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Sample GSM1127 Query DataSets for GSM1127
Status Public on Mar 29, 2002
Title Wild type voxel A2
Sample type RNA
 
Channel 1
Source name normal whole brain
Organism Mus musculus
Extracted molecule total RNA
 
Channel 2
Source name wild type 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 Feb 13, 2002
Last update date Apr 23, 2013
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 -0.2290553 3390 13960 80 12133 11914 2850 527 567 246 100 100 0 7420 7156 1519 571 587 153 100 100 0 1.695 1.729 1.621 1.811 0.64 1.605 0.878 52 250 18455 17972 0.761 11606 6849 11387 6585 0 0.590125797 -0.2290553
2 -0.1468543 3620 13960 90 9559 9342 2044 462 493 175 100 100 0 7082 7370 2191 595 644 264 100 100 0 1.402 1.311 1.382 1.451 0.765 1.199 0.912 52 420 15584 15655 0.488 9097 6487 8880 6775 0 0.713092228 -0.1468543
3 -0.0850113 3870 13960 90 1991 2058 507 461 602 1123 84 9 0 1828 1946 464 570 662 951 88 11 0 1.216 1.161 1.162 1.217 0.389 1.211 0.644 52 420 2788 2973 0.282 1530 1258 1597 1376 0 0.822222222 -0.0850113
4 0.0629923 4100 13950 90 2390 2577 1046 436 654 1208 75 42 0 2896 2823 1225 637 735 956 78 55 0 0.865 0.979 0.978 1.142 0.566 0.867 0.754 52 420 4213 4327 -0.209 1954 2259 2141 2186 0 1.156090072 0.0629923
5 -0.2062333 4380 13950 130 2017 2793 2883 451 895 1864 47 20 0 1394 1638 1284 420 538 508 57 47 0 1.608 1.923 1.439 2.391 3.399 2.017 0.468 120 907 2540 3560 0.685 1566 974 2342 1218 0 0.621966794 -0.2062333
6 -0.2909063 4600 13970 100 15195 17623 15096 906 1290 1390 93 91 2 8560 15522 17673 1247 1272 831 90 88 7 1.954 1.171 1.433 2.264 4.124 0.801 0.696 80 555 21602 30992 0.966 14289 7313 16717 14275 0 0.511792288 -0.2909063
7 -0.6990463 4850 13960 130 6420 6865 2536 734 1306 2289 95 71 0 1967 2831 2117 830 1422 2540 39 10 0 5.001 3.064 2.378 13.618 21.951 0.773 0.496 120 920 6823 8132 2.322 5686 1137 6131 2001 0 0.199964826 -0.6990463
8 5130 13920 140 536 652 427 498 560 283 25 10 0 456 465 147 471 482 108 10 4 0 -2.533 -25.667 2.385 5.73 11.795 0.697 0.169 156 1059 23 148 Error 38 -15 154 -6 -50 -0.394736842
9 -0.0512583 5330 13950 80 4017 3861 1145 424 481 321 100 100 0 3641 3572 899 448 467 132 100 100 0 1.125 1.1 1.123 1.13 0.325 1.034 0.844 52 336 6786 6561 0.17 3593 3193 3437 3124 0 0.888672419 -0.0512583
10 0.0158233 5590 13950 90 4090 3976 1098 371 421 274 100 100 0 4318 4211 1165 461 468 98 100 100 0 0.964 0.961 0.965 1.095 0.871 0.916 0.885 52 420 7576 7355 -0.053 3719 3857 3605 3750 0 1.037106749 0.0158233
11 -0.2065783 5830 13940 100 1813 1860 787 360 405 273 95 88 0 1374 1481 595 471 497 199 96 88 0 1.609 1.485 1.49 1.919 1.577 1.187 0.73 80 560 2356 2510 0.686 1453 903 1500 1010 0 0.621472815 -0.2065783
12 6100 13910 140 372 384 117 381 456 546 0 0 0 502 507 136 462 493 304 1 0 0 -0.225 0.067 1.098 3.377 6.859 1.486 0.696 156 1099 31 48 Error -9 40 3 45 -50 -4.444444444
13 -0.0247463 6350 13910 90 2650 2831 1004 357 387 179 100 100 0 2559 2624 906 393 410 112 100 100 0 1.059 1.109 1.105 1.175 0.385 1.06 0.863 52 420 4459 4705 0.082 2293 2166 2474 2231 0 0.944614043 -0.0247463
14 -0.1896723 6590 13920 100 10487 10674 4067 353 418 468 100 100 0 6940 6811 2820 392 425 270 100 100 0 1.548 1.608 1.575 2.045 2.182 1.419 0.843 80 560 16682 16740 0.63 10134 6548 10321 6419 0 0.646141701 -0.1896723
15 -0.2280643 6830 13910 90 16577 17434 4732 343 390 219 100 100 0 10067 10767 3090 465 491 177 100 100 0 1.691 1.659 1.736 1.695 0.307 1.618 0.87 52 420 25836 27393 0.758 16234 9602 17091 10302 0 0.591474683 -0.2280643
16 -0.2146823 7070 13920 100 11516 11502 5727 378 483 607 100 98 0 7302 6741 3491 508 607 739 93 86 0 1.639 1.785 1.871 2.611 4.097 1.574 0.883 80 560 17932 17357 0.713 11138 6794 11124 6233 0 0.609983839 -0.2146823
17 -0.2262223 7310 13910 90 6106 6468 3325 350 408 293 100 100 0 4050 4497 2394 631 685 295 100 98 0 1.684 1.583 1.603 1.766 0.629 1.394 0.886 52 420 9175 9984 0.751 5756 3419 6118 3866 0 0.593988881 -0.2262223
18 -0.1148933 7560 13910 110 2280 2546 1465 357 636 3620 10 2 0 2444 2444 1105 968 1247 3003 6 1 0 1.303 1.483 1.535 2.268 3.034 1.166 0.913 80 656 3399 3665 0.382 1923 1476 2189 1476 0 0.767550702 -0.1148933
19 -0.2092993 7800 13910 100 19704 18959 8758 387 532 781 100 100 0 12844 11417 5096 914 943 367 100 98 0 1.619 1.768 1.876 2.267 1.622 1.59 0.821 80 560 31247 29075 0.695 19317 11930 18572 10503 0 0.617590723 -0.2092993
20 -0.2650743 8040 13900 100 4624 5375 3685 349 435 406 100 98 0 2781 3268 2868 459 580 1227 75 45 0 1.841 1.789 1.828 2.31 1.942 1.346 0.828 80 560 6597 7835 0.881 4275 2322 5026 2809 0 0.543157895 -0.2650743

Total number of rows: 9504

Table truncated, full table size 1911 Kbytes.




Supplementary data files not provided
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