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Sample GSM9166 Query DataSets for GSM9166
Status Public on Jan 20, 2004
Title db/db 9-3
Sample type RNA
 
Channel 1
Source name ID:9-3, Genotype=(C57BKsJ) Lepr db/db, 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 18, 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 1890 18530 100 93 90 23 85 87 20 21 10 0 126 132 24 124 127 22 23 7 0 4.000 0.625 1.076 2.610 4.185 0.207 0.043 80 519 10 13 2.000 8 2 5 8 -50
2 -0.1583766764 1 1 2 1 2060 18450 90 22168 19966 7341 82 91 66 100 100 0 11855 11119 2913 127 132 28 100 100 0 1.883 1.809 1.828 1.742 0.346 1.875 0.970 52 414 33814 30876 0.913 22086 11728 19884 10992 0
3 0.7071416359 1 1 3 1 2220 18540 60 1653 2248 1510 76 76 17 100 100 0 889 1093 688 126 127 21 100 100 0 2.067 2.246 2.290 2.354 0.577 2.203 0.978 32 176 2340 3139 1.047 1577 763 2172 967 0
4 -3.4089683439 1 1 4 1 2390 18450 80 189 206 58 75 75 17 100 100 0 2011 1885 435 124 124 19 100 100 0 0.060 0.074 0.068 0.075 0.029 0.072 0.783 52 340 2001 1892 -4.049 114 1887 131 1761 0
5 0.1824026037 1 1 5 1 2550 18530 70 3168 3348 2274 75 77 19 100 100 0 2190 2112 1267 125 127 22 100 100 0 1.498 1.647 1.599 1.621 0.441 1.670 0.964 32 236 5158 5260 0.583 3093 2065 3273 1987 0
6 0.5215016172 1 1 6 1 2720 18440 60 860 958 512 72 73 17 100 100 0 735 708 337 124 126 20 100 100 0 1.290 1.517 1.549 1.675 0.598 1.461 0.916 32 176 1399 1470 0.367 788 611 886 584 0
7 0.4922738025 1 1 7 1 2870 18540 70 526 578 372 75 76 18 96 96 0 544 569 327 123 123 18 100 96 0 1.071 1.128 1.179 1.165 0.399 1.110 0.943 32 236 872 949 0.099 451 421 503 446 0
8 -0.4820632572 1 1 8 1 3050 18440 80 4518 3688 1598 72 74 16 100 100 0 4294 3434 1536 122 125 19 100 100 0 1.066 1.092 1.097 1.170 0.334 1.067 0.967 52 340 8618 6928 0.092 4446 4172 3616 3312 0
9 -0.4884162904 1 1 9 1 3210 18540 70 191 175 46 71 73 15 93 90 0 428 413 117 125 128 19 100 100 0 0.396 0.361 0.415 0.415 0.226 0.328 0.724 32 236 423 392 -1.336 120 303 104 288 0
10 -0.0209381415 1 1 10 1 3370 18430 80 4288 3934 1065 72 74 16 100 100 0 2848 2721 621 128 128 19 100 100 0 1.550 1.489 1.511 1.491 0.235 1.486 0.973 52 340 6936 6455 0.632 4216 2720 3862 2593 0
11 -0.1927899641 1 1 11 1 3540 18530 70 884 826 329 71 75 17 100 100 0 974 920 304 131 132 20 100 100 0 0.964 0.957 0.958 0.955 0.238 0.955 0.940 32 236 1656 1544 -0.052 813 843 755 789 0
12 -2.3705668674 1 1 12 1 3690 18430 70 486 476 76 71 73 15 100 100 0 2068 1978 404 127 129 21 100 100 0 0.214 0.219 0.225 0.230 0.061 0.206 0.904 32 236 2356 2256 -2.226 415 1941 405 1851 0
13 -0.5296529956 1 1 13 1 3850 18520 70 1785 1629 454 75 80 31 100 100 0 1812 1741 301 134 137 27 100 100 0 1.019 0.967 1.024 0.964 0.259 0.974 0.910 32 236 3388 3161 0.027 1710 1678 1554 1607 0
14 0.3743010790 1 1 14 1 4020 18420 90 8517 7880 2086 74 75 17 100 100 0 4139 3802 1021 130 131 21 100 100 0 2.106 2.126 2.119 2.182 0.304 2.107 0.981 52 420 12452 11478 1.075 8443 4009 7806 3672 0
15 -0.3394657068 1 1 15 1 4190 18510 70 2663 2501 557 73 76 19 100 100 0 2445 2277 432 131 133 23 100 100 0 1.119 1.131 1.167 1.142 0.223 1.109 0.917 32 236 4904 4574 0.163 2590 2314 2428 2146 0
16 -0.2388141996 1 1 16 1 4360 18420 90 1732 1709 567 76 77 16 100 100 0 1387 1520 575 125 127 20 100 100 0 1.312 1.171 1.193 1.231 0.251 1.126 0.963 52 403 2918 3028 0.392 1656 1262 1633 1395 0
17 0 1 17 1 4510 18510 100 93 108 56 79 81 20 43 25 0 146 189 136 127 128 21 45 32 0 0.737 0.468 0.633 1.128 1.438 0.325 0.474 80 471 33 91 -0.441 14 19 29 62 -50
18 0.4503808306 1 1 18 1 4670 18430 80 451 448 268 79 81 20 98 94 0 373 511 355 121 123 25 98 84 0 1.476 0.946 1.056 1.231 0.834 0.778 0.834 52 335 624 759 0.562 372 252 369 390 0
19 -0.6915505602 1 1 19 1 4840 18520 60 154 161 39 80 80 18 96 93 0 402 392 110 118 118 18 96 96 0 0.261 0.296 0.272 0.553 1.368 0.233 0.495 32 176 358 355 -1.940 74 284 81 274 0
20 -1.9697715884 1 1 20 1 5010 18420 80 1404 2021 1805 77 80 19 100 100 0 3976 5208 4640 111 111 20 100 100 0 0.343 0.381 0.375 0.444 0.328 0.381 0.981 52 332 5192 7041 -1.542 1327 3865 1944 5097 0

Total number of rows: 9568

Table truncated, full table size 1773 Kbytes.




Supplementary data files not provided
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