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Sample GSM1384 Query DataSets for GSM1384
Status Public on Mar 29, 2002
Title Parkinson's model voxel A2
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 A2
Organism Mus musculus
Extracted molecule total RNA
 
 
Description Voxel A2 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 -0.1332553 4050 9120 80 1691 1719 529 408 447 229 100 98 0 1148 1187 293 204 223 118 100 100 0 1.359 1.334 1.293 1.371 0.6 1.268 0.794 52 268 2227 2294 0.443 1283 944 1311 983 0 0.735775526 -0.1332553
2 0.0595123 4300 9110 120 1014 949 480 408 459 542 53 8 0 894 760 587 199 206 64 74 66 0 0.872 0.964 1.013 2.844 11.875 0.958 0.256 120 732 1301 1102 -0.198 606 695 541 561 0 1.146864686 0.0595123
3 -0.0441343 4550 9120 80 844 844 236 399 406 115 90 80 0 597 582 189 195 201 65 96 90 0 1.107 1.15 1.193 1.287 0.745 0.895 0.693 52 288 847 832 0.147 445 402 445 387 0 0.903370787 -0.0441343
4 0.1124883 4780 9130 100 581 592 157 351 452 611 0 0 0 485 468 147 187 198 73 88 83 0 0.772 0.858 0.911 1.796 4.268 0.736 0.516 80 522 528 522 -0.374 230 298 241 281 0 1.295652174 0.1124883
5 0.1425773 5030 9140 80 900 933 208 321 333 82 100 100 0 980 974 275 176 177 46 100 100 0 0.72 0.767 0.771 0.802 0.259 0.701 0.809 52 320 1383 1410 -0.474 579 804 612 798 0 1.388601036 0.1425773
6 0.0381883 5280 9130 90 1124 1207 382 308 313 78 100 100 0 1064 1262 697 173 175 41 100 100 0 0.916 0.826 0.885 0.916 0.291 0.68 0.743 52 400 1707 1988 -0.127 816 891 899 1089 0 1.091911765 0.0381883
7 0.1382603 5510 9130 80 1243 1276 218 312 318 73 100 100 0 1458 1486 313 178 182 47 100 100 0 0.727 0.737 0.72 0.756 0.15 0.7 0.922 52 306 2211 2272 -0.459 931 1280 964 1308 0 1.374865736 0.1382603
8 0.1569593 5750 9120 80 1317 1347 279 327 336 79 100 100 0 1602 1569 366 181 182 45 100 100 0 0.697 0.735 0.709 0.765 0.214 0.702 0.896 52 288 2411 2408 -0.521 990 1421 1020 1388 0 1.435353535 0.1569593
9 0.0415253 6000 9130 80 619 640 207 320 354 297 50 7 0 505 541 204 176 183 54 98 94 0 0.909 0.877 0.879 0.954 0.559 1.012 0.329 52 306 628 685 -0.138 299 329 320 365 0 1.100334448 0.0415253
10 0.0810653 6240 9120 90 886 948 240 311 320 115 100 98 0 862 873 250 169 175 46 100 100 0 0.83 0.905 0.868 0.95 0.325 0.86 0.789 52 384 1268 1341 -0.269 575 693 637 704 0 1.205217391 0.0810653
11 0.0877023 6490 9130 80 457 543 471 314 322 79 63 46 0 353 427 386 178 179 41 75 71 0 0.817 0.92 1.023 1.606 2.679 1.046 0.801 52 320 318 478 -0.291 143 175 229 249 0 1.223776224 0.0877023
12 0.0479243 6720 9130 80 569 543 192 329 439 858 0 0 0 442 496 236 174 188 90 88 65 0 0.896 0.665 0.753 0.812 0.484 0.702 0.392 52 320 508 536 -0.159 240 268 214 322 0 1.116666667 0.0479243
13 0.0380343 6950 9140 90 1198 1185 172 313 352 251 100 98 0 1145 1170 278 179 194 100 100 98 0 0.916 0.88 0.912 0.963 0.496 0.838 0.892 52 420 1851 1863 -0.126 885 966 872 991 0 1.091525424 0.0380343
14 -0.0153533 7190 9140 90 2040 2074 450 399 471 371 100 100 0 1794 1825 559 210 237 175 100 98 0 1.036 1.037 1.056 1.139 0.475 0.962 0.818 52 420 3225 3290 0.051 1641 1584 1675 1615 0 0.965265082 -0.0153533
15 -0.0642813 7450 9150 90 3704 3790 740 375 392 128 100 100 0 3059 3153 674 188 193 64 100 100 0 1.16 1.152 1.168 1.168 0.182 1.12 0.937 52 420 6200 6380 0.214 3329 2871 3415 2965 0 0.862421147 -0.0642813
16 -0.1823403 7670 9150 90 1414 1339 421 364 403 215 98 92 0 880 910 282 190 210 119 98 94 0 1.522 1.354 1.385 1.395 0.472 1.253 0.795 52 420 1740 1695 0.606 1050 690 975 720 0 0.657142857 -0.1823403
17 -0.0815063 7930 9150 100 982 1033 347 345 358 120 97 91 0 711 729 249 183 184 44 100 98 0 1.206 1.26 1.269 1.431 0.961 1.186 0.76 80 560 1165 1234 0.271 637 528 688 546 0 0.8288854 -0.0815063
18 -0.0761713 8200 9150 70 576 510 159 346 368 126 62 37 0 374 420 229 181 206 99 78 34 0 1.192 0.686 0.88 1.918 3.753 0.566 0.386 32 236 423 403 0.253 230 193 164 239 0 0.839130435 -0.0761713
19 -0.1910173 8410 9150 100 1670 1628 570 338 346 93 100 97 0 1035 1042 387 177 181 43 100 100 0 1.552 1.491 1.517 1.601 0.606 1.378 0.867 80 560 2190 2155 0.635 1332 858 1290 865 0 0.644144144 -0.1910173
20 -0.0293843 8650 9150 100 882 876 248 347 355 94 97 92 0 680 673 226 180 183 45 98 96 0 1.07 1.073 1.041 1.216 0.79 0.998 0.792 80 560 1035 1022 0.098 535 500 529 493 0 0.934579439 -0.0293843

Total number of rows: 9504

Table truncated, full table size 1892 Kbytes.




Supplementary data files not provided
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