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Sample GSM1395 Query DataSets for GSM1395
Status Public on Mar 29, 2002
Title Wild type voxel B3
Sample type RNA
 
Channel 1
Source name normal whole brain
Organism Mus musculus
Extracted molecule total RNA
 
Channel 2
Source name wild type voxel B3
Organism Mus musculus
Extracted molecule total RNA
 
 
Description Voxel B3 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 -0.0845623 3750 14630 90 2031 2641 1677 228 270 436 98 92 0 1650 2015 978 166 175 63 100 100 0 1.215 1.305 1.256 1.263 0.425 1.353 0.911 52 324 3287 4262 0.281 1803 1484 2413 1849 0 0.823072657 -0.0845623
2 -0.0745843 3990 14620 90 2431 3659 3054 251 946 5541 15 3 0 2014 2708 1963 178 739 5334 11 0 0 1.187 1.347 1.242 1.347 0.52 0.782 0.687 52 420 4016 5938 0.248 2180 1836 3408 2530 0 0.842201835 -0.0745843
3 -0.0310343 4240 14630 90 953 1154 581 228 265 286 98 71 0 842 956 351 167 174 51 100 100 0 1.074 1.174 1.119 1.161 0.414 1.169 0.846 52 420 1400 1715 0.103 725 675 926 789 0 0.931034483 -0.0310343
4 -0.0165193 4480 14620 110 1129 1239 689 218 277 628 73 33 0 1041 1042 565 164 168 50 91 87 0 1.039 1.163 1.117 2.197 7.914 1.169 0.296 80 656 1788 1899 0.055 911 877 1021 878 0 0.962678375 -0.0165193
5 0.0636193 4730 14630 80 1004 1126 434 218 236 193 100 94 0 1073 1232 677 163 168 58 100 98 0 0.864 0.849 0.904 0.996 0.456 0.701 0.682 52 340 1696 1977 -0.211 786 910 908 1069 0 1.157760814 0.0636193
6 -0.0412183 4970 14630 90 2691 3479 2523 206 216 71 100 100 0 2417 2940 1907 157 162 42 100 100 0 1.1 1.176 0.98 1.215 0.755 1.133 0.853 52 420 4745 6056 0.137 2485 2260 3273 2783 0 0.90945674 -0.0412183
7 0.1195373 5210 14620 80 1651 1831 692 215 218 65 100 100 0 2052 2120 866 161 165 38 100 100 0 0.759 0.825 0.822 0.884 0.338 0.782 0.926 52 332 3327 3575 -0.397 1436 1891 1616 1959 0 1.316852368 0.1195373
8 5500 14610 140 207 217 74 209 215 66 17 7 0 157 158 43 160 163 45 10 1 0 0.667 -4 1.66 3.159 4.583 0.095 0.003 156 1052 -5 6 -0.585 -2 -3 8 -2 -50 1.5 0.1760913
9 0.0047153 5710 14620 90 1400 1509 547 209 282 471 98 73 0 1366 1533 479 162 174 103 100 100 0 0.989 0.948 0.927 0.977 0.346 0.917 0.841 52 414 2395 2671 -0.016 1191 1204 1300 1371 0 1.010915197 0.0047153
10 -0.0858903 5950 14620 80 1854 1868 670 210 219 84 100 100 0 1505 1553 423 156 162 40 100 100 0 1.219 1.187 1.234 1.201 0.363 1.145 0.87 52 340 2993 3055 0.285 1644 1349 1658 1397 0 0.820559611 -0.0858903
11 -0.0967553 6190 14620 80 907 1245 1022 206 232 201 98 80 0 723 910 676 162 165 43 98 98 0 1.25 1.389 1.269 1.635 1.162 1.277 0.776 52 340 1262 1787 0.321 701 561 1039 748 0 0.800285307 -0.0967553
12 -1.0016673 6410 14600 130 485 623 427 224 237 147 60 47 0 188 201 84 162 165 46 33 13 0 10.038 10.231 4.873 10.64 14.115 1.923 0.186 120 908 287 438 3.327 261 26 399 39 0 0.099616858 -1.0016673
13 -0.0029153 6700 14600 90 1115 1125 323 218 242 102 100 98 0 1055 1033 346 164 174 90 98 98 0 1.007 1.044 1.072 1.217 0.913 0.96 0.864 52 412 1788 1776 0.01 897 891 907 869 0 0.993311037 -0.0029153
14 -0.1593563 6940 14610 80 3329 3564 1323 249 283 241 100 100 0 2293 2428 797 159 198 234 100 98 0 1.443 1.461 1.47 1.57 0.8 1.432 0.904 52 332 5214 5584 0.529 3080 2134 3315 2269 0 0.692857143 -0.1593563
15 -0.2441703 7190 14610 80 8989 9074 2533 246 317 576 100 100 0 5143 5290 1329 160 319 1801 100 86 0 1.755 1.721 1.73 1.722 0.265 1.694 0.944 52 337 13726 13958 0.811 8743 4983 8828 5130 0 0.569941668 -0.2441703
16 -0.1775833 7430 14610 80 3300 3424 1065 237 333 709 100 100 0 2194 2255 709 159 204 301 100 100 0 1.505 1.521 1.537 1.56 0.321 1.491 0.834 52 340 5098 5283 0.59 3063 2035 3187 2096 0 0.664381325 -0.1775833
17 -0.0879463 7670 14610 90 1202 1249 504 231 266 261 100 82 0 950 977 412 157 170 91 100 100 0 1.224 1.241 1.243 1.331 0.581 1.127 0.853 52 420 1764 1838 0.292 971 793 1018 820 0 0.816683831 -0.0879463
18 -0.0068393 7920 14610 100 406 415 145 214 223 80 78 60 0 342 379 171 153 157 42 88 82 0 1.016 0.889 0.947 1.696 4.225 0.71 0.605 80 560 381 427 0.023 192 189 201 226 0 0.984375 -0.0068393
19 -0.2122273 8160 14610 90 2197 2359 1169 218 231 107 100 100 0 1369 1579 783 155 159 42 100 100 0 1.63 1.504 1.505 1.607 0.611 1.296 0.855 52 420 3193 3565 0.705 1979 1214 2141 1424 0 0.613441132 -0.2122273
20 -0.0882703 8400 14610 100 866 966 585 219 245 260 81 61 0 685 744 466 157 176 330 71 31 0 1.225 1.273 1.32 1.811 2.908 1.084 0.645 80 560 1175 1334 0.293 647 528 747 587 0 0.816074189 -0.0882703

Total number of rows: 9504

Table truncated, full table size 1902 Kbytes.




Supplementary data files not provided
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