 .798 1.253 1.281 1.183 1.185 1.955 80 336 1.311 .9 100 2110 9060 23 33 138 148 0 2666 122 2543 1.392 2827 2704 .718 1.423 .477 .509
6 1089 495 139 107 950 388 1055 489 142 115 916 382 0 0 609 289 43 51 95 83 91 76 1338 1298 2.448 .408 .417 .42 .427 2.533 80 318 .393 .86 100 2250 9060 23 33 152 162 0 550 119 431 .454 543 424 2.204 .463 -1.14 -1.11
7 2374 1608 138 109 2236 1499 2096 1493 140 117 1958 1384 0 0 1569 1036 31 45 98 98 97 97 3735 3342 1.492 .67 .707 .679 .659 1.995 80 314 .638 .91 100 2400 9070 24 34 167 177 0 1787 121 1666 .745 1659 1538 1.342 .785 -.425 -.349
8 715 1528 135 108 580 1420 735 1586 138 113 600 1478 0 0 382 789 28 47 93 95 88 93 2000 2078 .408 2.448 2.463 2.627 2.531 1.801 80 306 2.499 .89 100 2550 9070 24 34 182 192 0 1698 120 1578 2.72 1762 1642 .368 2.737 1.444 1.453
9 870 1548 133 103 737 1445 918 1665 135 108 785 1562 0 0 292 594 30 51 96 100 95 98 2182 2347 .51 1.961 1.99 1.93 1.967 1.621 80 365 2.224 .89 110 2690 9060 22 33 195 206 0 1720 114 1606 2.179 1850 1736 .459 2.211 1.123 1.145
10 387 294 129 111 258 183 389 275 134 126 260 164 0 0 155 133 31 85 88 71 86 46 441 424 1.41 .709 .631 .693 .743 2.231 52 204 .766 .7 80 2840 9070 25 33 212 220 0 327 123 203 .788 306 182 1.269 .701 -.344 -.513
11 2551 2074 136 109 2415 1965 2736 2313 140 118 2600 2204 0 0 744 830 46 68 100 100 100 98 4380 4804 1.229 .814 .848 .746 .84 1.913 80 338 .842 .91 110 2980 9060 22 33 224 235 0 2304 121 2183 .904 2570 2449 1.106 .942 -.145 -.086
12 7116 8039 136 105 6980 7934 7752 8840 138 110 7616 8735 0 0 3715 4710 31 42 94 100 93 99 14914 16351 .88 1.137 1.147 1.064 1.178 2.856 120 370 1.198 .91 120 3120 9070 23 35 238 250 0 8932 117 8816 1.263 9822 9706 .792 1.274 .337 .35
13 1295 2939 139 114 1156 2825 1374 3183 140 117 1235 3069 0 0 430 1045 31 40 100 100 98 100 3981 4304 .409 2.444 2.485 2.424 2.464 1.852 80 350 2.74 .89 110 3270 9060 22 33 253 264 0 3266 127 3139 2.715 3537 3410 .368 2.761 1.441 1.465
14 637 385 139 105 498 280 669 371 136 107 530 266 0 0 202 154 36 37 97 96 97 91 778 796 1.779 .562 .502 .519 .566 2.249 80 362 .556 .79 110 3420 9060 22 33 268 279 0 428 117 311 .625 412 296 1.601 .558 -.679 -.843
15 617 395 125 92 492 303 618 402 121 96 493 310 0 0 176 136 46 42 100 95 98 93 795 803 1.624 .616 .629 .605 .637 1.944 80 332 .614 .78 110 3560 9060 22 33 282 293 0 439 102 337 .684 447 344 1.461 .699 -.547 -.517
16 10499 15163 131 103 10368 15060 11919 16522 131 108 11788 16419 0 0 5061 6827 41 43 100 100 100 100 25428 28207 .688 1.453 1.393 1.563 1.396 1.939 120 437 1.469 .92 130 3710 9070 22 35 296 309 0 16848 114 16733 1.614 18358 18243 .62 1.548 .691 .63
17 4336 6210 135 103 4201 6107 4615 6607 138 110 4480 6504 0 0 1504 2676 33 42 100 99 100 98 10308 10984 .688 1.454 1.452 1.323 1.496 2.107 120 375 1.559 .92 120 3850 9060 22 34 311 323 0 6900 114 6786 1.615 7341 7227 .619 1.613 .692 .69
18 238 204 132 103 106 101 169 133 133 109 37 30 0 0 214 179 31 38 51 42 40 30 207 67 1.05 .953 .811 .594 .721 3.427 52 174 .815 .64 80 3990 9060 24 32 327 335 -50 227 114 112 1.059 148 33 .945 .901 .082 -.151
19 6365 3766 129 103 6236 3663 6524 3681 131 106 6395 3578 0 0 3235 2224 28 36 100 98 100 97 9899 9973 1.702 .587 .559 .532 .581 2.457 120 389 .6 .94 120 4140 9060 22 34 340 352 0 4184 114 4070 .653 4090 3976 1.532 .622 -.616 -.686
20 2363 2164 133 104 2230 2060 2465 2426 136 109 2332 2322 0 0 754 966 30 39 100 96 100 95 4290 4654 1.083 .924 .996 .764 .959 2.488 120 348 .989 .91 120 4290 9060 22 34 355 367 0 2404 116 2289 1.026 2696 2580 .974 1.106 .038 .146

Total number of rows: 43104

Table truncated, full table size 9501 Kbytes.




Supplementary data files not provided
Processed data not provided for this record
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