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Sample GSM1390 Query DataSets for GSM1390
Status Public on Mar 29, 2002
Title Parkinson's model voxel B1
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 B1
Organism Mus musculus
Extracted molecule total RNA
 
 
Description Voxel B1 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 -0.0466613 2900 7760 90 1789 1852 697 346 372 194 100 98 0 1529 1507 516 233 238 79 100 98 0 1.113 1.182 1.258 1.239 0.426 1.1 0.783 52 420 2739 2780 0.155 1443 1296 1506 1274 0 0.898128898 -0.0466613
2 0.0486463 3120 7770 80 1344 1334 313 340 348 87 100 100 0 1357 1337 342 234 246 85 100 100 0 0.894 0.901 0.858 0.939 0.296 0.839 0.783 52 340 2127 2097 -0.162 1004 1123 994 1103 0 1.118525896 0.0486463
3 0.0541793 3380 7760 90 636 573 213 350 386 259 53 1 0 557 539 179 233 241 69 84 80 0 0.883 0.729 0.986 2.584 6.007 0.715 0.402 52 420 610 529 -0.18 286 324 223 306 0 1.132867133 0.0541793
4 0.1309063 3630 7770 70 569 553 175 316 339 111 71 56 0 564 610 263 222 251 190 84 40 0 0.74 0.611 0.697 0.713 0.376 0.481 0.542 32 236 595 625 -0.435 253 342 237 388 0 1.351778656 0.1309063
5 0.1315453 3870 7780 80 1531 1553 375 324 329 69 100 100 0 1858 1842 467 224 229 59 100 100 0 0.739 0.76 0.732 0.821 0.359 0.676 0.794 52 340 2841 2847 -0.437 1207 1634 1229 1618 0 1.353769677 0.1315453
6 0.0602113 4090 7770 80 1183 1248 471 329 334 75 100 100 0 1205 1225 475 224 345 1904 1 0 0 0.871 0.918 0.915 1.011 0.512 0.027 0.017 52 340 1835 1920 -0.2 854 981 919 1001 0 1.148711944 0.0602113
7 0.1265073 4330 7770 80 1084 1093 373 324 339 101 96 94 0 1235 1218 424 218 241 116 100 96 0 0.747 0.769 0.777 0.83 0.354 0.701 0.785 52 340 1777 1769 -0.42 760 1017 769 1000 0 1.338157895 0.1265073
8 0.1259013 4580 7770 80 1443 1456 418 316 325 84 100 100 0 1731 1727 463 225 235 75 100 100 0 0.748 0.759 0.727 0.782 0.265 0.72 0.841 52 340 2633 2642 -0.418 1127 1506 1140 1502 0 1.336291038 0.1259013
9 -0.1254093 4820 7760 90 1540 1554 563 308 310 72 100 100 0 1142 1153 510 219 223 53 100 100 0 1.335 1.334 1.363 1.609 1.144 1.191 0.814 52 420 2155 2180 0.417 1232 923 1246 934 0 0.749188312 -0.1254093
10 -0.1094883 5080 7760 90 1753 1797 525 308 315 101 100 100 0 1333 1444 541 210 219 60 100 100 0 1.287 1.207 1.28 1.273 0.384 1.13 0.819 52 420 2568 2723 0.364 1445 1123 1489 1234 0 0.77716263 -0.1094883
11 -0.2420033 5310 7760 80 1964 1931 951 288 296 78 100 96 0 1176 1189 666 216 222 74 96 92 0 1.746 1.689 1.771 2.849 5.934 1.469 0.864 52 340 2636 2616 0.804 1676 960 1643 973 0 0.572792363 -0.2420033
12 0.0255543 5560 7770 80 682 674 235 286 292 67 88 86 0 637 644 276 217 222 97 88 80 0 0.943 0.909 0.859 1.078 0.675 0.758 0.694 52 340 816 815 -0.085 396 420 388 427 0 1.060606061 0.0255543
13 0.0477373 5790 7760 100 1290 1313 592 283 290 67 93 91 0 1331 1292 735 207 211 56 93 88 0 0.896 0.949 0.896 1.293 1.475 0.805 0.635 80 560 2131 2115 -0.159 1007 1124 1030 1085 0 1.116186693 0.0477373
14 -0.1077063 6030 7760 100 4065 4072 1875 277 287 81 100 100 0 3158 3225 1657 202 210 62 97 95 0 1.281 1.255 1.313 1.725 1.717 1.163 0.91 80 560 6744 6818 0.358 3788 2956 3795 3023 0 0.780359029 -0.1077063
15 -0.1220723 6270 7760 100 10392 10293 3431 275 286 77 100 100 0 7844 7780 2596 206 208 50 100 98 0 1.325 1.323 1.336 1.382 0.454 1.276 0.919 80 560 17755 17592 0.406 10117 7638 10018 7574 0 0.754966887 -0.1220723
16 -0.1887803 6510 7750 90 6128 6188 1508 276 282 72 100 100 0 3990 3977 923 201 210 57 100 100 0 1.544 1.566 1.565 1.591 0.299 1.538 0.934 52 412 9641 9688 0.627 5852 3789 5912 3776 0 0.64747095 -0.1887803
17 -0.0842843 6760 7760 100 1964 2053 773 286 317 212 97 97 0 1594 1748 1060 212 215 62 97 97 0 1.214 1.15 1.205 1.311 0.555 0.845 0.688 80 560 3060 3303 0.28 1678 1382 1767 1536 0 0.823599523 -0.0842843
18 0.1954833 7010 7750 90 422 393 185 276 303 226 21 1 0 434 493 355 205 214 66 73 69 0 0.638 0.406 0.67 1.032 1.334 0.436 0.509 52 412 375 405 -0.649 146 229 117 288 0 1.568493151 0.1954833
19 -0.2080143 7220 7750 90 5861 7009 4344 259 282 175 100 100 0 3674 4466 2613 204 215 106 100 100 0 1.614 1.584 1.696 1.679 0.579 1.553 0.829 52 412 9072 11012 0.691 5602 3470 6750 4262 0 0.619421635 -0.2080143
20 0.0981743 7450 7740 90 948 973 343 262 292 362 86 46 0 1061 1037 443 201 228 451 80 42 0 0.798 0.85 0.931 1.063 0.928 0.809 0.727 52 400 1546 1547 -0.326 686 860 711 836 0 1.253644315 0.0981743

Total number of rows: 9504

Table truncated, full table size 1914 Kbytes.




Supplementary data files not provided
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