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Sample GSM1383 Query DataSets for GSM1383
Status Public on Mar 29, 2002
Title Parkinson's model voxel A1
Sample type RNA
 
Channel 1
Source name normal whole brain
Organism Mus musculus
Extracted molecule total RNA
 
Channel 2
Source name Parkinson's model voxel A1
Organism Mus musculus
Extracted molecule total RNA
 
 
Description Voxel A1 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 -0.1963613 3580 9650 80 2173 2214 501 298 313 109 100 100 0 1374 1430 446 181 191 87 100 100 0 1.572 1.534 1.613 1.609 0.37 1.395 0.851 52 312 3068 3165 0.652 1875 1193 1916 1249 0 0.636266667 -0.1963613
2 -0.0074623 3820 9650 90 1316 1310 227 318 361 382 100 78 0 1164 1204 325 183 191 60 100 100 0 1.017 0.972 1.037 1.025 0.255 0.889 0.855 52 412 1979 2013 0.025 998 981 992 1021 0 0.982965932 -0.0074623
3 -0.0384583 4070 9650 90 760 764 209 288 298 83 98 94 0 608 629 219 176 181 53 98 98 0 1.093 1.051 1.108 1.152 0.599 0.941 0.744 52 412 904 929 0.128 472 432 476 453 0 0.915254237 -0.0384583
4 -0.0195543 4310 9650 90 607 593 153 289 299 86 90 80 0 473 490 191 169 173 53 96 90 0 1.046 0.947 1.023 1.65 3.28 0.732 0.539 52 412 622 625 0.065 318 304 304 321 0 0.955974843 -0.0195543
5 0.0098713 4560 9660 90 1176 1135 245 306 306 79 100 100 0 1063 1070 271 173 179 56 100 100 0 0.978 0.924 0.93 0.969 0.299 0.838 0.839 52 420 1760 1726 -0.033 870 890 829 897 0 1.022988506 0.0098713
6 -0.1581073 4810 9660 90 2193 2169 545 289 303 123 100 100 0 1496 1634 468 173 187 140 100 100 0 1.439 1.287 1.306 1.336 0.337 1.196 0.896 52 420 3227 3341 0.525 1904 1323 1880 1461 0 0.694852941 -0.1581073
7 0.0479613 5030 9660 80 1175 1198 262 310 383 626 86 7 0 1141 1107 295 175 203 134 100 100 0 0.895 0.953 0.945 1.011 0.298 0.849 0.2 52 332 1831 1820 -0.159 865 966 888 932 0 1.116763006 0.0479613
8 0.0667883 5290 9650 90 1466 1449 364 293 310 144 100 98 0 1540 1588 463 172 191 105 100 100 0 0.857 0.816 0.825 0.847 0.246 0.745 0.85 52 412 2541 2572 -0.222 1173 1368 1156 1416 0 1.166240409 0.0667883
9 -0.1178443 5510 9660 80 710 745 323 285 296 85 92 84 0 498 508 181 174 182 62 96 82 0 1.312 1.377 1.232 1.58 1.161 1.069 0.564 52 332 749 794 0.391 425 324 460 334 0 0.762352941 -0.1178443
10 -0.0483053 5770 9650 80 1427 1386 307 287 301 95 100 100 0 1198 1175 294 178 186 69 100 100 0 1.118 1.102 1.115 1.144 0.314 1.014 0.837 52 320 2160 2096 0.16 1140 1020 1099 997 0 0.894736842 -0.0483053
11 -0.0541963 6000 9650 70 465 456 142 286 299 119 68 28 0 331 349 146 173 180 64 78 56 0 1.133 0.966 0.929 1.717 2.269 0.802 0.373 32 230 337 346 0.18 179 158 170 176 0 0.882681564 -0.0541963
12 -0.1398993 6230 9660 80 722 701 216 279 302 154 88 67 0 489 486 174 168 183 97 90 69 0 1.38 1.327 1.212 1.809 1.621 0.976 0.557 52 332 764 740 0.465 443 321 422 318 0 0.724604966 -0.1398993
13 -0.0923513 6480 9650 90 1514 1549 342 282 289 83 100 100 0 1169 1184 222 173 179 59 100 100 0 1.237 1.253 1.218 1.287 0.341 1.187 0.873 52 420 2228 2278 0.307 1232 996 1267 1011 0 0.808441558 -0.0923513
14 -0.1558143 6730 9650 100 4967 4726 1343 270 297 245 100 100 0 3455 3228 1052 174 178 54 98 98 0 1.432 1.459 1.479 1.669 1.028 1.384 0.936 80 552 7978 7510 0.518 4697 3281 4456 3054 0 0.698530977 -0.1558143
15 -0.1734723 6970 9650 100 11268 10486 3090 275 283 79 100 100 0 7542 6839 2413 169 176 56 100 97 0 1.491 1.531 1.507 2.769 5.245 1.464 0.959 80 552 18366 16881 0.576 10993 7373 10211 6670 0 0.670699536 -0.1734723
16 -0.2888303 7200 9650 80 3057 2943 767 284 312 229 100 100 0 1596 1590 474 170 191 159 100 98 0 1.945 1.873 1.853 2.042 1.048 1.671 0.88 52 332 4199 4079 0.959 2773 1426 2659 1420 0 0.514244501 -0.2888303
17 -0.2242833 7450 9650 80 1410 1400 389 277 286 77 100 100 0 844 895 308 168 170 49 100 100 0 1.676 1.545 1.539 1.698 0.623 1.329 0.816 52 332 1809 1850 0.745 1133 676 1123 727 0 0.596646072 -0.2242833
18 -0.0800173 7690 9650 80 502 472 150 294 307 92 75 55 0 351 348 132 178 180 56 80 69 0 1.202 1.047 1.041 2.284 5.189 0.735 0.422 52 332 381 348 0.266 208 173 178 170 0 0.831730769 -0.0800173
19 -0.2529523 7940 9650 80 3326 3326 1075 302 323 115 100 100 0 1873 1824 535 184 196 85 100 100 0 1.79 1.844 1.869 1.886 0.507 1.727 0.879 52 332 4713 4664 0.84 3024 1689 3024 1640 0 0.558531746 -0.2529523
20 -0.1822843 8180 9650 80 953 966 290 282 286 73 100 98 0 611 668 249 170 174 47 100 98 0 1.522 1.373 1.393 1.559 0.79 1.126 0.722 52 332 1112 1182 0.606 671 441 684 498 0 0.657228018 -0.1822843

Total number of rows: 9504

Table truncated, full table size 1900 Kbytes.




Supplementary data files not provided
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