NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1393 Query DataSets for GSM1393
Status Public on Mar 29, 2002
Title Wild type voxel B2
Sample type RNA
 
Channel 1
Source name normal whole brain
Organism Mus musculus
Extracted molecule total RNA
 
Channel 2
Source name wild type voxel B2
Organism Mus musculus
Extracted molecule total RNA
 
 
Description Voxel B2 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 0.0619203 3740 14670 90 1913 2737 1959 262 490 1288 71 30 0 2116 2680 1612 212 229 104 100 100 0 0.867 1.003 0.886 1.024 0.605 0.979 0.793 52 302 3555 4943 -0.206 1651 1904 2475 2468 0 1.15324046 0.0619203
2 0.1323633 3980 14670 80 1385 2952 3622 254 272 106 98 96 0 1747 3158 3091 213 227 82 100 100 0 0.737 0.916 0.759 0.825 0.412 0.992 0.812 52 340 2665 5643 -0.44 1131 1534 2698 2945 0 1.356321839 0.1323633
3 0.0928413 4220 14660 90 844 919 418 265 323 498 55 15 0 926 997 385 209 219 73 100 100 0 0.808 0.83 0.819 0.9 0.54 0.768 0.719 52 420 1296 1442 -0.308 579 717 654 788 0 1.238341969 0.0928413
4 0.1622503 4460 14660 90 1226 1302 551 259 273 113 100 94 0 1620 1587 834 215 226 66 100 98 0 0.688 0.76 0.777 0.988 0.613 0.663 0.625 52 420 2372 2415 -0.539 967 1405 1043 1372 0 1.45294726 0.1622503
5 0.1744243 4730 14660 90 923 973 360 314 530 1223 11 0 0 1128 1307 641 218 237 100 100 98 0 0.669 0.605 0.586 0.736 0.573 0.729 0.061 52 420 1519 1748 -0.579 609 910 659 1089 0 1.494252874 0.1744243
6 -0.0481343 4960 14660 90 2584 3071 1951 344 677 1732 53 28 0 2231 2636 1575 226 260 229 98 94 0 1.117 1.132 1.073 1.643 2.469 1.019 0.368 52 420 4245 5137 0.16 2240 2005 2727 2410 0 0.895089286 -0.0481343
7 0.1593403 5200 14650 80 1387 1501 578 277 314 210 98 96 0 1823 1950 747 221 233 83 100 100 0 0.693 0.708 0.739 0.746 0.279 0.657 0.814 52 340 2712 2953 -0.529 1110 1602 1224 1729 0 1.443243243 0.1593403
8 5490 14650 140 271 278 74 287 537 1458 0 0 0 225 250 127 222 237 102 11 4 0 -5.333 -0.321 1.192 3.452 8.309 0.116 0.011 156 1049 -13 19 Error -16 3 -9 28 -50 -0.1875
9 -0.0497373 5690 14650 80 1608 1790 933 268 297 220 96 92 0 1412 1654 656 217 224 56 100 100 0 1.121 1.059 0.972 1.057 0.477 1.007 0.776 52 334 2535 2959 0.165 1340 1195 1522 1437 0 0.891791045 -0.0497373
10 -0.6932503 5960 14660 140 1352 1984 1942 296 313 114 89 84 0 443 850 945 229 252 118 63 49 0 4.935 2.718 3.112 8.656 12.814 0.857 0.151 156 991 1270 2309 2.303 1056 214 1688 621 0 0.202651515 -0.6932503
11 -0.2016453 6170 14650 80 1117 1425 1417 277 287 77 94 84 0 751 1100 999 223 247 126 86 71 0 1.591 1.309 1.32 1.921 1.875 0.918 0.446 52 340 1368 2025 0.67 840 528 1148 877 0 0.628571429 -0.2016453
12 -0.3891663 6510 14590 130 337 327 105 288 305 102 25 5 0 254 270 105 234 263 119 21 3 0 2.45 1.083 0.936 2.786 6.038 0.477 0.224 120 770 69 75 1.293 49 20 39 36 0 0.408163265 -0.3891663
13 0.0886373 6690 14640 100 900 933 311 264 281 83 100 98 0 997 987 402 217 244 118 93 88 0 0.815 0.869 0.932 1.172 1.077 0.656 0.219 80 520 1416 1439 -0.294 636 780 669 770 0 1.226415094 0.0886373
14 -0.0808773 6930 14640 110 3199 3573 1891 274 332 436 98 91 0 2654 2970 1315 226 253 145 100 100 0 1.205 1.202 1.146 1.303 0.818 1.092 0.701 80 656 5353 6043 0.269 2925 2428 3299 2744 0 0.83008547 -0.0808773
15 -0.1287403 7170 14630 110 7195 9421 6795 272 316 224 98 97 0 5375 6402 4287 228 265 160 97 97 0 1.345 1.482 1.512 1.904 1.761 1.31 0.728 80 648 12070 15323 0.428 6923 5147 9149 6174 0 0.743463816 -0.1287403
16 -0.2604433 7410 14650 110 4293 4397 2871 271 326 301 96 92 0 2440 2577 1732 232 269 163 96 86 0 1.822 1.759 1.803 2.514 2.407 1.48 0.748 80 656 6230 6471 0.865 4022 2208 4126 2345 0 0.548980607 -0.2604433
17 -0.1021893 7660 14640 100 1544 1584 803 261 304 303 90 76 0 1244 1211 684 230 260 154 88 78 0 1.265 1.349 1.329 2.834 6.749 1.107 0.267 80 560 2297 2304 0.339 1283 1014 1323 981 0 0.790335152 -0.1021893
18 -0.0014803 7890 14640 90 851 944 423 263 434 1154 13 0 0 803 846 432 217 280 343 69 38 0 1.003 1.083 1.092 1.572 1.454 1.128 0.471 52 420 1174 1310 0.005 588 586 681 629 0 0.996598639 -0.0014803
19 -0.2554433 8140 14640 100 4884 4918 2940 294 323 215 100 96 0 2784 3049 1685 235 264 165 97 91 0 1.801 1.643 1.58 2.307 2.425 1.431 0.731 80 560 7139 7438 0.849 4590 2549 4624 2814 0 0.555337691 -0.2554433
20 -0.1703663 8380 14640 100 1464 1715 1211 296 348 420 81 66 0 1020 1130 772 231 256 130 88 76 0 1.48 1.578 1.592 3.707 8.927 1.184 0.631 80 560 1957 2318 0.566 1168 789 1419 899 0 0.675513699 -0.1703663

Total number of rows: 9504

Table truncated, full table size 1898 Kbytes.




Supplementary data files not provided
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap