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Sample GSM173032 Query DataSets for GSM173032
Status Public on Sep 28, 2007
Title SM, Uterus #2
Sample type RNA
 
Channel 1
Source name Stratagene
Organism Homo sapiens
Characteristics Stratagene
LabeledExtract: 34755.Channel_1
Extracted molecule total RNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name Uterus SM #2
Organism Homo sapiens
Characteristics Uterus SM #2
LabeledExtract: 34755.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/2002-11/34755.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
1 156 300 62 127 94 173 157 299 64 136 95 172 0 0 48 118 15 51 87 84 87 71 267 267 .543 1.84 1.811 1.417 1.818 4.504 32 136 4.698 .35 60 1390 9100 29 35 68 74 0 448 190 258 2.747 446 257 .364 2.702 1.458 1.434
2 1086 5576 61 118 1025 5458 1341 6257 69 134 1280 6139 0 0 627 2309 52 93 96 100 92 100 6483 7419 .188 5.325 4.796 6.488 4.795 2.537 52 290 6.348 .74 90 1530 9110 28 37 80 89 0 8322 176 8146 7.948 9339 9163 .126 7.158 2.991 2.84
3 766 505 61 111 705 394 724 512 77 130 663 401 0 0 327 253 66 108 100 81 100 71 1099 1064 1.789 .559 .605 .519 .487 2.92 32 213 .511 .48 70 1670 9100 28 35 95 102 0 754 166 588 .834 764 599 1.199 .903 -.262 -.148
4 427 380 61 94 366 286 422 361 68 105 361 267 0 0 133 143 39 51 100 96 100 93 652 628 1.28 .781 .74 .734 .769 2.079 32 218 .888 .64 70 1820 9100 28 35 110 117 0 567 140 427 1.166 539 399 .857 1.104 .222 .143
5 509 1928 58 92 451 1836 561 1926 60 98 503 1834 0 0 292 989 17 49 93 98 92 97 2287 2337 .246 4.071 3.646 4.574 4.032 2.599 80 444 4.543 .81 110 1970 9110 27 38 123 134 0 2878 137 2740 6.076 2875 2737 .165 5.442 2.603 2.444
6 355 396 61 81 294 315 365 413 65 98 304 332 0 0 87 127 31 67 100 96 100 87 609 636 .933 1.071 1.092 1.015 1.163 1.926 32 198 1.278 .68 70 2110 9100 28 35 139 146 0 591 121 470 1.599 616 496 .625 1.63 .677 .705
7 786 449 58 77 728 372 712 459 63 91 654 382 0 0 386 228 26 59 100 94 96 82 1100 1036 1.957 .511 .584 .487 .462 3.034 52 324 .464 .7 90 2260 9100 27 36 153 162 0 670 115 555 .763 685 570 1.311 .872 -.391 -.198
8 274 399 59 70 215 329 263 430 62 77 204 360 0 0 96 156 17 41 100 94 96 92 544 564 .653 1.53 1.765 1.461 1.383 2.672 52 301 1.909 .7 90 2410 9100 27 36 168 177 0 596 104 491 2.284 642 537 .438 2.634 1.192 1.397
9 244 1079 60 68 184 1011 256 1104 63 76 196 1036 0 0 97 320 18 35 92 100 88 100 1195 1232 .182 5.495 5.286 6.224 5.467 2.121 80 394 5.824 .79 110 2550 9120 28 39 181 192 0 1610 101 1509 8.201 1648 1546 .122 7.889 3.036 2.98
10 166 283 61 71 105 212 147 271 64 81 86 200 0 0 76 142 16 42 100 90 87 81 317 286 .495 2.019 2.326 1.873 2.489 2.985 32 145 3.058 .49 60 2710 9100 29 35 200 206 0 422 106 316 3.014 404 299 .332 3.471 1.591 1.795
11 1013 1063 62 67 951 996 1090 1091 66 78 1028 1024 0 0 292 345 24 96 100 100 100 98 1947 2052 .955 1.047 .996 1.028 1.046 1.714 80 383 1.067 .83 110 2840 9110 27 38 210 221 0 1587 100 1487 1.563 1628 1528 .64 1.487 .644 .572
12 2478 2297 61 68 2417 2229 2780 2406 67 79 2719 2338 0 0 1395 1336 31 60 94 92 92 91 4646 5057 1.084 .922 .86 .901 .887 4.055 120 441 .921 .83 120 2990 9110 27 39 225 237 0 3428 101 3327 1.376 3591 3490 .727 1.283 .461 .36
13 409 1036 61 71 348 965 403 1064 63 78 342 993 0 0 116 365 19 39 100 100 100 100 1313 1335 .361 2.773 2.904 2.681 2.819 1.78 80 342 3.405 .8 110 3140 9110 27 38 240 251 0 1546 106 1440 4.139 1588 1482 .242 4.334 2.049 2.116
14 203 131 61 70 142 61 206 123 64 99 145 53 0 0 52 47 20 300 100 0 98 0 203 198 2.328 .43 .366 .45 .476 2.048 80 363 -1 -1 110 3290 9100 26 37 255 266 0 196 104 91 .641 184 79 1.56 .546 -.641 -.874
15 218 167 58 68 160 99 220 152 61 98 162 84 0 0 54 65 19 314 100 1 98 0 259 246 1.616 .619 .519 .534 .535 2.472 80 331 108.111 .03 110 3430 9100 26 37 269 280 0 249 101 148 .924 227 125 1.083 .774 -.115 -.37
16 3669 4409 57 62 3612 4347 4177 4748 59 66 4120 4686 0 0 1701 1983 14 29 100 99 100 98 7959 8806 .831 1.203 1.137 1.298 1.175 4.013 120 384 1.256 .77 120 3580 9110 27 39 284 296 0 6581 93 6488 1.796 7087 6994 .557 1.698 .845 .763
17 1363 1076 57 56 1306 1020 1530 1148 58 60 1473 1092 0 0 589 410 13 25 95 100 94 100 2326 2565 1.28 .781 .741 .798 .72 3.21 120 364 .699 .64 120 3720 9110 27 39 298 310 0 1606 84 1522 1.166 1713 1630 .858 1.106 .221 .146
18 98 93 57 56 41 37 83 84 58 60 26 28 0 0 50 46 12 21 61 57 51 42 78 54 1.108 .902 1.077 1.509 1.354 3.855 52 175 1.55 .28 80 3860 9100 28 36 314 322 -50 139 84 55 1.347 125 42 .742 1.607 .43 .685
19 1937 1233 57 58 1880 1175 2125 1367 58 62 2068 1309 0 0 1203 658 13 24 94 97 91 95 3055 3377 1.6 .625 .633 .798 .654 5.122 120 376 .519 .76 120 4010 9110 27 39 327 339 0 1840 87 1754 .933 2040 1954 1.072 .945 -.1 -.082
20 661 508 57 60 604 448 764 540 59 65 707 480 0 0 303 179 14 29 94 97 91 95 1052 1187 1.348 .742 .679 .812 .672 3.537 120 352 .612 .71 120 4160 9110 27 39 342 354 0 758 90 669 1.107 806 716 .903 1.013 .147 .019

Total number of rows: 43104

Table truncated, full table size 8922 Kbytes.




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