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Sample GSM1388 Query DataSets for GSM1388
Status Public on Mar 29, 2002
Title Parkinson's model voxel A4
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 A4
Organism Mus musculus
Extracted molecule total RNA
 
 
Description Voxel A4 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 -0.0065313 3280 9810 90 1081 1091 238 411 423 103 100 100 0 873 882 204 213 221 67 100 100 0 1.015 1.016 0.961 1.13 0.624 0.848 0.68 52 412 1330 1349 0.022 670 660 680 669 0 0.985074627 -0.0065313
2 0.1214893 3530 9800 90 900 890 164 426 435 130 96 86 0 849 842 168 222 225 50 100 100 0 0.756 0.748 0.767 0.777 0.288 0.641 0.686 52 412 1101 1084 -0.404 474 627 464 620 0 1.32278481 0.1214893
3 0.1818903 3760 9810 90 644 650 138 396 407 94 90 69 0 586 579 144 209 212 50 94 90 0 0.658 0.686 0.68 0.795 0.464 0.531 0.335 52 420 625 624 -0.604 248 377 254 370 0 1.52016129 0.1818903
4 0.1461283 4000 9810 90 574 573 154 389 394 87 78 51 0 456 440 149 197 209 102 82 63 0 0.714 0.757 0.893 1.408 2.57 0.095 0.067 52 420 444 427 -0.485 185 259 184 243 0 1.4 0.1461283
5 0.1575443 4250 9800 80 1001 1018 283 411 423 134 98 90 0 1053 1060 219 205 211 49 100 100 0 0.696 0.71 0.685 0.72 0.287 0.787 0.533 52 332 1438 1462 -0.523 590 848 607 855 0 1.437288136 0.1575443
6 0.0947863 4490 9800 80 769 766 200 400 403 86 90 80 0 662 655 207 203 205 46 98 98 0 0.804 0.81 0.792 0.902 0.491 0.676 0.627 52 332 828 818 -0.315 369 459 366 452 0 1.243902439 0.0947863
7 0.2143743 4730 9800 80 961 983 195 375 384 82 98 98 0 1149 1181 277 189 198 60 100 100 0 0.61 0.613 0.621 0.626 0.178 0.551 0.804 52 332 1546 1600 -0.712 586 960 608 992 0 1.638225256 0.2143743
8 0.1787533 4960 9800 80 1101 1136 194 396 402 95 100 100 0 1265 1352 318 201 210 101 100 100 0 0.663 0.643 0.634 0.661 0.15 0.592 0.844 52 332 1769 1891 -0.594 705 1064 740 1151 0 1.509219858 0.1787533
9 0.1635453 5220 9800 80 598 594 167 399 400 87 65 57 0 484 468 237 194 198 44 73 71 0 0.686 0.712 0.865 1.479 2.181 0.446 0.317 52 332 489 469 -0.543 199 290 195 274 0 1.457286432 0.1635453
10 0.1058653 5460 9790 80 967 942 236 391 393 83 94 92 0 929 917 249 194 195 43 100 100 0 0.784 0.762 0.733 0.807 0.356 0.717 0.777 52 332 1311 1274 -0.352 576 735 551 723 0 1.276041667 0.1058653
11 -0.0813053 5720 9790 80 563 543 153 399 405 95 61 38 0 336 340 169 200 204 50 67 57 0 1.206 1.029 0.915 3.338 12.65 0.604 0.275 52 332 300 284 0.27 164 136 144 140 0 0.829268293 -0.0813053
12 0.1344293 5950 9800 90 614 594 200 399 415 156 59 25 0 491 474 223 198 203 46 78 69 0 0.734 0.707 1.058 2.975 6.439 0.507 0.214 52 420 508 471 -0.447 215 293 195 276 0 1.362790698 0.1344293
13 0.1126473 6190 9790 80 1051 1039 220 406 414 91 100 98 0 1035 977 240 199 205 90 100 98 0 0.772 0.814 0.844 0.85 0.269 0.742 0.809 52 332 1481 1411 -0.374 645 836 633 778 0 1.296124031 0.1126473
14 -0.0062693 6410 9790 80 2573 2727 674 410 444 250 100 100 0 2323 2497 636 191 231 234 100 100 0 1.015 1.005 1.01 1.014 0.169 0.974 0.921 52 332 4295 4623 0.021 2163 2132 2317 2306 0 0.985668054 -0.0062693
15 -0.0254543 6660 9790 80 6161 6389 1874 399 415 180 100 100 0 5637 5418 1661 203 222 207 100 100 0 1.06 1.149 1.142 1.211 0.511 1.111 0.949 52 332 11196 11205 0.085 5762 5434 5990 5215 0 0.943075321 -0.0254543
16 -0.0958363 6910 9790 80 1514 1526 407 403 406 84 100 100 0 1083 1094 419 192 196 43 98 96 0 1.247 1.245 1.174 1.56 1.782 1.043 0.808 52 332 2002 2025 0.318 1111 891 1123 902 0 0.801980198 -0.0958363
17 0.0058003 7150 9790 80 1021 1036 191 426 737 1796 0 0 0 804 822 208 201 218 95 100 98 0 0.987 0.982 0.962 1.058 0.415 0.831 0.733 52 332 1198 1231 -0.019 595 603 610 621 0 1.013445378 0.0058003
18 7390 9790 140 419 428 109 401 634 1492 0 0 0 225 267 120 200 212 89 32 19 0 0.72 0.403 1.08 3.367 5.221 8.351 0.398 156 1001 43 94 -0.474 18 25 27 67 -50 1.388888889 0.1426683
19 -0.1401633 7640 9800 130 1736 4032 11528 391 431 656 70 51 2 1173 3022 9637 199 202 44 81 77 1 1.381 1.29 1.31 2.37 4.22 1.11 0.814 120 886 2319 6464 0.466 1345 974 3641 2823 0 0.724163569 -0.1401633
20 0.0277423 7870 9790 80 790 767 199 411 482 657 3 0 0 612 634 224 208 215 70 98 94 0 0.938 0.836 0.774 0.918 0.517 0.7 0.602 52 340 783 782 -0.092 379 404 356 426 0 1.065963061 0.0277423

Total number of rows: 9504

Table truncated, full table size 1899 Kbytes.




Supplementary data files not provided
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