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Sample GSM1399 Query DataSets for GSM1399
Status Public on Mar 29, 2002
Title Wild type voxel C1
Sample type RNA
 
Channel 1
Source name normal whole brain
Organism Mus musculus
Extracted molecule total RNA
 
Channel 2
Source name wild type voxel C1
Organism Mus musculus
Extracted molecule total RNA
 
 
Description Voxel C1 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 0.2783993 3170 14660 80 1580 4150 5380 999 1240 1593 30 21 0 1390 2964 3431 287 323 184 98 98 0 0.527 1.177 0.652 0.943 0.974 1.341 0.798 52 234 1684 5828 -0.925 581 1103 3151 2677 0 1.898450947 0.2783993
2 -0.0402473 3410 14650 70 2972 4395 3642 814 864 321 100 96 0 2224 4235 4293 257 285 118 100 100 0 1.097 0.9 0.893 1.146 0.993 0.905 0.579 32 236 4125 7559 0.134 2158 1967 3581 3978 0 0.911492122 -0.0402473
3 0.0050633 3640 14660 80 1128 1436 1063 531 624 450 59 25 0 817 1020 772 213 253 329 80 40 0 0.988 1.121 1.025 1.468 2.086 1.123 0.587 52 340 1201 1712 -0.017 597 604 905 807 0 1.011725293 0.0050633
4 -0.3484553 3940 14600 240 400 859 1197 342 508 1287 14 5 0 214 499 654 188 267 1451 6 0 0 2.231 1.662 1.821 4.139 6.842 1.557 0.518 460 2329 84 828 1.158 58 26 517 311 0 0.448275862 -0.3484553
5 0.0728163 4140 14660 80 1054 1172 450 298 322 144 98 92 0 1072 1251 558 178 183 49 98 98 0 0.846 0.815 0.834 0.905 0.442 0.698 0.718 52 283 1650 1947 -0.242 756 894 874 1073 0 1.182539683 0.0728163
6 -0.1058483 4380 14660 90 2730 3094 2249 349 378 212 100 100 0 2044 2309 916 178 189 64 100 100 0 1.276 1.288 0.998 1.492 1.511 1.121 0.254 52 420 4247 4876 0.352 2381 1866 2745 2131 0 0.783704326 -0.1058483
7 0.1104793 4630 14650 80 1653 2211 2940 317 393 617 92 55 0 1897 2174 1303 174 180 51 100 100 0 0.775 0.947 0.755 0.822 0.305 1.368 0.76 52 340 3059 3894 -0.367 1336 1723 1894 2000 0 1.289670659 0.1104793
8 4920 14620 140 341 408 713 342 526 2129 0 0 0 181 190 76 177 203 559 0 0 0 -0.25 5.077 2.477 6.398 10.706 3.302 0.749 156 1065 3 79 Error -1 4 66 13 -50 -4
9 -0.0077753 5120 14660 80 1840 1951 707 431 668 3190 3 0 0 1563 1663 537 179 239 984 90 19 0 1.018 1.024 0.987 1.124 0.571 0.95 0.821 52 337 2793 3004 0.026 1409 1384 1520 1484 0 0.98225692 -0.0077753
10 -0.0453613 5360 14650 70 2745 2733 784 436 448 130 100 100 0 2257 2142 449 177 184 63 100 100 0 1.11 1.169 1.149 1.161 0.282 1.122 0.854 32 236 4389 4262 0.151 2309 2080 2297 1965 0 0.900822867 -0.0453613
11 0.0883863 5610 14650 80 782 980 1593 463 623 1527 1 1 0 576 697 856 185 192 60 98 98 0 0.816 1.01 0.818 0.914 0.588 1.544 0.835 52 340 710 1029 -0.294 319 391 517 512 0 1.225705329 0.0883863
12 -1.2494093 5910 14540 70 967 1476 1696 452 548 746 34 15 0 229 280 156 200 203 51 43 21 0 17.759 12.8 10.204 15.396 16.616 4.687 0.193 32 138 544 1104 4.15 515 29 1024 80 0 0.05631068 -1.2494093
13 0.0493993 6140 14620 100 1235 1318 600 380 604 2118 6 0 0 1137 1139 417 179 204 259 91 87 0 0.892 0.977 0.881 1.456 2.171 1.032 0.158 80 560 1813 1898 -0.164 855 958 938 960 0 1.120467836 0.0493993
14 -0.0499053 6370 14620 100 3137 3239 1188 355 385 210 98 97 0 2659 2654 809 179 191 99 100 98 0 1.122 1.165 1.175 1.191 0.376 1.132 0.881 80 560 5262 5359 0.166 2782 2480 2884 2475 0 0.891445004 -0.0499053
15 -0.1123633 6610 14610 90 6368 7292 3713 389 654 1793 98 98 0 4801 5240 1830 185 208 141 100 100 0 1.295 1.366 1.309 1.332 0.298 1.401 0.838 52 420 10595 11958 0.373 5979 4616 6903 5055 0 0.772035457 -0.1123633
16 -0.1309543 6850 14610 90 3962 4847 2996 351 379 158 100 100 0 2852 3551 2158 181 193 95 100 100 0 1.352 1.334 1.29 1.35 0.426 1.265 0.885 52 420 6282 7866 0.435 3611 2671 4496 3370 0 0.739684298 -0.1309543
17 -0.1189983 7100 14610 90 1860 2029 1025 408 566 1324 51 11 0 1282 1703 970 178 187 81 100 100 0 1.315 1.063 1.057 1.225 0.8 0.862 0.555 52 420 2556 3146 0.395 1452 1104 1621 1525 0 0.760330579 -0.1189983
18 0.0900343 7350 14610 90 787 856 344 405 419 142 84 65 0 647 754 611 177 182 45 98 94 0 0.813 0.782 0.968 1.022 0.616 0.462 0.36 52 420 852 1028 -0.299 382 470 451 577 0 1.230366492 0.0900343
19 -0.0894163 7580 14610 100 2665 3131 1935 295 324 346 95 91 0 2097 2503 1553 168 172 42 100 100 0 1.229 1.215 1.237 1.567 1.572 1.105 0.781 80 560 4299 5171 0.297 2370 1929 2836 2335 0 0.813924051 -0.0894163
20 -0.1001353 7830 14610 100 1086 1106 407 275 315 419 81 47 0 811 860 370 167 175 133 96 91 0 1.259 1.199 1.166 1.689 2.262 0.996 0.609 80 560 1455 1524 0.333 811 644 831 693 0 0.794081381 -0.1001353

Total number of rows: 9504

Table truncated, full table size 1922 Kbytes.




Supplementary data files not provided
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