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Sample GSM173027 Query DataSets for GSM173027
Status Public on Sep 28, 2007
Title SM, PA #2, low
Sample type RNA
 
Channel 1
Source name Stratagene
Organism Homo sapiens
Characteristics Stratagene
LabeledExtract: 35910.Channel_1
Extracted molecule total RNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name SM, PA #2, low
Organism Homo sapiens
Characteristics SM, PA #2, low
LabeledExtract: 35910.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/2002-12/35910.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
1 394 332 150 117 244 215 401 330 150 120 251 213 0 0 72 86 35 38 100 100 100 100 459 464 1.135 .881 .849 .852 .877 1.72 32 150 .976 .74 60 1570 8460 171 177 94 100 0 369 130 239 .979 367 237 1.021 .943 -.031 -.085
2 3262 324 133 102 3129 222 3207 344 135 106 3074 242 0 0 1194 115 33 39 100 88 100 84 3351 3316 14.095 .071 .079 .066 .069 1.618 52 286 .067 .86 80 1720 8440 168 176 108 116 0 360 113 247 .079 382 269 12.685 .087 -3.665 -3.515
3 1313 546 126 97 1187 449 1372 533 127 101 1246 436 0 0 488 214 27 38 100 96 100 96 1636 1682 2.644 .378 .35 .345 .397 1.703 32 172 .376 .94 60 1870 8440 169 175 124 130 0 607 108 499 .42 592 484 2.379 .389 -1.251 -1.363
4 683 258 120 94 563 164 663 247 121 98 543 153 0 0 172 68 29 32 100 100 100 96 727 696 3.433 .291 .282 .282 .303 1.544 32 200 .266 .78 70 2010 8450 169 176 137 144 0 287 104 182 .324 274 170 3.09 .313 -1.627 -1.675
5 1369 2941 124 105 1245 2836 1436 2970 127 108 1312 2865 0 0 673 1283 26 35 100 100 100 100 4081 4177 .439 2.278 2.184 2.542 2.184 1.683 52 277 2.25 .96 80 2150 8450 169 177 151 159 0 3268 117 3151 2.531 3300 3183 .395 2.426 1.34 1.279
6 517 352 125 104 392 248 527 354 128 108 402 250 0 0 77 77 27 38 100 100 100 100 640 652 1.581 .633 .622 .612 .611 1.366 32 219 .629 .87 70 2300 8440 168 175 166 173 0 391 116 276 .703 393 278 1.423 .691 -.509 -.533
7 1354 704 125 110 1229 594 1321 703 128 125 1196 593 0 0 469 276 28 64 100 100 100 98 1823 1789 2.069 .483 .496 .459 .48 1.502 52 278 .473 .92 80 2450 8440 168 176 181 189 0 782 122 660 .537 781 659 1.862 .551 -.897 -.86
8 516 451 129 100 387 351 516 466 135 110 387 366 0 0 113 109 43 56 100 100 100 100 738 753 1.103 .907 .946 .898 .893 1.581 32 212 .959 .84 70 2580 8440 168 175 194 201 0 501 111 390 1.008 518 407 .992 1.051 .011 .072
9 475 383 132 99 343 284 464 359 137 110 332 260 0 0 110 108 38 52 100 100 98 98 627 592 1.208 .828 .783 .82 .802 1.622 52 285 .817 .84 80 2740 8440 168 176 210 218 0 426 110 316 .92 399 289 1.087 .87 -.12 -.201
10 360 202 143 123 217 79 353 205 144 133 210 82 0 0 82 56 31 49 96 65 96 37 296 292 2.747 .364 .39 .418 .472 1.982 32 152 .345 .52 60 2880 8440 169 175 225 231 0 224 137 88 .405 228 91 2.472 .434 -1.306 -1.205
11 1500 1879 141 119 1359 1760 1519 1958 144 127 1378 1839 0 0 474 615 34 49 100 100 100 100 3119 3217 .772 1.295 1.335 1.294 1.277 1.536 52 317 1.32 .93 90 3020 8440 167 176 237 246 0 2088 132 1956 1.439 2176 2043 .695 1.483 .525 .568
12 2868 2333 141 122 2727 2211 3152 2426 152 133 3011 2304 0 0 1645 1212 56 64 94 100 92 98 4938 5315 1.233 .811 .765 .873 .803 2.07 52 254 .778 .96 80 3170 8440 168 176 253 261 0 2592 136 2457 .901 2696 2560 1.11 .85 -.151 -.234
13 790 1556 144 122 646 1434 841 1478 222 414 697 1356 0 0 306 476 599 2437 60 1 3 0 2080 2053 .45 2.22 1.945 2.365 2.195 1.815 80 358 2.014 .84 100 3320 8450 168 178 267 277 0 1729 136 1593 2.466 1642 1507 .405 2.162 1.302 1.112
14 554 638 160 122 394 516 512 396 267 221 352 274 0 0 395 971 648 522 17 23 3 9 910 626 .764 1.31 .778 1.082 1.058 2.022 52 200 1.641 .97 80 3470 8470 171 179 283 291 0 709 136 573 1.455 440 304 .687 .865 .541 -.209
15 454 260 141 112 313 148 463 252 187 156 322 140 0 0 120 70 464 386 7 0 0 0 461 462 2.115 .473 .435 .44 .442 1.713 80 344 .98 .61 100 3610 8440 167 177 296 306 0 289 124 164 .525 280 156 1.903 .483 -.929 -1.05
16 4411 3741 137 114 4274 3627 4508 3807 153 137 4371 3693 0 0 1035 821 135 144 100 100 100 100 7901 8064 1.178 .849 .845 .875 .851 1.399 52 288 .847 .96 90 3750 8440 167 176 310 319 0 4157 127 4030 .943 4230 4103 1.061 .939 -.085 -.091
17 1480 1108 131 114 1349 994 1498 1103 148 138 1367 989 0 0 357 381 132 148 100 98 100 94 2343 2356 1.357 .737 .723 .689 .755 1.416 52 302 .774 .94 90 3900 8440 167 176 325 334 0 1231 127 1104 .819 1226 1099 1.221 .804 -.289 -.315
18 220 329 126 114 94 215 174 152 130 124 48 38 0 0 157 751 31 71 67 30 32 15 309 86 .437 2.287 .792 1.174 1.139 3.698 52 236 5.498 .76 80 4040 8430 167 175 340 348 -50 366 127 239 2.541 169 42 .393 .88 1.346 -.185
19 3321 2452 116 113 3205 2339 3689 2726 120 117 3573 2613 0 0 1798 1277 31 43 100 100 97 98 5544 6186 1.37 .73 .731 .758 .705 1.876 80 351 .711 .95 100 4190 8440 167 177 354 364 0 2724 126 2599 .811 3029 2903 1.233 .813 -.302 -.299
20 1400 1144 108 110 1292 1034 1474 1185 109 114 1366 1075 0 0 414 359 24 39 100 100 100 96 2326 2441 1.25 .8 .787 .747 .783 1.61 52 302 .807 .94 90 4340 8430 166 175 369 378 0 1271 122 1149 .889 1317 1194 1.125 .874 -.169 -.194

Total number of rows: 43104

Table truncated, full table size 9452 Kbytes.




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

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