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Sample GSM10401 Query DataSets for GSM10401
Status Public on Jan 20, 2004
Title db/m 3-1
Sample type RNA
 
Channel 1
Source name ID:3-1, 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 Sep 22, 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 1850 18580 100 104 108 25 98 101 23 25 6 0 140 140 24 142 144 26 6 2 0 -3.000 -5.000 1.375 3.622 4.801 0.084 0.008 80 507 4 8 Error 6 -2 10 -2 -50
2 -6.012913e-01 1 1 2 1 2020 18510 80 13627 13463 2191 102 105 22 100 100 0 15263 15530 1990 142 144 24 100 100 0 0.894 0.868 0.875 0.868 0.088 0.866 0.970 52 337 28646 28749 -0.161 13525 15121 13361 15388 0
3 2.584318e+00 1 1 3 1 2200 18590 60 728 1070 827 115 166 430 62 46 0 680 887 646 139 670 4040 0 0 0 1.133 1.277 1.297 1.360 0.666 1.249 0.945 32 176 1154 1703 0.180 613 541 955 748 0
4 -2.859200e+00 1 1 4 1 2340 18500 90 190 200 63 126 127 27 73 59 0 1091 1041 294 133 135 24 100 100 0 0.067 0.081 0.073 0.087 0.049 0.094 0.525 52 414 1022 982 -3.904 64 958 74 908 0
5 3.633248e-01 1 1 5 1 2520 18580 70 950 1058 536 134 136 33 100 100 0 943 1008 536 127 126 25 100 100 0 1.000 1.049 1.047 1.152 0.378 1.008 0.955 32 236 1632 1805 0.000 816 816 924 881 0
6 -3.680587e-02 1 1 6 1 2670 18490 70 778 749 376 132 135 30 93 93 0 898 932 438 119 122 27 100 100 0 0.829 0.759 0.775 0.769 0.214 0.760 0.916 32 236 1425 1430 -0.270 646 779 617 813 0
7 5.501369e-01 1 1 7 1 2840 18590 60 340 397 147 136 136 29 100 100 0 373 424 210 116 119 25 100 93 0 0.794 0.847 0.879 1.126 0.881 0.757 0.860 32 176 461 569 -0.333 204 257 261 308 0
8 -4.592411e-01 1 1 8 1 3010 18500 80 1467 1316 529 135 138 32 100 100 0 2068 1897 756 113 116 24 100 100 0 0.681 0.662 0.647 0.666 0.182 0.656 0.946 52 328 3287 2965 -0.554 1332 1955 1181 1784 0
9 0 1 9 1 3160 18580 100 124 125 36 138 144 37 7 0 0 145 151 39 116 119 32 46 22 0 -0.483 -0.371 0.721 4.198 11.925 0.149 0.024 80 500 15 22 Error -14 29 -13 35 -50
10 -4.273929e-02 1 1 10 1 3340 18490 80 1014 991 179 140 144 35 100 100 0 1184 1176 205 118 120 24 100 100 0 0.820 0.804 0.791 0.818 0.168 0.770 0.918 52 340 1940 1909 -0.287 874 1066 851 1058 0
11 1.448888e-01 1 1 11 1 3500 18590 70 212 240 78 143 145 30 87 59 0 349 357 75 116 119 24 100 100 0 0.296 0.402 0.355 0.475 0.332 0.424 0.417 32 236 302 338 -1.756 69 233 97 241 0
12 -1.423751e+00 1 1 12 1 3660 18490 70 310 329 89 139 143 33 100 96 0 846 856 161 115 120 26 100 100 0 0.234 0.256 0.241 0.250 0.094 0.244 0.713 32 236 902 931 -2.096 171 731 190 741 0
13 -7.785807e-01 1 1 13 1 3830 18580 70 479 488 146 144 146 34 100 100 0 896 896 183 117 122 34 100 100 0 0.430 0.442 0.442 0.441 0.166 0.433 0.820 32 236 1114 1123 -1.217 335 779 344 779 0
14 5.575125e-01 1 1 14 1 3990 18490 80 2366 2354 519 142 143 34 100 100 0 1665 1705 380 114 116 25 100 100 0 1.434 1.390 1.350 1.409 0.234 1.360 0.946 52 338 3775 3803 0.520 2224 1551 2212 1591 0
15 5.139089e-01 1 1 15 1 4140 18580 80 1198 1208 314 143 147 33 100 100 0 1080 1014 272 112 114 23 100 100 0 1.090 1.181 1.196 1.221 0.266 1.161 0.947 52 338 2023 1967 0.124 1055 968 1065 902 0
16 -2.637508e-01 1 1 16 1 4320 18480 80 618 611 129 144 148 33 100 100 0 839 849 204 117 119 26 100 100 0 0.657 0.638 0.630 0.668 0.216 0.610 0.879 52 328 1196 1199 -0.607 474 722 467 732 0
17 0 1 17 1 4470 18580 100 153 160 38 140 142 32 35 10 0 129 140 41 117 119 24 41 17 0 1.083 0.870 1.244 2.219 2.515 0.077 0.004 80 484 25 43 0.115 13 12 20 23 -50
18 9.596539e-01 1 1 18 1 4640 18470 70 212 218 41 138 139 30 93 65 0 261 276 78 115 116 23 100 93 0 0.507 0.497 0.511 0.663 0.624 0.426 0.390 32 220 220 241 -0.980 74 146 80 161 0
19 0 1 19 1 4800 18580 100 121 121 39 144 147 38 5 1 0 149 169 56 114 120 62 35 12 0 -0.657 -0.418 0.989 3.457 7.282 -0.198 0.055 80 532 12 32 Error -23 35 -23 55 -50
20 -2.235237e+00 1 1 20 1 4970 18490 80 785 837 453 145 150 43 94 90 0 3562 3550 1914 116 120 35 100 100 0 0.186 0.202 0.193 0.192 0.072 0.208 0.930 52 340 4086 4126 -2.429 640 3446 692 3434 0

Total number of rows: 9568

Table truncated, full table size 1773 Kbytes.




Supplementary data files not provided
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