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Sample GSM1391 Query DataSets for GSM1391
Status Public on Mar 29, 2002
Title Wild type voxel C2
Sample type RNA
 
Channel 1
Source name normal whole brain
Organism Mus musculus
Extracted molecule total RNA
 
Channel 2
Source name wild type voxel C2
Organism Mus musculus
Extracted molecule total RNA
 
 
Description Voxel C2 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 -0.8042013 3070 15500 120 16894 25856 19124 12428 15824 9865 35 25 13 3742 5629 4702 3041 3934 3720 19 12 0 6.371 5.189 5.095 9.688 13.025 1.981 0.51 120 653 5167 16016 2.671 4466 701 13428 2588 0 0.156963726 -0.8042013
2 3230 15490 140 9345 10978 4503 9844 12936 8381 7 2 0 2688 3031 1041 2720 3420 3195 2 0 0 15.594 3.646 4.11 6.352 10.156 2.193 0.324 156 831 -531 1445 3.963 -499 -32 1134 311 -50 0.064128257 -1.1929513
3 3470 15490 140 11574 13063 4727 10244 11035 3418 31 9 0 3079 3237 794 2751 2986 898 19 6 0 4.055 5.8 4.535 8.959 13.212 2.246 0.358 156 1001 1658 3305 2.02 1330 328 2819 486 -50 0.246616541 -0.6079783
4 -0.7969823 3700 15450 130 13382 20528 16593 10719 12386 6855 35 22 6 3324 4337 2811 2899 3167 1066 26 17 0 6.266 6.821 5.868 9.772 12.145 5.374 0.705 120 802 3088 11247 2.648 2663 425 9809 1438 0 0.159594442 -0.7969823
5 3950 15490 140 7553 8163 2300 8530 10508 5789 1 0 0 2371 2651 800 2637 2931 1067 9 3 0 3.673 -26.214 3.589 6.353 10.475 2.387 0.419 156 984 -1243 -353 1.877 -977 -266 -367 14 -50 0.272262027 -0.5650133
6 4200 15490 140 7464 8001 2021 9130 13843 13125 0 0 0 2500 2600 534 2780 3552 2316 0 0 0 5.95 6.272 4.376 6.24 6.989 4.892 0.663 156 943 -1946 -1309 2.573 -1666 -280 -1129 -180 -50 0.168067227 -0.7745173
7 4440 15490 140 6434 7026 1823 9288 14825 14970 0 0 0 2361 2546 710 2787 3603 2488 0 0 0 6.7 9.386 4.996 6.443 5.186 4.967 0.745 156 926 -3280 -2503 2.744 -2854 -426 -2262 -241 -50 0.149264191 -0.8260443
8 4680 15490 140 8102 8456 2096 8629 12579 11688 0 0 0 2461 2563 391 2746 3248 1973 0 0 0 1.849 0.945 3.096 7.706 14.728 5.091 0.66 156 926 -812 -356 0.887 -527 -285 -173 -183 -50 0.540796964 -0.2669663
9 4920 15490 140 8074 15553 17052 7787 10369 8682 21 13 7 2533 3768 2974 2526 2889 1316 25 14 0 41 6.253 4.402 6.71 8.657 5.198 0.766 156 994 294 9008 5.358 287 7 7766 1242 -50 0.024390244 -1.6127843
10 5160 15490 140 8224 8893 3059 8715 10857 8492 1 0 0 2694 2922 908 2576 3013 1815 11 0 0 -4.161 0.514 5.044 9.049 14.251 3.488 0.417 156 926 -373 524 Error -491 118 178 346 -50 -0.240325866
11 5400 15490 140 9654 10734 4594 9586 11428 6925 5 1 0 2648 2862 926 2574 2918 1470 5 1 0 0.919 3.986 4.539 8.959 13.27 1.64 0.333 156 875 142 1436 -0.122 68 74 1148 288 -50 1.088235294 0.0367233
12 5640 15490 140 8224 9368 4521 7774 9279 5387 8 5 0 3031 3259 1069 2727 2955 867 16 7 0 1.48 2.996 4.086 9.466 14.295 4.605 0.674 156 901 754 2126 0.566 450 304 1594 532 -50 0.675555556 -0.1703393
13 5880 15490 140 5704 6388 2832 5109 5700 2616 15 6 0 2965 3328 1234 2426 2611 1365 35 7 0 1.104 1.418 1.438 3.425 5.764 1.386 0.379 156 948 1134 2181 0.143 595 539 1279 902 -50 0.905882353 -0.0429283
14 -0.1463353 6100 15490 80 9344 9932 2618 4317 4463 715 100 98 0 5720 6128 1681 2131 2168 298 100 98 0 1.401 1.405 1.275 1.548 0.928 1.279 0.832 52 332 8616 9612 0.486 5027 3589 5615 3997 0 0.713944699 -0.1463353
15 -0.1456893 6350 15500 100 7911 8616 3251 3160 3295 1165 98 91 0 4991 5338 2298 1594 1641 306 97 95 0 1.399 1.457 1.38 1.975 2.41 1.371 0.839 80 560 8148 9200 0.484 4751 3397 5456 3744 0 0.715007367 -0.1456893
16 -0.1569803 6600 15490 90 4180 4800 1828 1935 1989 405 100 100 0 2871 3083 1087 1307 1316 180 94 94 0 1.435 1.613 1.467 2.272 3.586 1.494 0.876 52 420 3809 4641 0.521 2245 1564 2865 1776 0 0.696659243 -0.1569803
17 6850 15490 140 2453 2648 867 1874 2042 565 50 31 0 1568 1688 491 1318 1354 228 50 41 0 2.316 2.092 1.611 3.096 6.782 1.352 0.487 156 1039 829 1144 1.212 579 250 774 370 -50 0.431778929 -0.3647393
18 -0.7719303 7070 15530 110 11655 16864 13855 2576 3228 2840 83 61 0 3250 3894 1878 1715 1910 842 75 43 0 5.915 6.557 6.424 7.518 5.661 4.818 0.535 80 588 10614 16467 2.564 9079 1535 14288 2179 0 0.169071484 -0.7719303
19 -0.1080993 7330 15490 80 4716 5136 1306 2760 3073 984 96 50 0 3192 3347 1001 1667 1737 395 90 86 0 1.283 1.414 1.317 1.491 0.714 1.196 0.678 52 332 3481 4056 0.359 1956 1525 2376 1680 0 0.779652352 -0.1080993
20 -0.2219503 7570 15500 70 5726 7071 3558 2872 2955 618 93 78 0 3281 4346 3110 1569 1651 508 93 81 0 1.667 1.512 1.735 1.901 0.876 1.094 0.738 32 236 4566 6976 0.737 2854 1712 4199 2777 0 0.599859846 -0.2219503

Total number of rows: 9504

Table truncated, full table size 1946 Kbytes.




Supplementary data files not provided
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