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Sample GSM9083 Query DataSets for GSM9083
Status Public on Jan 20, 2004
Title c 4-3
Sample type RNA
 
Channel 1
Source name ID:c 4-3, Genotype=(C57BL/6J), 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 1770 18500 100 279 285 59 225 254 108 17 2 0 155 165 47 121 144 86 15 3 0 1.588 1.364 1.398 1.926 1.753 1.074 0.721 80 479 88 104 0.667 54 34 60 44 -50
2 3.800342e-01 1 1 2 1 1930 18420 110 47782 45793 12274 219 250 110 100 100 0 28669 27103 6028 114 138 86 100 100 0 1.666 1.689 1.689 1.670 0.211 1.711 0.977 80 549 76118 72563 0.736 47563 28555 45574 26989 0
3 1.500435e+00 1 1 3 1 2090 18510 70 2088 2166 642 180 192 78 100 100 0 843 887 264 83 88 23 100 100 0 2.511 2.470 2.390 2.589 0.845 2.291 0.850 32 236 2668 2790 1.328 1908 760 1986 804 0
4 -2.499685e+00 1 1 4 1 2260 18420 80 379 377 91 168 170 29 98 92 0 925 940 301 81 83 18 100 100 0 0.250 0.243 0.241 0.255 0.112 0.227 0.764 52 339 1055 1068 -2.000 211 844 209 859 0
5 -2.695373e-02 1 1 5 1 2420 18500 80 2324 2207 832 170 172 30 100 100 0 2116 2145 760 83 84 20 100 100 0 1.060 0.988 0.951 1.002 0.313 0.960 0.876 52 339 4187 4099 0.083 2154 2033 2037 2062 0
6 1.048261e-02 1 1 6 1 2590 18410 80 836 854 312 166 168 26 100 100 0 680 694 269 81 83 19 100 100 0 1.119 1.122 1.121 1.193 0.487 1.088 0.923 52 340 1269 1301 0.162 670 599 688 613 0
7 1.095528e+00 1 1 7 1 2760 18500 80 722 726 194 171 173 34 100 100 0 342 362 101 86 90 24 100 100 0 2.152 2.011 1.932 2.215 1.290 1.795 0.808 52 338 807 831 1.106 551 256 555 276 0
8 -3.783440e-01 1 1 8 1 2910 18410 90 2618 2547 400 162 163 32 100 100 0 3074 2967 456 80 83 20 100 100 0 0.820 0.826 0.832 0.827 0.092 0.828 0.971 52 402 5450 5272 -0.286 2456 2994 2385 2887 0
9 0 1 9 1 3080 18500 100 189 192 33 165 167 30 38 13 0 95 94 21 79 82 20 35 8 0 1.500 1.800 1.885 3.663 6.493 0.325 0.040 80 478 40 42 0.585 24 16 27 15 -50
10 -1.605618e-01 1 1 10 1 3250 18410 80 1471 1488 194 158 159 31 100 100 0 1541 1537 225 75 78 19 100 100 0 0.896 0.910 0.926 0.919 0.119 0.886 0.949 52 335 2779 2792 -0.159 1313 1466 1330 1462 0
11 -5.034169e-01 1 1 11 1 3400 18490 90 493 481 92 161 163 26 100 98 0 495 493 126 80 81 20 100 100 0 0.800 0.775 0.801 0.810 0.254 0.723 0.847 52 400 747 733 -0.322 332 415 320 413 0
12 -1.538144e+00 1 1 12 1 3560 18410 80 610 603 94 164 162 26 100 100 0 1088 1075 173 79 84 23 100 100 0 0.442 0.441 0.431 0.443 0.083 0.435 0.910 52 339 1455 1435 -1.178 446 1009 439 996 0
13 4.669119e-02 1 1 13 1 3740 18500 70 1159 1133 133 169 169 32 100 100 0 1030 965 222 78 81 24 100 100 0 1.040 1.087 1.081 1.215 0.678 1.004 0.876 32 236 1942 1851 0.056 990 952 964 887 0
14 7.174873e-01 1 1 14 1 3900 18400 90 5307 5015 1122 165 171 38 100 100 0 3193 3032 630 77 81 29 100 100 0 1.650 1.641 1.646 1.664 0.339 1.635 0.961 52 415 8258 7805 0.723 5142 3116 4850 2955 0
15 0 1 15 1 4060 18500 100 154 153 33 164 168 35 7 1 0 81 83 19 78 81 19 20 5 0 -3.333 -2.200 1.417 4.787 7.396 0.022 0.000 80 451 -7 -6 Error -10 3 -11 5 -50
16 0 1 16 1 4220 18400 100 153 156 29 156 156 30 15 1 0 74 78 19 73 78 22 12 2 0 -3.000 0.000 1.454 3.457 4.927 -0.011 0.000 80 491 -2 5 Error -3 1 0 5 -50
17 0 1 17 1 4390 18500 100 149 147 30 154 157 28 10 1 0 79 83 23 76 79 22 22 5 0 -1.667 -1.000 1.591 3.288 5.116 0.191 0.017 80 469 -2 0 Error -5 3 -7 7 -50
18 3.312406e-01 1 1 18 1 4570 18410 80 227 241 64 154 155 27 92 67 0 140 148 47 73 76 19 92 76 0 1.090 1.160 1.100 1.553 1.392 0.793 0.368 52 335 140 162 0.124 73 67 87 75 0
19 3.173447e-01 1 1 19 1 4740 18510 60 238 246 75 158 156 29 68 56 0 158 159 52 82 83 21 84 75 0 1.053 1.143 1.041 1.392 1.347 0.683 0.291 32 176 156 165 0.074 80 76 88 77 0
20 -1.985400e+00 1 1 20 1 4890 18410 80 1442 1503 330 153 155 25 100 100 0 4353 4385 1081 77 80 22 100 100 0 0.301 0.313 0.317 0.319 0.057 0.302 0.949 52 332 5565 5658 -1.730 1289 4276 1350 4308 0

Total number of rows: 9568

Table truncated, full table size 1728 Kbytes.




Supplementary data files not provided
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