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Sample GSM1126 Query DataSets for GSM1126
Status Public on Mar 29, 2002
Title Wild type voxel A1
Sample type RNA
 
Channel 1
Source name normal whole brain
Organism Mus musculus
Extracted molecule total RNA
 
Channel 2
Source name wild type voxel A1
Organism Mus musculus
Extracted molecule total RNA
 
 
Description Voxel A1 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 m 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_R 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_R 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 0.0413183 3410 12580 80 4122 4442 1673 1487 1895 1628 73 42 0 3265 3716 1502 367 577 2640 61 15 0 0.909 0.882 0.864 0.893 0.411 0.302 0.24 52 270 5533 6304 -0.137 2635 2898 2955 3349 0 1.099810247 0.0413183
2 -0.0191683 3650 12580 80 8574 8474 1012 1510 1617 896 100 100 0 7103 7091 1219 344 381 225 100 100 0 1.045 1.032 1.004 1.071 0.297 0.987 0.93 52 340 13823 13711 0.064 7064 6759 6964 6747 0 0.95682333 -0.0191683
3 0.0385983 3870 12570 120 1705 1783 590 1124 1212 499 60 17 0 923 1252 2837 288 315 136 66 59 0 0.915 0.684 0.807 4.138 10.52 0.098 0.045 120 806 1216 1623 -0.128 581 635 659 964 0 1.092943201 0.0385983
4 0.2022373 4120 12580 90 2844 2997 900 1168 1249 631 92 76 0 2951 2948 873 281 306 148 100 100 0 0.628 0.686 0.639 0.677 0.26 0.66 0.635 52 420 4346 4496 -0.672 1676 2670 1829 2667 0 1.593078759 0.2022373
5 0.3510943 4380 12580 80 1779 1925 701 1202 1279 424 57 32 0 1559 1611 699 264 320 250 96 86 0 0.446 0.537 0.544 0.653 0.559 0.375 0.201 52 340 1872 2070 -1.166 577 1295 723 1347 0 2.244367418 0.3510943
6 -1.0770703 4620 12620 170 3441 4833 4571 1184 1392 1162 75 49 0 452 1754 2212 263 295 197 47 39 0 11.942 2.447 4.66 12.99 18.781 1.191 0.278 208 1379 2446 5140 3.578 2257 189 3649 1491 0 0.083739477 -1.0770703
7 0.1688653 4850 12580 110 2307 2312 656 1095 1275 1221 47 2 0 2041 2066 1262 253 281 205 83 80 0 0.678 0.671 0.553 3.458 9.012 0.405 0.322 80 635 3000 3030 -0.561 1212 1788 1217 1813 0 1.475247525 0.1688653
8 5150 12550 140 924 983 316 900 1138 2617 0 0 0 232 252 82 246 346 2074 0 0 0 -1.714 13.833 3.848 7.577 10.522 0.975 0.621 156 1040 10 89 Error 24 -14 83 6 -50 -0.583333333
9 0.1572553 5340 12580 90 2403 2902 2179 1170 1639 4145 5 1 0 2029 1856 970 258 505 3350 1 0 0 0.696 1.084 0.772 2.744 6.542 2.509 0.584 52 399 3004 3330 -0.522 1233 1771 1732 1598 0 1.436334144 0.1572553
10 0.1464323 5600 12580 100 2527 2381 887 1098 1331 1228 55 6 0 2264 1969 1222 262 333 308 81 76 0 0.714 0.752 0.769 1.91 5.088 0.656 0.452 80 560 3431 2990 -0.486 1429 2002 1283 1707 0 1.400979706 0.1464323
11 5880 12540 140 1070 1208 541 1039 1367 1177 3 1 0 285 397 298 256 299 294 19 8 0 1.069 1.199 4.077 7.786 13.677 1.313 0.103 156 1062 60 310 0.096 31 29 169 141 -50 0.935483871 -0.0289643
12 6120 12540 140 1105 1480 2614 999 1193 1078 7 1 0 253 332 617 263 282 123 11 5 0 -10.6 6.971 3.935 7.959 11.083 3.932 0.75 156 1026 96 550 Error 106 -10 481 69 -50 -0.094339623
13 0.1148303 6370 12550 100 1918 2062 1263 864 1190 1645 18 3 0 1647 1610 786 274 344 284 87 82 0 0.768 0.897 0.813 1.738 6.254 1.082 0.242 80 554 2427 2534 -0.381 1054 1373 1198 1336 0 1.302656546 0.1148303
14 -0.1497863 6620 12550 100 6424 6962 3644 939 1043 489 100 100 0 4152 4362 2550 267 320 209 100 100 0 1.412 1.471 1.458 1.65 1.09 1.37 0.897 80 560 9370 10118 0.498 5485 3885 6023 4095 0 0.708295351 -0.1497863
15 -0.2220613 6860 12550 110 15322 15976 8029 1015 1553 2213 93 87 0 8855 8999 4587 275 555 1257 87 85 0 1.667 1.715 1.737 2.002 1.276 1.659 0.95 80 656 22887 23685 0.738 14307 8580 14961 8724 0 0.599706437 -0.2220613
16 -0.2161823 7100 12550 100 7927 8574 4423 998 1717 2396 88 77 0 4483 4779 2712 271 547 1243 90 81 0 1.645 1.681 1.649 1.739 0.794 1.523 0.791 80 560 11141 12084 0.718 6929 4212 7576 4508 0 0.607879925 -0.2161823
17 -0.1505343 7340 12550 110 3206 3201 1693 888 1033 748 77 68 0 1893 1982 1290 254 286 139 82 81 0 1.414 1.339 1.387 2.423 3.611 1.158 0.69 80 651 3957 4041 0.5 2318 1639 2313 1728 0 0.707075065 -0.1505343
18 7580 12530 140 937 1038 403 840 1076 1237 2 0 0 357 458 286 257 342 625 10 0 0 0.97 0.985 1.462 5.723 11.965 1.172 0.327 156 1068 197 399 -0.044 97 100 198 201 -50 1.030927835 0.0132283
19 -1.1845793 7900 12560 130 5766 9601 11361 1116 1693 2260 90 50 1 577 1559 2145 273 564 1248 23 17 0 15.296 6.598 18.852 20.639 16.915 1.579 0.206 120 773 4954 9771 3.935 4650 304 8485 1286 0 0.065376344 -1.1845793
20 -0.1789803 8060 12540 120 2267 2709 1815 985 1155 767 74 38 0 1107 1263 1023 258 286 130 81 77 0 1.51 1.715 1.395 5.734 13.442 1.27 0.448 120 688 2131 2729 0.595 1282 849 1724 1005 0 0.66224649 -0.1789803

Total number of rows: 9504

Table truncated, full table size 1894 Kbytes.




Supplementary data files not provided

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