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Sample GSM173047 Query DataSets for GSM173047
Status Public on Sep 28, 2007
Title SM, uterus #3, low
Sample type RNA
 
Channel 1
Source name Stratagene
Organism Homo sapiens
Characteristics Stratagene
LabeledExtract: 36005.Channel_1
Extracted molecule total RNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name SM, uterus #3, low
Organism Homo sapiens
Characteristics SM, uterus #3, low
LabeledExtract: 36005.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/2002-12/36005.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
1 515 557 144 152 371 405 532 563 150 162 388 411 0 0 147 193 38 58 98 98 96 92 776 799 .916 1.092 1.059 1.051 1.143 1.745 52 254 1.175 .85 80 1570 8670 191 199 93 101 0 844 230 614 1.654 853 623 .605 1.605 .726 .683
2 4464 14724 150 163 4314 14561 4483 15335 156 179 4333 15172 0 0 2053 7266 39 92 100 100 100 100 18875 19505 .296 3.375 3.502 3.247 3.392 1.203 52 314 3.441 .99 90 1700 8660 189 198 105 114 0 22309 247 22062 5.114 23235 22988 .196 5.305 2.354 2.407
3 2924 1221 143 146 2781 1075 2526 1087 151 165 2383 941 0 0 1392 498 39 100 100 100 100 100 3856 3324 2.587 .387 .395 .4 .384 1.288 32 219 .364 .98 70 1850 8670 191 198 121 128 0 1850 221 1629 .586 1647 1426 1.707 .598 -.772 -.741
4 1207 424 136 156 1071 268 1122 407 142 160 986 251 0 0 356 140 30 63 100 93 100 87 1339 1237 3.996 .25 .255 .221 .246 1.804 32 204 .237 .79 70 2000 8670 191 198 136 143 0 642 236 406 .379 617 380 2.638 .386 -1.399 -1.374
5 2285 4738 149 152 2136 4586 2039 4650 156 162 1890 4498 0 0 1092 1645 42 75 100 100 100 100 6722 6388 .466 2.147 2.38 2.237 2.241 1.411 52 329 1.084 .58 90 2140 8670 190 199 149 158 0 7179 230 6948 3.253 7045 6815 .307 3.606 1.702 1.85
6 877 589 150 149 727 440 900 594 157 155 750 445 0 0 182 151 37 54 100 100 100 100 1167 1195 1.652 .605 .593 .586 .583 1.358 32 219 .613 .91 70 2290 8660 190 197 165 172 0 892 226 667 .917 900 674 1.091 .899 -.125 -.154
7 4645 2817 144 144 4501 2673 3316 1265 169 166 3172 1121 0 0 3797 3594 285 252 98 92 98 88 7174 4293 1.684 .594 .353 .413 .404 1.594 52 350 .798 .95 90 2440 8660 189 198 179 188 0 4268 218 4050 .9 1917 1698 1.111 .535 -.152 -.901
8 1281 1679 149 149 1132 1530 1247 1597 187 187 1098 1448 0 0 351 519 370 325 100 100 90 96 2662 2546 .74 1.352 1.319 1.331 1.322 1.336 32 206 1.416 .95 70 2580 8660 190 197 194 201 0 2544 226 2318 2.048 2420 2194 .488 1.998 1.034 .999
9 799 1776 156 156 643 1620 796 1749 162 176 640 1593 0 0 196 441 44 85 100 100 100 100 2263 2233 .397 2.519 2.489 2.544 2.485 1.312 52 340 2.527 .94 90 2720 8660 189 198 207 216 0 2691 236 2455 3.817 2650 2414 .262 3.771 1.933 1.915
10 499 351 155 160 344 191 509 351 161 178 354 191 0 0 124 98 42 93 100 81 100 50 535 545 1.801 .555 .54 .523 .65 1.97 32 206 .592 .68 70 2870 8660 190 197 223 230 0 532 242 289 .841 532 289 1.189 .817 -.249 -.291
11 1989 5441 157 157 1832 5284 1973 5625 160 165 1816 5468 0 0 924 2602 34 68 97 100 97 100 7116 7284 .347 2.884 3.011 3.028 2.922 1.38 80 375 2.909 .98 100 3020 8670 190 200 237 247 0 8244 238 8006 4.37 8523 8285 .229 4.562 2.128 2.19
12 6153 5291 155 151 5998 5140 6089 5664 173 170 5934 5513 0 0 4201 3784 98 119 98 100 96 100 11138 11447 1.167 .857 .929 .876 .857 1.455 52 300 .876 .99 90 3160 8660 189 198 251 260 0 8017 229 7788 1.298 8582 8353 .77 1.408 .377 .493
13 1135 3186 155 153 980 3033 1053 2886 171 168 898 2733 0 0 425 1149 90 110 100 100 100 100 4013 3631 .323 3.095 3.043 3.192 3.078 1.299 80 370 3.101 .96 100 3320 8670 190 200 267 277 0 4827 232 4595 4.689 4373 4141 .213 4.611 2.229 2.205
14 623 437 156 152 467 285 609 442 161 156 453 290 0 0 163 106 35 52 100 100 100 94 752 743 1.639 .61 .64 .594 .593 1.553 52 300 .62 .85 90 3460 8660 189 198 281 290 0 662 230 432 .925 670 439 1.081 .97 -.113 -.044
15 789 341 158 157 631 184 806 316 162 157 648 159 0 0 192 87 35 54 100 98 100 76 815 807 3.429 .292 .245 .277 .283 1.679 52 272 .292 .79 90 3610 8670 190 199 296 305 0 517 238 279 .442 479 241 2.263 .372 -1.178 -1.428
16 10603 8548 158 165 10445 8383 10687 9090 162 180 10529 8925 0 0 4340 3417 40 96 100 100 98 98 18828 19454 1.246 .803 .848 .842 .807 1.324 80 340 .795 .99 100 3750 8670 190 200 310 320 0 12952 250 12702 1.216 13773 13523 .822 1.284 .282 .361
17 3300 1765 152 143 3148 1622 3139 1755 159 154 2987 1612 0 0 1254 730 36 58 100 100 100 100 4770 4599 1.941 .515 .54 .49 .519 1.378 52 244 .514 .98 80 3900 8660 190 198 326 334 0 2674 217 2458 .781 2659 2442 1.281 .818 -.357 -.29
18 185 176 155 145 30 31 161 159 160 156 6 14 0 0 93 69 46 59 23 30 11 13 61 20 .968 1.033 2.333 1.875 1.656 4.02 52 256 1.002 .28 80 4040 8650 189 197 340 348 -50 267 220 47 1.566 241 21 .639 3.535 .647 1.822
19 9559 5776 156 155 9403 5621 9310 5853 177 173 9154 5698 0 0 2732 2025 165 109 100 100 100 100 15024 14852 1.673 .598 .622 .573 .599 1.256 52 316 .609 .99 90 4190 8650 188 197 354 363 0 8752 235 8517 .906 8868 8633 1.104 .943 -.143 -.084
20 3701 2272 156 159 3545 2113 3633 2233 176 172 3477 2074 0 0 1364 889 164 108 100 100 100 100 5658 5551 1.678 .596 .596 .584 .581 1.248 52 300 .597 .98 90 4340 8660 189 198 369 378 0 3442 241 3202 .903 3383 3142 1.107 .904 -.147 -.146

Total number of rows: 43104

Table truncated, full table size 9545 Kbytes.




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

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