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Sample GSM9076 Query DataSets for GSM9076
Status Public on Jan 20, 2004
Title db/m 5-3
Sample type RNA
 
Channel 1
Source name ID:5-3, 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 2150 16750 100 171 167 46 172 176 39 13 3 0 140 141 32 137 142 25 21 5 0 -0.333 -1.250 1.831 3.793 6.667 0.429 0.098 80 415 2 -1 Error -1 3 -5 4 -50
2 4.726876e-02 1 1 2 1 2290 16650 130 11083 12528 7831 167 172 39 100 100 0 8626 9381 5425 133 138 26 100 100 0 1.285 1.337 1.354 1.401 0.614 1.325 0.916 120 662 19409 21609 0.362 10916 8493 12361 9248 0
3 4.335690e-01 1 1 3 1 2480 16750 120 2170 2146 1378 174 179 37 92 91 0 1421 1437 1108 136 138 24 90 90 0 1.553 1.516 1.542 2.230 3.766 1.324 0.914 120 476 3281 3273 0.635 1996 1285 1972 1301 0
4 -4.841540e+00 1 1 4 1 2640 16660 120 238 225 67 166 175 52 57 22 0 1095 952 386 135 139 37 95 95 0 0.075 0.072 0.088 0.215 0.575 0.075 0.352 120 572 1032 876 -3.737 72 960 59 817 0
5 4.188186e-02 1 1 5 1 2800 16750 110 3687 3226 1096 180 184 44 100 100 0 2791 2505 842 145 148 38 100 100 0 1.325 1.291 1.289 1.326 0.310 1.261 0.959 80 433 6153 5406 0.406 3507 2646 3046 2360 0
6 -3.136398e-01 1 1 6 1 2970 16670 110 1012 973 477 173 176 36 91 90 0 998 1003 542 141 143 24 95 92 0 0.979 0.928 0.963 1.002 0.346 0.856 0.910 80 583 1696 1662 -0.031 839 857 800 862 0
7 7.014442e-01 1 1 7 1 3150 16780 80 529 510 149 187 189 40 94 92 0 411 381 115 148 153 28 96 92 0 1.300 1.386 1.434 1.612 0.837 1.286 0.837 52 286 605 556 0.379 342 263 323 233 0
8 -3.925887e-01 1 1 8 1 3300 16670 120 2699 2287 967 181 183 38 100 100 0 2595 2281 927 146 150 31 100 100 0 1.028 0.986 0.986 1.043 0.503 0.971 0.945 120 643 4967 4241 0.040 2518 2449 2106 2135 0
9 -3.011551e-01 1 1 9 1 3460 16760 110 400 366 141 191 193 36 82 77 0 391 371 144 150 153 25 86 85 0 0.867 0.792 0.857 0.994 0.710 0.739 0.712 80 439 450 396 -0.206 209 241 175 221 0
10 -3.133439e-02 1 1 10 1 3630 16660 120 1562 1453 704 176 180 37 94 92 0 1450 1284 645 139 144 27 95 93 0 1.057 1.115 1.136 1.321 0.942 1.059 0.917 120 653 2697 2422 0.080 1386 1311 1277 1145 0
11 -3.535457e-01 1 1 11 1 3790 16760 110 594 526 214 195 196 41 85 81 0 651 575 231 148 153 29 90 90 0 0.793 0.775 0.832 0.871 0.405 0.783 0.864 80 404 902 758 -0.334 399 503 331 427 0
12 -2.039011e+00 1 1 12 1 3950 16660 110 465 409 158 173 179 39 83 83 0 1004 897 351 142 146 27 90 90 0 0.339 0.313 0.355 0.990 2.687 0.305 0.810 80 517 1154 991 -1.562 292 862 236 755 0
13 -4.265171e-01 1 1 13 1 4110 16750 110 903 799 352 169 173 36 92 91 0 1022 894 403 147 151 28 93 90 0 0.839 0.843 0.866 0.998 0.578 0.819 0.919 80 430 1609 1377 -0.254 734 875 630 747 0
14 5.539983e-01 1 1 14 1 4270 16650 120 3573 3094 1424 165 171 35 100 100 0 2197 1867 941 142 144 25 98 96 0 1.658 1.698 1.742 2.524 2.684 1.588 0.935 120 599 5463 4654 0.730 3408 2055 2929 1725 0
15 1.382295e-01 1 1 15 1 4430 16740 120 1275 1200 541 179 186 43 92 90 0 1117 998 436 149 156 35 90 90 0 1.132 1.203 1.179 1.299 0.610 1.174 0.942 120 556 2064 1870 0.179 1096 968 1021 849 0
16 1.438805e-01 1 1 16 1 4600 16660 110 1200 1067 377 183 187 41 95 92 0 972 887 318 146 151 34 95 92 0 1.231 1.193 1.185 1.389 1.476 1.126 0.914 80 531 1843 1625 0.300 1017 826 884 741 0
17 9.040192e-01 1 1 17 1 4760 16750 110 843 744 286 179 181 37 90 90 0 540 497 179 147 151 31 91 88 0 1.690 1.614 1.608 1.682 0.511 1.509 0.874 80 481 1057 915 0.757 664 393 565 350 0
18 2.596136e-01 1 1 18 1 4920 16660 110 416 388 115 181 180 37 90 87 0 360 338 101 144 147 25 91 88 0 1.088 1.067 1.115 1.326 1.051 0.959 0.761 80 542 451 401 0.122 235 216 207 194 0
19 0 1 19 1 5080 16750 100 162 169 52 177 172 60 10 1 0 201 202 50 152 157 27 71 46 0 -0.306 -0.160 0.763 1.200 1.618 0.435 0.086 80 439 34 42 Error -15 49 -8 50 -50
20 -2.177369e+00 1 1 20 1 5250 16670 120 2142 1877 702 189 195 90 97 95 0 5358 4708 1800 156 167 70 100 100 0 0.375 0.371 0.374 0.389 0.180 0.361 0.937 120 628 7155 6240 -1.413 1953 5202 1688 4552 0

Total number of rows: 9568

Table truncated, full table size 1788 Kbytes.




Supplementary data files not provided
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