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Sample GSM9078 Query DataSets for GSM9078
Status Public on Jan 20, 2004
Title db/m 6-2
Sample type RNA
 
Channel 1
Source name ID:6-2, Genotype=(C57BKsJ) Lepr db/m, Treatment= none
Organism Mus musculus
Extracted molecule total RNA
 
Channel 2
Source name common reference RNA (from mouse liver,spleen and kidney)
Organism Mus musculus
Extracted molecule total RNA
 
 
Description Total RNA from whole kidney was hybridized
Keywords = diabetes mouse models diabetic nephropathy streptozotocin db/db
 
Submission date Aug 13, 2003
Last update date May 28, 2005
Contact name Weijia Zhang
E-mail(s) [email protected]
Phone 718-430-3616
Fax 718-430-2732
URL http://www.aecom.yu.edu/BottingerLab/
Organization name Albert Einstein College of Medicine
Department Medicine
Lab Nephrology
Street address 1300 Morris Park Ave
City Bronx
State/province NY
ZIP/Postal code 10461
Country USA
 
Platform ID GPL409
Series (1)
GSE710 diabetic nephropathy streptozotocin db db

Data table header descriptions
ID_REF
VALUE log (base 2) transform of the ratio of the background subtracted means after lowess within and between chip normalization.
QUAL 1 means the quality of the spot is good, 0 means the quality of the spot is not good
Block the block number of the feature.
Column the column number of the feature.
Row the row number of the feature.
X the X-coordinate in �m of the center of the feature-indicator associated with the feature, where (0,0) is the top left of the image.
Y the Y-coordinate in �m of the center of the feature-indicator associated with the feature, where (0,0) is the top left of the image.
Dia. the diameter in �m of the feature-indicator.
F635 Median
F635 Mean
F635 SD
B635 Median
B635 Mean
B635 SD
% > B635+1SD the percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength #1 (635 nm).
% > B635+2SD the percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength #1 (635 nm).
F635 % Sat. the percentage of feature pixels at wavelength #1 that are saturated.
F532 Median median feature pixel intensity at wavelength #2 (532 nm).
F532 Mean mean feature pixel intensity at wavelength #2 (532 nm).
F532 SD the standard deviation of the feature intensity at wavelength #2 (532 nm).
B532 Median the median feature background intensity at wavelength #2 (532 nm).
B532 Mean the mean feature background intensity at wavelength #2 (532 nm).
B532 SD the standard deviation of the feature background intensity at wavelength #2 (532 nm).
% > B532+1SD the percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength #2 (532 nm).
% > B532+2SD the percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength #2 (532 nm).
F532 % Sat. the percentage of feature pixels at wavelength #2 that are saturated.
Ratio of Medians the ratio of the median intensities of each feature for each wavelength, with the median background subtracted.
Ratio of Means the ratio of the arithmetic mean intensities of each feature for each wavelength, with the median background subtracted.
Median of Ratios the median of pixel-by-pixel ratios of pixel intensities, with the median background subtracted.
Mean of Ratios the geometric mean of the pixel-by-pixel ratios of pixel intensities, with the median background subtracted.
Ratios SD the geometric standard deviation of the pixel intensity ratios.
Rgn Ratio the regression ratio of every pixel in a 2-feature-diameter circle around the center of the feature.
Rgn R.
F Pixels the total number of feature pixels.
B Pixels the total number of background pixels.
Sum of Medians the sum of the median intensities for each wavelength, with the median background subtracted.
Sum of Means the sum of the arithmetic mean intensities for each wavelength, with the median background subtracted.
Log Ratio
F635 Median - B635 the median feature pixel intensity at wavelength #1 with the median background subtracted.
F532 Median - B532 the median feature pixel intensity at wavelength #2 with the median background subtracted.
F635 Mean - B635 the mean feature pixel intensity at wavelength #1 with the median background subtracted.
F532 Mean - B532 the mean feature pixel intensity at wavelength #2 with the median background subtracted.
Flags the type of flag associated with a feature.

Data table
ID_REF VALUE QUAL Block Column Row 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
1 1 1 1 1650 16970 100 249 242 51 268 276 85 0 0 0 175 178 24 187 197 96 0 0 0 1.583 2.889 2.000 3.094 4.479 0.234 0.019 80 494 -31 -35 0.663 -19 -12 -26 -9 -50
2 1.926585e-01 1 1 2 1 1810 16870 100 24081 22732 7930 285 324 217 100 100 0 12745 12263 3871 204 226 151 100 100 0 1.897 1.861 1.889 1.924 0.618 1.854 0.935 80 492 36337 34506 0.924 23796 12541 22447 12059 0
3 2.715702e-01 1 1 3 1 2000 16980 110 2858 2873 1230 261 275 104 100 100 0 1879 1876 730 205 212 37 100 98 0 1.551 1.563 1.523 1.679 0.790 1.511 0.931 80 466 4271 4283 0.634 2597 1674 2612 1671 0
4 0 1 4 1 2150 16870 110 216 200 65 236 241 37 5 1 0 1184 1027 402 197 200 29 95 91 0 -0.020 -0.043 0.022 1.825 7.568 -0.003 0.001 80 547 967 794 Error -20 987 -36 830 0
5 -5.226936e-01 1 1 5 1 2310 16960 110 2959 2617 845 241 247 47 98 98 0 3144 2776 894 209 215 38 98 98 0 0.926 0.926 0.934 0.945 0.206 0.917 0.954 80 538 5653 4943 -0.111 2718 2935 2376 2567 0
6 -3.793279e-01 1 1 6 1 2480 16890 90 1339 1352 352 219 227 50 100 100 0 1389 1438 412 196 203 44 100 100 0 0.939 0.912 0.914 0.955 0.279 0.843 0.907 52 411 2313 2375 -0.091 1120 1193 1133 1242 0
7 7.272402e-01 1 1 7 1 2650 16980 90 592 576 143 233 237 38 96 94 0 443 431 93 190 192 27 98 98 0 1.419 1.423 1.332 1.516 0.743 1.255 0.788 52 374 612 584 0.505 359 253 343 241 0
8 -6.216249e-01 1 1 8 1 2800 16880 110 3152 2908 746 231 236 44 100 100 0 3344 3184 730 185 188 26 100 100 0 0.925 0.893 0.915 0.894 0.167 0.889 0.950 80 560 6080 5676 -0.113 2921 3159 2677 2999 0
9 -1.077066e-01 1 1 9 1 2970 16970 90 408 389 129 239 244 53 84 75 0 426 401 114 194 196 27 90 90 0 0.728 0.725 0.819 0.902 0.469 0.717 0.572 52 379 401 357 -0.457 169 232 150 207 0
10 -4.294323e-01 1 1 10 1 3120 16880 100 1885 1675 506 230 234 41 100 98 0 1945 1765 510 185 187 26 100 100 0 0.940 0.915 0.931 0.936 0.294 0.915 0.929 80 499 3415 3025 -0.089 1655 1760 1445 1580 0
11 -2.675811e-01 1 1 11 1 3300 16970 100 562 535 134 238 240 38 91 91 0 612 584 139 191 192 25 98 96 0 0.770 0.756 0.774 0.784 0.233 0.753 0.850 80 429 745 690 -0.378 324 421 297 393 0
12 -1.801092e+00 1 1 12 1 3450 16860 110 472 442 121 218 222 42 90 87 0 1049 967 264 182 184 26 98 97 0 0.293 0.285 0.306 0.391 0.700 0.295 0.798 80 529 1121 1009 -1.771 254 867 224 785 0
13 -2.288292e-01 1 1 13 1 3610 16960 100 1098 1014 253 225 231 49 100 100 0 1093 997 255 184 186 26 100 100 0 0.960 0.970 0.961 0.990 0.209 0.948 0.930 80 450 1782 1602 -0.058 873 909 789 813 0
14 5.539474e-01 1 1 14 1 3770 16860 110 5483 4935 1507 207 211 36 100 100 0 2728 2441 724 178 178 25 100 100 0 2.069 2.089 2.086 2.202 0.760 2.035 0.946 80 556 7826 6991 1.049 5276 2550 4728 2263 0
15 6.063617e-01 1 1 15 1 3940 16960 110 1924 1799 434 213 214 36 100 100 0 1117 1058 226 178 179 27 100 100 0 1.822 1.802 1.782 1.835 0.488 1.779 0.955 80 510 2650 2466 0.866 1711 939 1586 880 0
16 1.354887e-02 1 1 16 1 4100 16860 100 1138 1048 231 204 205 37 100 100 0 964 912 180 172 173 23 100 100 0 1.179 1.141 1.162 1.159 0.242 1.146 0.913 80 486 1726 1584 0.238 934 792 844 740 0
17 8.099175e-01 1 1 17 1 4270 16950 110 719 657 187 209 210 36 91 91 0 487 455 120 176 177 22 93 92 0 1.640 1.606 1.582 1.604 0.466 1.488 0.887 80 495 821 727 0.714 510 311 448 279 0
18 2.411554e-01 1 1 18 1 4430 16870 110 363 351 79 199 202 35 90 88 0 350 344 70 174 176 23 95 92 0 0.932 0.894 0.977 1.490 3.939 0.835 0.646 80 524 340 322 -0.102 164 176 152 170 0
19 0 1 19 1 4590 16960 100 224 220 51 202 205 36 38 13 0 244 240 43 180 182 23 80 68 0 0.344 0.300 0.757 1.380 2.019 0.304 0.086 80 438 86 78 -1.541 22 64 18 60 -50
20 -1.841543e+00 1 1 20 1 4760 16870 110 1752 1666 270 197 198 35 100 100 0 4314 4150 677 180 181 24 100 100 0 0.376 0.370 0.368 0.374 0.059 0.365 0.936 80 540 5689 5439 -1.411 1555 4134 1469 3970 0

Total number of rows: 9568

Table truncated, full table size 1787 Kbytes.




Supplementary data files not provided
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