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Sample GSM1400 Query DataSets for GSM1400
Status Public on Mar 29, 2002
Title Parkinson's model voxel C1
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 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 -0.2151483 2980 9000 120 1072 1657 1882 386 401 117 83 76 0 562 711 631 144 150 50 82 69 0 1.641 2.242 1.733 6.53 15.373 1.491 0.293 120 776 1104 1838 0.715 686 418 1271 567 0 0.609329446 -0.2151483
2 0.0731163 3230 8970 90 1102 1172 307 393 432 284 94 73 0 980 1010 261 141 142 34 100 100 0 0.845 0.896 0.865 0.952 0.472 0.827 0.752 52 420 1548 1648 -0.243 709 839 779 869 0 1.183356841 0.0731163
3 0.1036553 3460 8970 90 605 608 135 375 385 105 84 57 0 430 424 115 138 144 44 100 96 0 0.788 0.815 0.858 0.975 0.628 0.681 0.38 52 420 522 519 -0.344 230 292 233 286 0 1.269565217 0.1036553
4 0.1088643 3700 8970 100 550 547 140 378 425 362 7 0 0 367 371 118 146 149 43 96 88 0 0.778 0.751 0.696 0.989 0.914 0.697 0.049 80 560 393 394 -0.362 172 221 169 225 0 1.284883721 0.1088643
5 0.1962953 3940 8960 90 776 787 179 384 407 278 75 19 0 756 734 146 140 150 46 100 100 0 0.636 0.678 0.631 0.703 0.329 0.654 0.641 52 420 1008 997 -0.652 392 616 403 594 0 1.571428571 0.1962953
6 0.0919793 4180 8970 80 872 899 231 376 397 117 98 90 0 756 770 179 143 153 50 100 100 0 0.809 0.834 0.862 0.858 0.366 0.727 0.678 52 340 1109 1150 -0.306 496 613 523 627 0 1.235887097 0.0919793
7 0.2196323 4420 8970 80 922 978 188 372 381 112 100 100 0 1050 996 312 138 141 33 100 98 0 0.603 0.706 0.657 0.997 1.325 0.615 0.749 52 340 1462 1464 -0.73 550 912 606 858 0 1.658181818 0.2196323
8 0.1768473 4660 8960 80 1145 1151 253 379 383 110 100 100 0 1300 1340 365 149 150 43 100 100 0 0.666 0.648 0.64 0.681 0.252 0.601 0.818 52 340 1917 1963 -0.587 766 1151 772 1191 0 1.502610966 0.1768473
9 0.1546863 4880 8950 70 601 611 203 400 420 134 59 37 0 435 428 174 148 166 82 81 68 0 0.7 0.754 0.943 1.438 2.578 0.639 0.377 32 236 488 491 -0.514 201 287 211 280 0 1.427860697 0.1546863
10 -0.0527063 5150 8940 90 725 783 259 375 384 101 90 78 0 452 534 273 142 145 37 100 98 0 1.129 1.041 1.063 1.32 0.972 0.667 0.425 52 412 660 800 0.175 350 310 408 392 0 0.885714286 -0.0527063
11 5390 8940 140 433 453 155 386 395 114 33 13 0 157 188 100 144 148 41 31 23 0 3.615 1.523 1.894 4.623 7.144 0.489 0.06 156 1015 60 111 1.854 47 13 67 44 -50 0.276595745 -0.5581553
12 5630 8940 140 445 452 134 385 396 107 35 14 0 174 217 129 140 144 38 46 31 0 1.765 0.87 1.679 4.111 7.048 0.427 0.084 156 1015 94 144 0.819 60 34 67 77 -50 0.566666667 -0.2466723
13 0.1110963 5870 8930 80 891 883 165 373 380 102 100 98 0 810 818 239 141 144 36 100 100 0 0.774 0.753 0.755 0.822 0.336 0.676 0.681 52 320 1187 1187 -0.369 518 669 510 677 0 1.291505792 0.1110963
14 -0.0436343 6110 8930 90 1473 1455 392 385 402 122 100 96 0 1128 1221 543 144 154 94 98 96 0 1.106 0.994 1.019 1.118 0.458 0.863 0.812 52 400 2072 2147 0.145 1088 984 1070 1077 0 0.904411765 -0.0436343
15 -0.1104283 6350 8930 80 2663 2510 888 387 465 632 94 80 0 1912 1994 910 147 174 242 98 92 0 1.29 1.149 1.164 1.329 0.774 1.079 0.817 52 320 4041 3970 0.367 2276 1765 2123 1847 0 0.775483304 -0.1104283
16 -0.1774093 6590 8930 80 884 920 336 389 469 662 26 3 0 474 497 188 145 189 586 15 0 0 1.505 1.509 1.568 1.926 2.102 1.43 0.106 52 320 824 883 0.589 495 329 531 352 0 0.664646465 -0.1774093
17 -0.1455943 6830 8930 90 869 929 275 381 396 181 94 80 0 490 541 214 141 147 59 98 96 0 1.398 1.37 1.373 1.529 0.712 1.181 0.705 52 412 837 948 0.484 488 349 548 400 0 0.715163934 -0.1455943
18 -0.3957073 7050 8900 100 559 1413 3273 365 382 102 65 48 0 223 266 154 145 149 37 71 51 0 2.487 8.661 2.587 8.14 14.142 4.933 0.091 80 480 272 1169 1.315 194 78 1048 121 0 0.402061856 -0.3957073
19 -0.3094433 7330 8940 90 1217 1310 426 383 395 133 98 98 0 549 651 294 140 145 36 100 98 0 2.039 1.814 1.899 2.128 1.09 1.63 0.781 52 420 1243 1438 1.028 834 409 927 511 0 0.490407674 -0.3094433
20 0.1965063 7570 8920 80 588 647 204 401 419 188 50 23 0 441 488 220 147 148 37 98 94 0 0.636 0.721 0.736 0.909 0.672 0.595 0.426 52 320 481 587 -0.653 187 294 246 341 0 1.572192513 0.1965063

Total number of rows: 9504

Table truncated, full table size 1879 Kbytes.




Supplementary data files not provided
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