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Sample GSM173069 Query DataSets for GSM173069
Status Public on Sep 28, 2007
Title SM, PA #4
Sample type RNA
 
Channel 1
Source name Stratagene
Organism Homo sapiens
Characteristics Stratagene
LabeledExtract: 34743.Channel_1
Extracted molecule total RNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name SM, PA #4
Organism Homo sapiens
Characteristics SM, PA #4
LabeledExtract: 34743.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/2002-11/34743.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
1 579 268 307 187 272 81 576 279 317 202 269 92 0 0 127 96 98 86 96 51 73 19 353 361 3.358 .298 .342 .391 .446 1.947 52 285 .602 .34 80 1680 8630 179 187 120 128 0 367 256 111 .408 382 126 2.451 .469 -1.294 -1.094
2 1335 515 306 176 1029 339 1349 522 306 194 1043 346 0 0 538 262 47 79 96 81 92 76 1368 1389 3.035 .329 .332 .393 .357 3.052 80 342 .316 .73 100 1850 8620 177 187 136 146 0 705 241 464 .451 715 474 2.216 .454 -1.148 -1.138
3 1025 427 304 172 721 255 1048 432 304 185 744 260 0 0 503 197 44 78 92 75 86 65 976 1004 2.827 .354 .349 .415 .397 2.527 52 232 .315 .76 80 1960 8620 178 186 148 156 0 585 236 349 .484 592 356 2.064 .479 -1.045 -1.063
4 1178 284 312 129 866 155 1177 284 305 144 865 155 0 0 248 80 80 58 100 83 100 75 1021 1020 5.587 .179 .179 .176 .165 1.632 12 68 .157 .65 40 2110 8620 180 184 165 169 0 389 177 212 .245 389 212 4.079 .245 -2.028 -2.026
5 1307 1967 295 161 1012 1806 1337 1889 308 196 1042 1728 0 0 490 954 68 182 100 100 100 100 2818 2770 .56 1.785 1.658 1.772 1.653 1.449 12 104 2.745 .74 50 2260 8620 179 184 179 184 0 2695 221 2474 2.445 2588 2367 .409 2.272 1.29 1.184
6 319 297 296 194 23 103 300 210 300 222 4 16 0 0 96 271 51 179 25 15 13 13 126 20 .223 4.478 4 2.083 1.798 5.935 52 299 .059 .23 80 2390 8610 177 185 191 199 -50 407 266 141 6.135 288 22 .163 5.479 2.617 2.454
7 2456 966 320 149 2136 817 2511 919 348 184 2191 770 0 0 633 301 180 152 100 100 100 100 2953 2961 2.614 .382 .351 .374 .351 1.523 12 104 .33 .76 50 2540 8620 179 184 207 212 0 1323 204 1119 .524 1259 1055 1.909 .481 -.932 -1.055
8 849 261 359 121 490 140 855 237 373 138 496 116 0 0 133 100 104 59 100 83 91 50 630 612 3.5 .286 .234 .225 .271 2.588 12 68 .169 .36 40 2690 8620 180 184 223 227 0 358 166 192 .391 325 159 2.555 .32 -1.353 -1.642
9 707 561 351 168 356 393 665 548 362 181 314 380 0 0 286 215 76 97 86 90 78 80 749 694 .906 1.104 1.21 1.058 .938 2.513 80 436 .983 .63 100 2830 8620 177 187 234 244 0 768 230 538 1.512 751 521 .661 1.658 .597 .729
10 481 461 327 187 154 274 502 314 332 193 175 127 0 0 148 481 53 71 75 78 65 43 428 302 .562 1.779 .726 .583 .505 2.867 32 179 21.043 .15 70 3000 8620 178 185 252 259 0 632 256 375 2.437 430 174 .41 .994 1.285 -.008
11 2148 25687 336 199 1812 25488 2226 26803 344 236 1890 26604 0 0 1198 15574 64 218 91 100 88 98 27300 28494 .071 14.066 14.076 11.98 13.271 2.004 80 440 15.17 .9 110 3120 8620 176 187 262 273 0 35188 273 34915 19.269 36716 36444 .052 19.282 4.268 4.269
12 2481 2995 325 215 2156 2780 2484 2819 329 256 2159 2604 0 0 1840 1789 51 253 90 96 82 94 4936 4763 .776 1.289 1.206 1.973 1.213 3.674 52 264 1.162 .88 80 3280 8620 178 186 280 288 0 4103 295 3808 1.766 3862 3567 .566 1.652 .821 .724
13 596 1448 303 184 293 1264 603 1207 307 198 300 1023 0 0 252 720 43 120 75 100 73 96 1557 1323 .232 4.314 3.41 3.972 3.677 2.033 52 222 4.348 .79 80 3430 8620 178 186 295 303 0 1984 252 1732 5.91 1653 1401 .169 4.671 2.563 2.224
14 793 498 317 185 476 313 775 484 324 210 458 299 0 0 255 194 59 173 93 75 92 41 789 757 1.521 .658 .653 .658 .627 2.04 80 432 .926 .57 110 3550 8610 175 186 305 316 0 682 253 429 .901 663 410 1.11 .894 -.151 -.161
15 324 430 313 191 11 239 324 237 319 200 11 46 0 0 72 547 60 89 15 40 7 25 250 57 .046 21.727 4.182 3.745 3.016 4.907 52 256 43.437 .17 80 3710 8610 177 185 323 331 -50 589 262 327 29.763 325 63 .034 5.729 4.895 2.518
16 3659 2976 314 193 3345 2783 3107 2805 317 208 2793 2612 0 0 2826 2140 47 93 98 98 98 95 6128 5405 1.202 .832 .935 .882 .944 2.711 80 419 .778 .86 110 3860 8610 175 186 336 347 0 4077 264 3812 1.14 3842 3578 .877 1.281 .189 .357
17 3724 2855 319 187 3405 2668 4095 3167 339 215 3776 2980 0 0 1217 1280 173 171 98 96 96 93 6073 6756 1.276 .784 .789 .727 .812 2.271 80 433 .838 .87 110 3990 8610 175 186 349 360 0 3911 256 3655 1.073 4338 4082 .932 1.081 .102 .112
18 315 469 309 168 6 301 306 213 333 190 -3 45 0 0 107 627 223 128 3 32 0 25 307 42 .02 50.167 null 2.704 2.957 4.773 52 244 16.665 .38 80 4150 8610 177 185 367 375 -50 642 230 412 68.721 292 62 .015 null 6.103 null
19 5108 2749 317 185 4791 2564 5292 2752 322 198 4975 2567 0 0 2430 1593 52 81 100 97 100 96 7355 7542 1.869 .535 .516 .497 .562 2.075 80 392 .548 .91 110 4290 8610 175 186 379 390 0 3766 253 3512 .733 3770 3516 1.364 .707 -.448 -.501
20 2787 1392 325 186 2462 1206 2887 1503 340 205 2562 1317 0 0 864 569 163 138 97 93 96 90 3668 3879 2.041 .49 .514 .482 .49 2.324 80 381 .491 .83 110 4430 8610 175 186 393 404 0 1907 255 1652 .671 2059 1804 1.49 .704 -.576 -.506

Total number of rows: 43008

Table truncated, full table size 9611 Kbytes.




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