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Sample GSM1448 Query DataSets for GSM1448
Status Public on Mar 29, 2002
Title Parkinson's model voxel I2
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 I2
Organism Mus musculus
Extracted molecule total RNA
 
 
Description Voxel I2 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 0.0705603 2830 8350 80 1543 1594 388 517 528 185 98 98 0 1452 1545 385 245 254 88 100 100 0 0.85 0.828 0.807 0.869 0.365 0.789 0.767 52 340 2233 2377 -0.234 1026 1207 1077 1300 0 1.176413255 0.0705603
2 0.1430353 3070 8340 80 1649 1629 369 562 581 206 100 96 0 1764 1757 534 253 277 239 98 96 0 0.719 0.709 0.729 0.759 0.296 0.613 0.72 52 340 2598 2571 -0.475 1087 1511 1067 1504 0 1.390064397 0.1430353
3 3300 8320 140 753 800 292 646 684 264 31 10 0 424 567 338 333 371 183 43 33 0 1.176 0.658 1.089 3.29 8.114 0.547 0.25 156 1023 198 388 0.234 107 91 154 234 -50 0.85046729 -0.0703423
4 3540 8320 140 701 728 257 642 663 230 23 4 0 363 473 276 315 333 124 42 32 0 1.229 0.544 1.141 3.064 5.962 0.35 0.086 156 1044 107 244 0.298 59 48 86 158 -50 0.813559322 -0.0896113
5 0.1042623 3780 8330 70 1894 1944 467 582 597 249 100 96 0 1956 2024 674 288 300 158 100 100 0 0.787 0.785 0.787 0.858 0.37 0.56 0.636 32 236 2980 3098 -0.346 1312 1668 1362 1736 0 1.271341463 0.1042623
6 0.1268123 4020 8330 80 1229 1264 345 477 501 191 98 90 0 1245 1261 392 238 249 100 100 100 0 0.747 0.769 0.712 0.869 0.557 0.614 0.615 52 340 1759 1810 -0.421 752 1007 787 1023 0 1.339095745 0.1268123
7 0.1379823 4270 8330 80 1531 1475 425 424 475 288 96 84 0 1749 1766 475 228 232 74 100 100 0 0.728 0.683 0.661 0.718 0.327 0.596 0.736 52 340 2628 2589 -0.458 1107 1521 1051 1538 0 1.37398374 0.1379823
8 0.2108533 4500 8340 80 1650 1744 473 482 508 191 100 98 0 2130 2151 554 232 243 73 100 100 0 0.615 0.658 0.655 0.721 0.361 0.605 0.76 52 340 3066 3181 -0.7 1168 1898 1262 1919 0 1.625 0.2108533
9 -0.0845663 4750 8320 90 1113 1178 476 480 636 859 32 1 0 761 906 579 240 263 124 82 75 0 1.215 1.048 0.96 2.385 3.951 0.58 0.255 52 420 1154 1364 0.281 633 521 698 666 0 0.823064771 -0.0845663
10 0.1125573 4980 8330 80 1143 1201 433 467 474 162 94 84 0 1106 1160 568 230 240 78 98 90 0 0.772 0.789 0.918 1.139 1.089 0.628 0.592 52 340 1552 1664 -0.374 676 876 734 930 0 1.295857988 0.1125573
11 5230 8320 140 509 560 269 463 485 185 26 15 0 259 317 226 235 240 77 32 24 0 1.917 1.183 1.328 4.492 9.901 0.502 0.119 156 1058 70 179 0.939 46 24 97 82 -50 0.52173913 -0.2825473
12 0.0077553 5470 8320 80 920 921 290 476 496 170 82 69 0 684 720 452 232 238 75 86 82 0 0.982 0.912 0.892 2.224 3.56 0.481 0.323 52 332 896 933 -0.026 444 452 445 488 0 1.018018018 0.0077553
13 0.1552383 5710 8320 80 1403 1561 539 500 519 187 100 98 0 1526 1624 972 235 245 78 100 98 0 0.699 0.764 0.87 1.029 0.691 0.546 0.538 52 332 2194 2450 -0.516 903 1291 1061 1389 0 1.429678848 0.1552383
14 0.1411653 5960 8310 80 2285 2164 748 525 537 184 100 96 0 2675 2738 1190 239 244 75 100 100 0 0.722 0.656 0.623 0.749 0.641 0.58 0.786 52 320 4196 4138 -0.469 1760 2436 1639 2499 0 1.384090909 0.1411653
15 0.1385373 6190 8310 90 3559 3577 1431 533 636 746 98 90 0 4412 4446 1982 249 266 108 100 100 0 0.727 0.725 0.703 0.782 0.339 0.679 0.876 52 412 7189 7241 -0.46 3026 4163 3044 4197 0 1.375743556 0.1385373
16 0.0682413 6440 8310 100 1221 1401 700 551 1240 5709 0 0 0 1027 1063 545 243 671 4398 0 0 0 0.855 1.037 1.033 1.453 1.765 0.752 0.358 80 538 1454 1670 -0.227 670 784 850 820 0 1.170149254 0.0682413
17 0.0223373 6670 8300 120 920 1071 608 560 1079 4837 0 0 0 625 758 549 246 631 4290 0 0 0 0.95 0.998 1.052 2.718 8.579 0.896 0.633 120 764 739 1023 -0.074 360 379 511 512 0 1.052777778 0.0223373
18 0.1967973 6920 8310 100 871 915 316 557 587 259 56 25 0 739 889 600 245 257 135 77 65 0 0.636 0.556 0.58 2.211 6.372 0.365 0.286 80 538 808 1002 -0.654 314 494 358 644 0 1.573248408 0.1967973
19 0.0762473 7160 8320 80 1707 1756 599 519 530 183 98 96 0 1660 1805 728 244 253 77 98 98 0 0.839 0.792 0.737 1.043 1.114 0.667 0.659 52 340 2604 2798 -0.253 1188 1416 1237 1561 0 1.191919192 0.0762473
20 0.2154273 7410 8320 80 1040 1120 421 495 535 215 84 69 0 1138 1210 558 243 283 364 90 57 0 0.609 0.646 0.554 0.755 0.568 0.498 0.485 52 340 1440 1592 -0.716 545 895 625 967 0 1.642201835 0.2154273

Total number of rows: 9504

Table truncated, full table size 1885 Kbytes.




Supplementary data files not provided
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