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Sample GSM9077 Query DataSets for GSM9077
Status Public on Jan 20, 2004
Title db/m 5-4
Sample type RNA
 
Channel 1
Source name ID:5-4, 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 1620 17360 100 177 175 37 182 188 39 10 1 0 162 164 26 164 168 31 7 2 0 2.500 100000.000 1.545 4.442 6.993 0.386 0.081 80 454 -7 -7 1.322 -5 -2 -7 0 -50
2 8.783014e-02 1 1 2 1 1780 17250 130 14415 13861 5789 207 214 53 100 100 0 9205 9412 4229 180 187 42 100 100 0 1.574 1.479 1.441 1.642 0.839 1.400 0.940 120 698 23233 22886 0.655 14208 9025 13654 9232 0
3 3.273930e-01 1 1 3 1 1950 17370 120 2339 2440 1210 225 232 52 99 98 0 1459 1653 845 197 202 38 100 100 0 1.675 1.521 1.530 1.606 0.693 1.449 0.943 120 459 3376 3671 0.744 2114 1262 2215 1456 0
4 0 1 4 1 2110 17270 110 199 196 56 196 200 45 15 2 0 1009 932 272 175 177 32 97 95 0 0.004 0.000 0.051 1.210 6.736 0.014 0.010 80 542 837 757 -8.119 3 834 0 757 0
5 -8.842108e-02 1 1 5 1 2280 17360 110 3567 3216 1053 179 183 44 100 100 0 2907 2566 852 166 170 41 100 98 0 1.236 1.265 1.276 1.347 0.507 1.180 0.916 80 504 6129 5437 0.306 3388 2741 3037 2400 0
6 -3.926565e-01 1 1 6 1 2460 17270 100 1278 1282 531 191 192 43 97 96 0 1451 1378 589 168 173 34 98 96 0 0.847 0.902 0.922 1.030 0.483 0.864 0.920 80 509 2370 2301 -0.239 1087 1283 1091 1210 0
7 2.264321e-01 1 1 7 1 2620 17380 90 500 485 101 221 223 41 98 92 0 427 424 75 194 196 31 98 96 0 1.197 1.148 1.164 1.506 2.280 1.070 0.757 52 343 512 494 0.260 279 233 264 230 0
8 -2.578985e-01 1 1 8 1 2760 17270 120 3381 2927 1135 213 218 45 100 99 0 3026 2604 1086 185 191 39 100 98 0 1.115 1.122 1.119 1.365 1.329 1.059 0.923 120 684 6009 5133 0.157 3168 2841 2714 2419 0
9 -8.962834e-02 1 1 9 1 2940 17360 70 395 379 85 247 250 46 87 87 0 405 383 85 226 235 90 87 50 0 0.827 0.841 0.781 1.008 0.694 0.789 0.699 32 236 327 289 -0.274 148 179 132 157 0
10 6.958051e-02 1 1 10 1 3090 17260 120 2665 2361 731 218 220 40 100 100 0 2046 1853 595 192 199 59 100 96 0 1.320 1.290 1.283 1.488 1.448 1.245 0.945 120 676 4301 3804 0.400 2447 1854 2143 1661 0
11 -2.805699e-01 1 1 11 1 3260 17360 110 643 584 184 232 234 40 87 85 0 663 601 196 203 208 45 86 86 0 0.893 0.884 0.914 1.098 1.003 0.828 0.847 80 474 871 750 -0.162 411 460 352 398 0
12 -2.366863e+00 1 1 12 1 3410 17250 110 438 413 102 209 220 127 83 32 0 1101 1033 228 187 198 143 98 95 0 0.251 0.241 0.257 0.306 0.505 0.327 0.588 80 543 1143 1050 -1.997 229 914 204 846 0
13 -5.602359e-01 1 1 13 1 3570 17350 110 1054 1005 236 219 224 40 100 98 0 1243 1174 279 196 202 35 100 98 0 0.798 0.804 0.798 0.833 0.280 0.779 0.897 80 510 1882 1764 -0.326 835 1047 786 978 0
14 4.276468e-01 1 1 14 1 3740 17240 110 6215 5631 1642 222 226 43 100 100 0 3479 3126 938 195 200 38 100 100 0 1.825 1.845 1.865 1.912 0.452 1.775 0.940 80 604 9277 8340 0.868 5993 3284 5409 2931 0
15 2.996697e-01 1 1 15 1 3910 17350 100 2082 1934 498 243 247 44 100 100 0 1486 1383 360 216 219 43 100 100 0 1.448 1.449 1.432 1.516 0.541 1.356 0.918 80 448 3109 2858 0.534 1839 1270 1691 1167 0
16 8.609560e-03 1 1 16 1 4060 17240 110 1425 1336 338 223 224 53 98 98 0 1228 1150 267 195 200 37 98 98 0 1.164 1.165 1.209 1.190 0.283 1.139 0.922 80 572 2235 2068 0.219 1202 1033 1113 955 0
17 8.250286e-01 1 1 17 1 4240 17340 100 890 814 242 269 273 58 92 90 0 571 519 159 224 230 58 90 85 0 1.790 1.847 1.711 2.142 1.800 1.405 0.723 80 487 968 840 0.840 621 347 545 295 0
18 2.955998e-01 1 1 18 1 4410 17250 90 468 450 75 250 253 59 94 90 0 392 386 51 205 215 65 96 86 0 1.166 1.105 1.157 1.166 0.367 1.012 0.720 52 379 405 381 0.221 218 187 200 181 0
19 0 1 19 1 4550 17340 100 259 245 77 305 302 66 5 0 0 238 228 62 246 245 52 11 0 0 5.750 3.333 1.655 3.830 7.077 0.762 0.318 80 453 -54 -78 2.524 -46 -8 -60 -18 -50
20 -2.110168e+00 1 1 20 1 4720 17240 120 2148 1930 541 264 272 64 98 97 0 5690 5133 1473 231 233 44 100 100 0 0.345 0.340 0.344 0.349 0.098 0.330 0.944 120 612 7343 6568 -1.535 1884 5459 1666 4902 0

Total number of rows: 9568

Table truncated, full table size 1787 Kbytes.




Supplementary data files not provided
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