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Sample GSM1449 Query DataSets for GSM1449
Status Public on Mar 29, 2002
Title Wild type voxel I3
Sample type RNA
 
Channel 1
Source name normal whole brain
Organism Mus musculus
Extracted molecule total RNA
 
Channel 2
Source name wild type voxel I3
Organism Mus musculus
Extracted molecule total RNA
 
 
Description Voxel I3 of mouse brain.
Voxelation is a novel technology designed to produce high throughput, three-dimensional imaging of gene expression patterns in the brain. In these experiments, mouse brains were dissected into 40 voxels, or cubes, by cutting 10 serial coronal sections and transecting each coronal section into fourths. Using microarrays, the gene expression pattern of 9000 genes was acquired for both a normal and a pharmacological model of Parkinson's disease (PD) mouse brain. The mice used in these experiments were C57BL/6J males 10-24 weeks in age.
 
Submission date Mar 14, 2002
Last update date Nov 21, 2005
Contact name Vanessa Marie Brown
E-mail(s) dsmith@mednet.ucla.edu
Phone 310-794-5711
Fax 310-825-6267
URL http://www.pharmacology.ucla.edu/smithlab
Organization name UCLA
Department Department of Molecular & Medical Pharmacology
Lab Desmond Smith, M.D., Ph.D.
Street address 650 Charles E. Young Dr. South, CHS 23-151
City Los Angeles
State/province CA
ZIP/Postal code 90095
Country USA
 
Platform ID GPL69
Series (1)
GSE30 Multiplex three dimensional brain gene expression mapping in a mouse model of Parkinson's disease

Data table header descriptions
ID_REF
VALUE same as UNF_VALUE but with flagged values removed
X X-coordinate of the center of the feature-indicator associated with the feature, where (0,0) is the top left of the image
Y Y-coordinate of the center of the feature-indicator associated with the feature, where (0,0) is the top left of the image
DIA. diameter in µm of the feature-indicator
F635_MEDIAN median pixel intensity of feature for Cy5 channel - in this experiment Cy5 channel is normal whole brain (reference) throughout the data set
F635_MEAN mean pixel intensity of feature for Cy5 channel
F635_SD Cy5 pixel intensity standard deviation
B635_MEDIAN median Cy5 feature background intensity
B635_MEAN mean Cy5 feature background intensity
B635_SD Cy5 background pixel intensity standard deviation
%_>_B635+1SD percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength #1 (635 nm, Cy5)
%_>_B635+2SD percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength #1 (635 nm, Cy5)
F635_%_SAT. percentage of pixel saturation within feature
F532_MEDIAN median feature pixel intensity at wavelength #2 (532 nm, Cy3)
F532_MEAN mean feature background intensity at wavelength #2 (532 nm, Cy3)
F532_SD standard deviation of the feature background intensity at wavelength #2 (532 nm, Cy3)
B532_MEDIAN median feature background intensity at wavelength #2 (532 nm, Cy3)
B532_MEAN mean feature background intensity at wavelength #2 (532 nm, Cy3)
B532_SD standard deviation of the feature background intensity at wavelength #2 (532 nm, Cy3)
%_>_B532+1SD percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength #2 (532 nm, Cy3)
%_>_B532+2SD percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength #2 (532 nm, Cy3)
F532_%_SAT. percentage of feature pixels at wavelength #2 (Cy3) that are saturated
RATIO_OF_MEDIANS ratio of the background subtracted median pixel intensity at the second wavelength (Cy3), to the background subtracted median pixel intensity at the first wavelength(Cy5)
RATIO_OF_MEANS ratio of the arithmetic mean of the background subtracted raw pixel intensities at the second wavelength (Cy3), to the arithmetic mean of the background subtracted raw pixel intensities at the first wavelength (Cy5)
MEDIAN_OF_RATIOS median of the pixel-by-pixel ratios of pixel intensities that have had the median background intensity subtracted of wavelength 2 (Cy3) to wavelength one (Cy5)
MEAN_OF_RATIOS arithmetic mean of the pixel-by-pixel ratios of the raw pixel intensities of wavelength 2 (Cy3) to wavelength 1 (Cy5)
RATIOS_SD standard deviation of the log of pixel intensity ratios. Note: ratios greater than 100 and less than 0.01 are excluded when calculating this data type
RGN_RATIO regression ratio is determined by computing a linear regression between the population of pixels represented by wavelength 1 and wavelength 2
RGN_R² coefficient of determination provides a measure of the level of accuracy of the fit of the linear regression curve
F_PIXELS number of feature pixels
B_PIXELS number of background pixels
SUM_OF_MEDIANS sum of the median of the pixel intensities at each wavelength, with the median background pixel intensity at each wavelength subtracted
SUM_OF_MEANS sum of the arithmetic mean of the pixel intensities at each wavelength, with the median background pixel intensity at each wavelength subtracted
LOG_RATIO base two logarithm of the ratio of medians
F635_MEDIAN_B635 Cy5 median feature intensity subtracted by Cy5 median background intensity
F532_MEDIAN_B532 Cy3 median feature intensity subtracted by Cy3 median background intensity
F635_MEAN_B635 Cy5 mean feature intensity subtracted by Cy5 mean background intensity
F532_MEAN_B532 Cy3 mean feature intensity subtracted by Cy3 mean background intensity
FLAGS sub-standard features will have a negative value, while a good feature will have a positive value
PRE_VALUE Cy3 background subtracted median intensity divided by Cy5 background subtracted intensity
UNF_VALUE log ratio of PRE_VALUE

Data table
ID_REF VALUE X Y DIA. F635_MEDIAN F635_MEAN F635_SD B635_MEDIAN B635_MEAN B635_SD %_>_B635+1SD %_>_B635+2SD F635_%_SAT. F532_MEDIAN F532_MEAN F532_SD B532_MEDIAN B532_MEAN B532_SD %_>_B532+1SD %_>_B532+2SD F532_%_SAT. RATIO_OF_MEDIANS RATIO_OF_MEANS MEDIAN_OF_RATIOS MEAN_OF_RATIOS RATIOS_SD RGN_RATIO RGN_R² F_PIXELS B_PIXELS SUM_OF_MEDIANS SUM_OF_MEANS LOG_RATIO F635_MEDIAN_B635 F532_MEDIAN_B532 F635_MEAN_B635 F532_MEAN_B532 FLAGS PRE_VALUE UNF_VALUE
1 0.0146433 2960 14820 80 2102 2132 926 294 323 264 98 90 0 2241 2253 1208 371 376 65 94 94 0 0.967 0.977 0.939 1.467 2.15 0.853 0.902 52 250 3678 3720 -0.049 1808 1870 1838 1882 0 1.034292035 0.0146433
2 0.0055563 3200 14810 80 2390 2411 774 293 295 50 100 100 0 2499 2561 1290 375 377 60 100 100 0 0.987 0.969 1.04 1.198 0.702 0.804 0.866 52 340 4221 4304 -0.018 2097 2124 2118 2186 0 1.012875536 0.0055563
3 -0.0428843 3440 14810 90 1435 1426 260 297 298 56 100 100 0 1410 1396 298 379 377 61 100 100 0 1.104 1.11 1.101 1.169 0.348 1.028 0.893 52 420 2169 2146 0.142 1138 1031 1129 1017 0 0.905975395 -0.0428843
4 0.0579923 3680 14810 90 1205 1340 419 295 314 132 100 100 0 1421 1563 603 381 389 73 98 98 0 0.875 0.884 0.822 1.264 1.641 0.779 0.865 52 420 1950 2227 -0.193 910 1040 1045 1182 0 1.142857143 0.0579923
5 -0.0261093 3950 14810 90 2038 1911 797 307 339 159 90 90 0 2018 1914 615 388 421 151 98 96 0 1.062 1.051 1.057 1.009 0.374 1.052 0.913 52 420 3361 3130 0.087 1731 1630 1604 1526 0 0.941652224 -0.0261093
6 0.0003623 4180 14810 80 2686 2616 984 287 296 78 98 96 0 2766 2680 828 365 371 57 98 98 0 0.999 1.006 0.998 0.972 0.288 0.994 0.907 52 340 4800 4644 -0.001 2399 2401 2329 2315 0 1.000833681 0.0003623
7 -0.0378203 4420 14810 80 2791 2714 878 297 301 59 100 100 0 2671 2697 837 385 397 103 98 98 0 1.091 1.045 1.055 1.1 0.4 0.995 0.88 52 340 4780 4729 0.126 2494 2286 2417 2312 0 0.91659984 -0.0378203
8 4700 14780 140 266 340 372 284 296 96 14 6 0 385 420 326 385 393 73 15 6 0 100000 1.6 1.23 3.482 9.262 0.208 0.015 156 1089 -18 91 16.61 -18 0 56 35 -50 0
9 -0.0150163 4920 14820 80 2264 2257 580 322 354 424 98 96 0 2254 2243 525 378 388 139 100 100 0 1.035 1.038 1.022 1.093 0.413 0.926 0.374 52 340 3818 3800 0.05 1942 1876 1935 1865 0 0.966014418 -0.0150163
10 0.0131103 5170 14810 80 2129 2014 657 367 395 171 98 94 0 2186 2052 503 370 379 81 100 100 0 0.97 0.979 0.957 0.986 0.346 0.955 0.861 52 340 3578 3329 -0.044 1762 1816 1647 1682 0 1.030646992 0.0131103
11 5430 14780 140 583 576 271 337 442 220 56 17 0 568 591 226 414 455 140 53 22 0 1.597 1.35 1.256 1.915 2.221 0.819 0.476 156 1052 400 416 0.676 246 154 239 177 -50 0.62601626 -0.2034143
12 5670 14780 140 712 662 254 292 427 313 66 11 0 614 645 665 404 448 141 66 22 0 2 1.535 1.959 2.985 7.768 0.469 0.158 156 1034 630 611 1 420 210 370 241 -50 0.5 -0.3010303
13 -0.0278363 5910 14790 80 2207 2160 499 258 280 156 100 100 0 2190 2078 451 362 364 63 100 100 0 1.066 1.108 1.099 1.14 0.282 1.043 0.909 52 340 3777 3618 0.092 1949 1828 1902 1716 0 0.93791688 -0.0278363
14 -0.0426693 6150 14790 90 3170 3034 841 274 280 89 100 98 0 2999 3051 767 374 378 70 98 98 0 1.103 1.031 1.085 1.317 1.923 1 0.9 52 420 5521 5437 0.142 2896 2625 2760 2677 0 0.906422652 -0.0426693
15 0.0165623 6400 14790 90 4317 4617 1615 278 292 116 100 100 0 4571 4794 1399 375 380 68 100 100 0 0.963 0.982 0.987 0.984 0.162 0.933 0.902 52 420 8235 8758 -0.055 4039 4196 4339 4419 0 1.038871008 0.0165623
16 0.0297803 6640 14790 90 1854 1735 544 276 290 110 100 100 0 2065 2071 679 375 380 66 100 100 0 0.934 0.86 0.843 0.884 0.214 0.737 0.843 52 420 3268 3155 -0.099 1578 1690 1459 1696 0 1.070975919 0.0297803
17 0.0341993 6880 14790 80 1157 1119 313 266 272 59 100 100 0 1327 1344 358 363 371 67 100 100 0 0.924 0.87 0.904 0.9 0.261 0.797 0.844 52 340 1855 1834 -0.114 891 964 853 981 0 1.081930415 0.0341993
18 0.0050883 7120 14790 80 830 889 337 236 248 92 100 96 0 949 986 342 348 347 61 94 94 0 0.988 1.024 1.013 1.089 0.409 0.889 0.813 52 340 1195 1291 -0.017 594 601 653 638 0 1.011784512 0.0050883
19 0.1798843 7350 14780 90 992 1137 514 232 257 138 100 92 0 1490 1441 515 340 366 177 96 88 0 0.661 0.822 0.86 0.953 0.564 0.712 0.752 52 420 1910 2006 -0.598 760 1150 905 1101 0 1.513157895 0.1798843
20 0.0787313 7610 14790 90 833 887 311 189 193 57 100 98 0 1069 1017 340 297 306 69 94 92 0 0.834 0.969 0.937 1.586 2.646 0.787 0.773 52 420 1416 1418 -0.262 644 772 698 720 0 1.198757764 0.0787313

Total number of rows: 9504

Table truncated, full table size 1913 Kbytes.




Supplementary data files not provided
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