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Sample GSM173033 Query DataSets for GSM173033
Status Public on Sep 28, 2007
Title SM, Uterus #3
Sample type RNA
 
Channel 1
Source name Stratagene
Organism Homo sapiens
Characteristics Stratagene
LabeledExtract: 34756.Channel_1
Extracted molecule total RNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name Uterus SM #3
Organism Homo sapiens
Characteristics Uterus SM #3
LabeledExtract: 34756.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/2002-11/34756.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 GPL3322
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
1 482 524 108 124 374 400 504 522 111 128 396 398 0 0 170 260 33 42 100 98 98 90 774 794 .935 1.07 1.005 .969 .911 2.265 52 244 1.268 .76 80 1340 9160 34 42 62 70 0 845 200 645 1.725 842 642 .58 1.621 .787 .697
2 4220 12087 106 124 4114 11963 4343 11454 113 137 4237 11330 0 0 2256 6553 53 109 100 100 98 100 16077 15567 .344 2.908 2.674 3.003 3.105 2.24 80 378 3.075 .92 110 1490 9170 33 44 75 86 0 19495 200 19295 4.69 18474 18274 .213 4.313 2.23 2.109
3 2422 1320 115 137 2307 1183 2240 1248 138 162 2125 1111 0 0 1044 573 110 148 100 100 100 93 3490 3236 1.95 .513 .523 .5 .498 2.017 32 198 .453 .8 70 1630 9160 34 41 91 98 0 2129 221 1908 .827 2013 1792 1.209 .843 -.274 -.246
4 1357 486 113 125 1244 361 1267 444 126 138 1154 319 0 0 635 230 86 79 100 86 98 80 1605 1473 3.446 .29 .276 .248 .25 2.471 52 266 .244 .71 80 1780 9160 34 42 106 114 0 784 202 582 .468 716 515 2.137 .446 -1.095 -1.165
5 2018 4903 101 113 1917 4790 2085 5113 106 120 1984 5000 0 0 960 2854 36 63 100 98 100 98 6707 6984 .4 2.499 2.52 2.119 2.461 2.262 80 407 2.799 .92 110 1930 9160 32 43 119 130 0 7908 182 7726 4.03 8247 8065 .248 4.065 2.011 2.023
6 1158 823 110 114 1048 709 1188 801 113 120 1078 687 0 0 364 301 33 48 100 100 100 100 1757 1765 1.478 .677 .637 .648 .647 1.589 52 234 .697 .88 80 2070 9160 34 42 135 143 0 1327 184 1144 1.091 1292 1108 .916 1.028 .126 .04
7 2805 1142 100 114 2705 1028 2609 1022 108 119 2509 908 0 0 1444 561 54 50 100 100 98 100 3733 3417 2.631 .38 .362 .406 .377 2.109 52 300 .345 .85 90 2220 9160 33 42 149 158 0 1842 184 1658 .613 1648 1465 1.631 .584 -.706 -.777
8 756 1376 100 112 656 1264 727 1417 107 119 627 1305 0 0 302 707 52 51 100 97 100 97 1920 1932 .519 1.927 2.081 1.67 2.007 2.224 80 344 2.233 .87 100 2370 9160 33 43 164 174 0 2219 181 2039 3.108 2285 2105 .322 3.357 1.636 1.747
9 760 2018 103 119 657 1899 793 2106 107 123 690 1987 0 0 195 521 35 49 100 100 98 100 2556 2677 .346 2.89 2.88 2.955 2.887 1.486 80 344 3.053 .91 110 2510 9170 33 44 177 188 0 3255 192 3063 4.662 3397 3205 .215 4.645 2.221 2.216
10 396 353 107 124 289 229 403 312 109 128 296 188 0 0 115 187 30 51 100 92 100 73 518 484 1.262 .792 .635 .599 .663 2.442 52 208 1.053 .72 80 2660 9160 34 42 194 202 0 569 200 369 1.278 503 303 .782 1.024 .354 .035
11 2015 8350 102 122 1913 8228 2093 8798 106 127 1991 8676 0 0 479 2212 34 55 100 100 100 100 10141 10667 .232 4.301 4.358 4.25 4.27 1.376 80 344 4.661 .94 110 2800 9160 32 43 206 217 0 13468 197 13271 6.937 14190 13994 .144 7.028 2.794 2.813
12 4894 4651 99 119 4795 4532 5320 4764 103 126 5221 4645 0 0 2533 2236 33 58 96 100 95 100 9327 9866 1.058 .945 .89 1.1 .913 2.447 120 386 .923 .95 120 2950 9170 33 45 221 233 0 7502 192 7310 1.524 7684 7492 .656 1.435 .608 .521
13 1012 2828 97 110 915 2718 1010 2914 100 122 913 2804 0 0 305 852 32 57 100 100 100 100 3633 3717 .337 2.97 3.071 2.989 2.921 1.387 80 351 3.144 .93 110 3090 9160 32 43 235 246 0 4561 177 4384 4.791 4700 4523 .209 4.954 2.26 2.308
14 463 330 95 115 368 215 471 322 106 140 376 207 0 0 128 102 96 282 98 32 91 0 583 583 1.712 .584 .551 .555 .604 1.721 80 378 .605 .76 110 3240 9160 32 43 250 261 0 532 185 347 .942 519 334 1.061 .888 -.086 -.171
15 470 287 87 113 383 174 466 288 97 141 379 175 0 0 122 88 102 300 98 8 96 0 557 554 2.201 .454 .462 .424 .461 1.957 80 333 .407 .66 110 3380 9160 32 43 264 275 0 463 182 281 .733 465 282 1.365 .745 -.449 -.425
16 7866 5503 79 114 7787 5389 8059 5472 91 179 7980 5358 0 0 2721 2137 58 553 100 98 100 96 13176 13338 1.445 .692 .671 .675 .707 1.575 120 431 .694 .95 130 3530 9160 31 44 278 291 0 8876 184 8692 1.116 8826 8642 .896 1.083 .159 .115
17 2746 1561 75 106 2671 1455 2923 1611 90 184 2848 1505 0 0 747 448 74 595 100 93 100 80 4126 4353 1.836 .545 .528 .538 .542 1.727 120 376 .526 .91 120 3680 9160 32 44 294 306 0 2518 171 2347 .879 2598 2427 1.138 .852 -.187 -.231
18 212 181 65 95 147 86 126 150 70 99 61 55 0 0 169 107 22 39 80 59 63 44 233 116 1.709 .585 .902 .717 .746 2.766 52 179 .589 .63 80 3820 9160 34 42 310 318 -50 292 153 139 .944 242 89 1.06 1.454 -.084 .54
19 4048 1859 70 99 3978 1760 4331 1799 75 107 4261 1700 0 0 2180 1070 26 48 99 94 98 92 5738 5961 2.26 .442 .399 .405 .452 3.147 120 389 .423 .89 120 3970 9160 32 44 323 335 0 2998 160 2839 .714 2902 2742 1.401 .643 -.487 -.636
20 1857 1022 73 104 1784 918 1949 1060 78 113 1876 956 0 0 651 378 28 50 100 97 100 96 2702 2832 1.943 .515 .51 .502 .508 2.275 120 338 .484 .85 120 4120 9160 32 44 338 350 0 1648 168 1481 .83 1710 1542 1.205 .822 -.269 -.283

Total number of rows: 43104

Table truncated, full table size 9287 Kbytes.




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