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Sample GSM9084 Query DataSets for GSM9084
Status Public on Jan 20, 2004
Title c 4-4
Sample type RNA
 
Channel 1
Source name ID:c 4-4, 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 1730 18860 100 366 387 86 272 356 225 15 0 0 257 273 80 191 262 189 10 0 0 1.424 1.402 1.280 2.195 3.452 1.151 0.918 80 449 160 197 0.510 94 66 115 82 -50
2 2.442958e-01 1 1 2 1 1890 18780 120 30133 29893 17036 322 390 216 100 100 0 23858 20968 11196 231 282 176 100 100 0 1.262 1.426 1.425 1.490 0.622 1.428 0.962 120 626 53438 50308 0.335 29811 23627 29571 20737 0
3 1.473309e+00 1 1 3 1 2070 18870 80 2902 3018 864 197 204 43 100 100 0 1368 1366 489 125 131 39 100 100 0 2.176 2.273 2.197 2.635 1.476 2.051 0.896 52 340 3948 4062 1.122 2705 1243 2821 1241 0
4 -2.412380e+00 1 1 4 1 2230 18770 80 405 417 60 172 172 37 100 100 0 1390 1387 333 105 109 34 100 100 0 0.181 0.191 0.186 0.200 0.055 0.179 0.860 52 338 1518 1527 -2.463 233 1285 245 1282 0
5 -1.344581e-02 1 1 5 1 2380 18860 80 2679 2538 1134 152 149 37 100 100 0 2858 2790 1234 88 89 32 100 100 0 0.912 0.883 0.892 0.949 0.475 0.849 0.905 52 338 5297 5088 -0.132 2527 2770 2386 2702 0
6 1.395481e-02 1 1 6 1 2570 18770 70 999 1117 482 136 132 36 100 100 0 1079 1097 515 70 74 32 100 100 0 0.855 0.955 0.905 1.015 0.398 0.856 0.887 32 236 1872 2008 -0.225 863 1009 981 1027 0
7 9.496294e-01 1 1 7 1 2720 18860 80 1127 1113 262 183 199 64 100 100 0 641 640 171 113 122 48 98 98 0 1.788 1.765 1.718 1.974 1.030 1.611 0.892 52 338 1472 1457 0.838 944 528 930 527 0
8 -3.313739e-01 1 1 8 1 2870 18770 90 3690 3459 796 165 175 59 100 100 0 4552 4412 787 101 112 44 100 100 0 0.792 0.764 0.781 0.755 0.107 0.782 0.945 52 402 7976 7605 -0.337 3525 4451 3294 4311 0
9 0 1 9 1 3040 18860 100 198 210 49 190 204 68 13 1 0 134 141 34 123 130 46 20 2 0 0.727 1.111 1.444 7.809 12.790 0.647 0.210 80 486 19 38 -0.459 8 11 20 18 -50
10 -1.067181e-01 1 1 10 1 3210 18760 90 2421 2266 493 157 168 45 100 100 0 2658 2642 544 97 106 43 100 100 0 0.884 0.829 0.841 0.841 0.179 0.832 0.946 52 405 4825 4654 -0.178 2264 2561 2109 2545 0
11 -4.068479e-01 1 1 11 1 3370 18840 90 614 583 161 156 161 35 100 100 0 731 726 162 105 113 44 100 100 0 0.732 0.688 0.675 0.694 0.271 0.652 0.845 52 413 1084 1048 -0.451 458 626 427 621 0
12 -1.382283e+00 1 1 12 1 3540 18760 90 736 727 107 143 148 34 100 100 0 1602 1574 204 94 106 53 100 100 0 0.393 0.395 0.382 0.400 0.089 0.387 0.901 52 411 2101 2064 -1.347 593 1508 584 1480 0
13 2.516505e-02 1 1 13 1 3700 18850 70 1548 1490 253 153 154 27 100 100 0 1646 1549 359 93 96 35 100 100 0 0.898 0.918 0.943 0.972 0.309 0.852 0.905 32 236 2948 2793 -0.155 1395 1553 1337 1456 0
14 7.663815e-01 1 1 14 1 3860 18750 90 6917 6631 1359 142 150 41 100 100 0 4153 4076 580 82 88 27 100 100 0 1.664 1.625 1.612 1.613 0.238 1.646 0.957 52 407 10846 10483 0.735 6775 4071 6489 3994 0
15 0 1 15 1 4020 18850 100 133 134 22 134 139 36 3 1 0 70 74 21 75 80 24 12 1 0 0.200 0.000 1.040 2.319 3.710 0.113 0.011 80 470 -6 -1 -2.322 -1 -5 0 -1 -50
16 0 1 16 1 4190 18760 100 137 139 25 125 127 23 33 11 0 69 73 20 69 71 19 18 10 0 100000.000 3.500 1.302 2.932 3.623 0.119 0.010 80 480 12 18 16.610 12 0 14 4 -50
17 0 1 17 1 4350 18850 100 143 143 26 131 132 22 28 5 0 82 88 34 70 73 19 35 13 0 1.000 0.667 1.000 1.907 2.509 0.154 0.028 80 479 24 30 0.000 12 12 12 18 -50
18 9.906900e-01 1 1 18 1 4530 18760 80 335 365 124 130 131 22 100 100 0 208 218 69 72 75 19 100 96 0 1.507 1.610 1.506 1.722 0.780 1.493 0.823 52 332 341 381 0.592 205 136 235 146 0
19 -2.983449e-01 1 1 19 1 4680 18860 60 199 212 34 140 140 24 100 75 0 181 178 42 80 82 20 93 90 0 0.584 0.735 0.636 1.089 1.281 0.476 0.368 32 176 160 170 -0.776 59 101 72 98 0
20 -1.729683e+00 1 1 20 1 4840 18760 90 2323 2253 365 139 140 23 100 100 0 6978 6909 953 79 84 24 100 100 0 0.317 0.310 0.319 0.311 0.048 0.306 0.945 52 420 9083 8944 -1.659 2184 6899 2114 6830 0

Total number of rows: 9568

Table truncated, full table size 1761 Kbytes.




Supplementary data files not provided
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