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Sample GSM173067 Query DataSets for GSM173067
Status Public on Sep 28, 2007
Title SM, PA #2
Sample type RNA
 
Channel 1
Source name Stratagene
Organism Homo sapiens
Characteristics Stratagene
LabeledExtract: 34741.Channel_1
Extracted molecule total RNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name SM, PA #2
Organism Homo sapiens
Characteristics SM, PA #2
LabeledExtract: 34741.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/2002-11/34741.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 GPL3268
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
1 596 378 426 291 170 87 478 285 625 750 52 -6 0 0 290 274 1049 2578 0 0 0 0 257 46 1.954 .512 null 1.015 .917 3.981 52 252 3.404 .76 80 1770 8270 143 151 129 137 -50 347 267 80 .47 261 null 2.13 null -1.091 null
2 1502 487 406 283 1096 204 1520 492 418 291 1114 209 0 0 520 176 108 108 97 72 96 47 1300 1323 5.373 .186 .188 .196 .191 2.239 80 389 .174 .57 100 1900 8270 142 152 141 151 0 447 260 187 .171 451 192 5.856 .172 -2.55 -2.539
3 1487 1303 410 213 1077 1090 1436 1364 438 255 1026 1151 0 0 422 528 171 189 100 100 100 91 2167 2177 .988 1.012 1.122 .957 1.108 2.17 12 104 1.012 .6 50 2070 8270 144 149 160 165 0 1195 195 1000 .929 1251 1056 1.077 1.029 -.107 .042
4 1813 803 397 180 1416 623 1828 878 397 200 1431 698 0 0 324 293 90 92 100 83 100 83 2039 2129 2.273 .44 .488 .342 .498 3.03 12 104 .448 .66 50 2220 8270 144 149 175 180 0 737 165 572 .404 806 640 2.477 .447 -1.309 -1.16
5 1467 3349 346 238 1121 3111 1531 3699 415 373 1185 3461 0 0 669 1643 309 552 83 100 75 75 4232 4646 .36 2.775 2.921 3.231 3.399 2.113 12 104 3.098 .81 50 2350 8270 144 149 188 193 0 3072 218 2854 2.546 3394 3175 .393 2.68 1.348 1.422
6 517 671 404 257 113 414 480 624 409 280 76 367 0 0 242 455 74 155 50 62 43 59 527 443 .273 3.664 4.829 1.333 1.723 4.856 32 172 127.35 .03 60 2520 8270 144 150 205 211 0 616 236 380 3.361 572 337 .298 4.43 1.749 2.147
7 2515 2304 427 231 2088 2073 2890 2250 430 250 2463 2019 0 0 1285 1301 75 97 93 87 93 87 4161 4482 1.007 .993 .82 .812 1.095 3.164 32 167 .959 .83 60 2650 8270 144 150 218 224 0 2114 212 1902 .911 2064 1852 1.098 .752 -.135 -.411
8 1189 910 423 211 766 699 1200 1025 462 263 777 814 0 0 153 369 173 172 100 83 100 75 1465 1591 1.096 .913 1.048 .688 1.004 2.515 12 98 1.116 .71 50 2790 8260 143 148 232 237 0 835 194 641 .837 940 747 1.194 .961 -.256 -.057
9 867 994 424 241 443 753 851 960 436 272 427 719 0 0 406 382 107 141 73 97 68 91 1196 1146 .588 1.7 1.684 1.714 1.349 2.903 80 406 1.54 .66 100 2940 8270 142 152 245 255 0 912 221 691 1.559 881 660 .641 1.545 .641 .627
10 658 878 424 233 234 645 722 652 426 271 298 419 0 0 224 458 80 182 75 87 75 62 879 717 .363 2.756 1.406 1.488 1.321 3.449 32 174 14.443 .14 70 3100 8260 142 149 262 269 0 806 214 592 2.529 598 384 .395 1.29 1.338 .367
11 3127 14628 417 252 2710 14376 3395 16570 422 270 2978 16318 0 0 1942 8229 76 134 95 100 92 100 17086 19296 .189 5.305 5.48 5.906 5.654 2.104 80 428 5.31 .89 110 3220 8270 141 152 272 283 0 13420 231 13189 4.867 15202 14971 .205 5.027 2.283 2.33
12 4032 6739 417 248 3615 6491 3721 7419 431 282 3304 7171 0 0 2474 4251 112 162 100 100 100 100 10106 10475 .557 1.796 2.17 1.867 1.819 1.895 32 220 1.774 .93 70 3370 8270 143 150 289 296 0 6183 228 5955 1.647 6806 6579 .607 1.991 .72 .994
13 761 2713 408 243 353 2470 750 2774 415 277 342 2531 0 0 367 1459 105 168 69 100 57 96 2823 2873 .143 6.997 7.401 6.11 5.384 2.007 52 320 6.279 .81 90 3530 8270 142 151 304 313 0 2489 223 2266 6.419 2545 2322 .156 6.79 2.682 2.763
14 1129 602 393 233 736 369 1016 609 398 252 623 376 0 0 496 239 77 109 90 81 88 77 1105 999 1.995 .501 .604 .541 .517 2.393 80 486 .488 .73 110 3660 8260 140 151 316 327 0 552 214 339 .46 559 345 2.174 .554 -1.12 -.853
15 361 790 386 219 -25 571 360 592 390 273 -26 373 0 0 71 677 72 225 9 59 0 43 546 347 null null null 2.932 2.829 6.149 32 140 -1 -1 60 3830 8250 142 148 336 342 0 725 201 524 null 543 342 null null null null
16 5570 7641 411 268 5159 7373 6153 7411 417 286 5742 7143 0 0 3216 4527 80 162 100 100 98 98 12532 12885 .7 1.429 1.244 1.472 1.469 2.585 52 300 1.46 .91 90 3950 8260 141 150 346 355 0 7010 246 6764 1.311 6799 6553 .763 1.141 .391 .191
17 4894 6546 421 287 4473 6259 5488 7483 436 323 5067 7196 0 0 1947 3177 98 213 99 96 98 95 10732 12263 .715 1.399 1.42 1.211 1.397 2.566 120 497 1.502 .9 120 4100 8260 140 152 360 372 0 6006 263 5742 1.284 6865 6602 .779 1.303 .36 .382
18 507 690 416 260 91 430 412 354 416 278 -4 94 0 0 305 722 65 109 28 48 17 38 521 90 .212 4.725 null 2.076 1.748 5.185 52 206 9.787 .25 80 4240 8260 142 150 376 384 -50 633 239 394 4.335 325 86 .231 null 2.116 null
19 5812 5393 413 244 5399 5149 6225 5714 434 269 5812 5470 0 0 2670 2516 211 190 98 98 97 96 10548 11282 1.049 .954 .941 .938 .934 2.076 80 391 .945 .92 110 4390 8260 140 151 389 400 0 4948 224 4724 .875 5242 5018 1.143 .863 -.193 -.212
20 3800 3866 419 244 3381 3622 3735 4005 456 294 3316 3761 0 0 1283 1509 268 254 100 98 98 98 7003 7077 .933 1.071 1.134 1.065 1.071 1.673 80 390 1.091 .86 110 4530 8260 140 151 403 414 0 3547 224 3323 .983 3674 3450 1.017 1.041 -.025 .057

Total number of rows: 43008

Table truncated, full table size 9716 Kbytes.




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