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Sample GSM173077 Query DataSets for GSM173077
Status Public on Sep 28, 2007
Title SM, PA #1, low
Sample type RNA
 
Channel 1
Source name Stratagene
Organism Homo sapiens
Characteristics Stratagene
LabeledExtract: 35909.Channel_1
Extracted molecule total RNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name SM, PA #1, low
Organism Homo sapiens
Characteristics SM, PA #1, low
LabeledExtract: 35909.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/2002-12/35909.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
1 568 490 144 105 424 385 542 440 148 106 398 335 0 0 133 165 30 31 100 100 100 100 809 733 1.101 .908 .842 .879 .951 1.366 32 184 .871 .87 70 1660 8430 167 174 102 109 0 766 164 602 1.419 688 523 .705 1.315 .505 .395
2 5617 460 128 94 5489 366 5445 463 130 96 5317 369 0 0 2250 138 34 30 100 100 100 96 5855 5686 14.997 .067 .069 .071 .068 1.821 52 266 .059 .32 80 1800 8420 166 174 116 124 0 719 147 572 .104 723 577 9.598 .108 -3.263 -3.205
3 2724 1137 128 89 2596 1048 2622 1143 125 91 2494 1054 0 0 1141 513 31 28 100 100 100 100 3644 3548 2.477 .404 .423 .383 .388 1.645 32 171 .4 .92 60 1950 8410 166 172 132 138 0 1777 139 1638 .631 1786 1647 1.585 .66 -.665 -.599
4 1206 444 129 91 1077 353 1161 391 131 95 1032 300 0 0 419 168 25 29 100 100 100 100 1430 1332 3.051 .328 .291 .313 .297 1.535 32 216 .292 .87 70 2090 8420 166 173 145 152 0 694 142 552 .512 611 469 1.953 .454 -.965 -1.139
5 3055 6199 135 93 2920 6106 3303 5796 136 98 3168 5703 0 0 1271 2171 25 31 100 100 100 100 9026 8871 .478 2.091 1.8 2.266 2.13 1.518 52 328 2.049 .95 90 2240 8420 165 174 159 168 0 9686 145 9541 3.267 9056 8911 .306 2.813 1.708 1.492
6 907 382 148 97 759 285 919 383 153 105 771 286 0 0 166 98 40 44 100 100 100 100 1044 1057 2.663 .375 .371 .364 .38 1.396 32 171 .353 .88 60 2380 8410 166 172 175 181 0 597 152 445 .587 598 447 1.704 .58 -.769 -.787
7 2383 1035 141 96 2242 939 2450 1022 145 100 2309 926 0 0 1032 423 34 40 100 100 100 100 3181 3235 2.388 .419 .401 .436 .436 1.471 52 314 .399 .95 90 2530 8420 165 174 188 197 0 1617 150 1467 .654 1597 1447 1.528 .627 -.612 -.674
8 1044 1519 125 92 919 1427 1033 1447 129 95 908 1355 0 0 499 749 31 29 100 100 100 100 2346 2263 .644 1.553 1.492 1.65 1.623 1.58 52 258 1.597 .9 80 2670 8420 166 174 203 211 0 2373 144 2230 2.426 2261 2117 .412 2.332 1.279 1.221
9 1040 712 122 89 918 623 1064 718 147 100 942 629 0 0 281 231 255 82 98 98 96 96 1541 1571 1.474 .679 .668 .644 .667 1.747 52 304 .551 .84 90 2820 8410 164 173 217 226 0 1113 139 973 1.06 1122 983 .943 1.043 .085 .061
10 596 636 121 93 475 543 585 570 126 96 464 477 0 0 202 310 26 31 100 96 100 96 1018 941 .875 1.143 1.028 1.072 1.111 1.538 32 153 1.287 .89 60 2960 8410 166 172 233 239 0 994 145 848 1.786 891 745 .56 1.606 .837 .684
11 3405 6810 138 95 3267 6715 3890 7389 3053 369 3752 7294 0 0 2047 3837 10839 1084 0 88 0 81 9982 11046 .487 2.055 1.944 2.254 2.059 1.803 80 381 .276 .34 100 3110 8420 165 175 246 256 0 10641 148 10492 3.212 11545 11397 .311 3.038 1.683 1.603
12 7527 5279 132 93 7395 5186 5742 4438 134 96 5610 4345 0 0 6319 4514 27 32 100 100 98 100 12581 9955 1.426 .701 .775 .773 .75 1.94 52 264 .697 .96 80 3260 8410 165 173 262 270 0 8248 145 8103 1.096 6934 6789 .913 1.21 .132 .275
13 2027 5026 136 97 1891 4929 1519 4127 137 99 1383 4030 0 0 1545 2643 26 33 100 100 98 100 6820 5413 .384 2.607 2.914 3.042 3.164 1.835 80 339 2.556 .81 100 3420 8420 165 175 277 287 0 7853 152 7702 4.073 6448 6297 .246 4.553 2.026 2.187
14 621 412 142 99 479 313 585 366 145 101 443 267 0 0 187 180 29 31 100 100 100 98 792 710 1.53 .653 .603 .588 .596 1.638 52 262 .704 .9 90 3550 8410 164 173 290 299 0 644 155 489 1.021 572 417 .979 .942 .03 -.087
15 950 381 142 99 808 282 859 322 145 104 717 223 0 0 362 184 31 33 100 96 100 96 1090 940 2.865 .349 .311 .303 .345 1.811 52 289 .35 .89 90 3690 8410 164 173 304 313 0 595 155 441 .545 503 348 1.834 .486 -.875 -1.041
16 13179 11090 145 101 13034 10989 12068 10983 150 104 11923 10882 0 0 8151 6254 32 33 100 100 98 100 24023 22805 1.186 .843 .913 .968 .889 1.911 80 369 .812 .97 100 3840 8420 165 175 319 329 0 17328 158 17170 1.317 17161 17003 .759 1.426 .398 .512
17 4802 3146 143 100 4659 3046 5000 3251 149 102 4857 3151 0 0 1685 1304 32 31 100 100 100 100 7705 8008 1.53 .654 .649 .608 .66 1.582 52 232 .659 .94 80 3990 8410 165 173 335 343 0 4916 156 4759 1.022 5080 4923 .979 1.014 .031 .02
18 338 380 144 102 194 278 160 136 152 104 16 34 0 0 437 746 38 30 38 50 28 38 472 50 .698 1.433 2.125 1.215 1.409 3.116 52 246 1.871 .8 80 4130 8400 164 172 349 357 -50 594 159 434 2.239 213 53 .447 3.32 1.163 1.731
19 10437 6539 152 103 10285 6436 11181 7016 170 116 11029 6913 0 0 4073 2559 121 92 100 100 100 100 16721 17942 1.598 .626 .627 .631 .627 1.745 52 312 .605 .96 90 4270 8410 164 173 362 371 0 10217 161 10056 .978 10963 10802 1.023 .979 -.032 -.03
20 4656 2878 151 103 4505 2775 4728 2787 171 117 4577 2684 0 0 1731 1139 132 98 100 100 100 100 7280 7261 1.623 .616 .586 .617 .626 1.443 52 262 .603 .94 80 4430 8410 165 173 379 387 0 4497 161 4336 .962 4355 4194 1.039 .916 -.055 -.126

Total number of rows: 43104

Table truncated, full table size 9549 Kbytes.




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

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