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Sample GSM9090 Query DataSets for GSM9090
Status Public on Jan 20, 2004
Title c 2-3
Sample type RNA
 
Channel 1
Source name ID:c 2-3, 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 18970 100 158 161 26 156 162 32 13 2 0 57 63 23 60 68 50 2 1 0 -0.667 1.667 1.690 3.629 7.280 0.314 0.056 80 513 -1 8 Error 2 -3 5 3 -50
2 2.528830e-01 1 1 2 1 1950 18890 110 21623 21051 5772 152 156 32 100 100 0 18164 16971 5987 57 65 47 100 100 0 1.186 1.236 1.198 1.466 0.853 1.174 0.965 80 566 39578 37813 0.246 21471 18107 20899 16914 0
3 1.168442e+00 1 1 3 1 2100 18990 80 723 778 391 147 149 23 100 100 0 309 329 177 53 55 14 98 94 0 2.250 2.286 2.354 3.329 4.712 2.117 0.900 52 328 832 907 1.170 576 256 631 276 0
4 -8.156852e-01 1 1 4 1 2260 18890 80 417 396 95 141 142 20 98 98 0 634 637 257 52 53 12 100 100 0 0.474 0.436 0.428 0.473 0.167 0.394 0.842 52 340 858 840 -1.076 276 582 255 585 0
5 -1.550287e-01 1 1 5 1 2430 18970 80 858 851 386 141 140 22 100 98 0 1031 980 572 51 52 11 100 100 0 0.732 0.764 0.802 1.005 0.882 0.666 0.825 52 340 1697 1639 -0.451 717 980 710 929 0
6 3.281991e-01 1 1 6 1 2590 18870 70 637 650 186 137 138 21 100 100 0 493 513 186 51 52 12 100 100 0 1.131 1.110 1.137 1.293 0.920 0.893 0.792 32 230 942 975 0.178 500 442 513 462 0
7 7.831908e-01 1 1 7 1 2760 18980 80 427 429 123 138 139 22 100 100 0 232 234 81 51 54 22 100 96 0 1.597 1.590 1.531 1.855 1.205 1.434 0.820 52 334 470 474 0.675 289 181 291 183 0
8 1.201287e-01 1 1 8 1 2920 18860 90 2388 2260 476 140 142 30 100 100 0 2315 2198 552 52 57 21 100 100 0 0.993 0.988 0.981 1.048 0.398 0.918 0.910 52 398 4511 4266 -0.010 2248 2263 2120 2146 0
9 0 1 9 1 3080 18970 100 155 154 29 138 140 26 35 8 0 75 77 24 52 54 20 52 21 0 0.739 0.640 1.023 3.540 7.538 0.236 0.030 80 496 40 41 -0.436 17 23 16 25 -50
10 2.443232e-03 1 1 10 1 3250 18880 90 1078 1027 197 139 155 109 100 100 0 1116 1065 193 53 72 136 100 98 0 0.883 0.877 0.882 0.887 0.182 0.871 0.928 52 414 2002 1900 -0.179 939 1063 888 1012 0
11 -3.783271e-01 1 1 11 1 3410 18970 80 310 307 52 137 141 37 100 98 0 345 334 85 52 56 18 100 98 0 0.590 0.603 0.661 0.700 0.532 0.529 0.700 52 334 466 452 -0.760 173 293 170 282 0
12 -2.801850e-01 1 1 12 1 3580 18870 80 597 608 89 131 133 23 100 100 0 795 774 142 51 54 12 100 100 0 0.626 0.660 0.645 0.683 0.173 0.618 0.912 52 320 1210 1200 -0.675 466 744 477 723 0
13 -1.707503e-01 1 1 13 1 3740 18970 80 619 567 180 131 133 24 100 92 0 707 650 259 49 52 12 98 98 0 0.742 0.725 0.747 0.879 0.668 0.672 0.871 52 340 1146 1037 -0.431 488 658 436 601 0
14 2.045252e-01 1 1 14 1 3900 18880 90 2373 2339 420 136 137 21 100 100 0 2139 2127 353 51 53 13 100 100 0 1.071 1.061 1.071 1.071 0.185 1.016 0.911 52 414 4325 4279 0.099 2237 2088 2203 2076 0
15 0 1 15 1 4070 18970 100 126 131 23 132 134 22 12 5 0 52 60 33 50 53 13 21 12 0 -3.000 -0.100 1.333 4.080 8.248 0.208 0.034 80 466 -4 9 Error -6 2 -1 10 -50
16 0 1 16 1 4230 18880 100 127 127 24 129 131 21 10 6 0 53 61 30 50 55 71 5 1 0 -0.667 -0.182 1.629 3.252 5.679 0.146 0.016 80 480 1 9 Error -2 3 -2 11 -50
17 0 1 17 1 4400 18970 100 138 139 22 132 133 20 25 7 0 54 70 43 51 53 11 30 22 0 2.000 0.368 1.483 5.129 8.756 0.215 0.065 80 474 9 26 1.000 6 3 7 19 -50
18 3.906423e-01 1 1 18 1 4570 18890 70 204 207 39 137 138 27 90 65 0 128 133 37 52 56 17 93 90 0 0.882 0.864 0.898 1.328 1.790 0.629 0.366 32 236 143 151 -0.182 67 76 70 81 0
19 0 1 19 1 4730 18970 60 193 196 41 140 204 487 0 0 0 111 119 39 53 109 528 0 0 0 0.914 0.848 0.860 1.385 1.306 0.485 0.211 32 176 111 122 -0.130 53 58 56 66 0
20 -1.156888e+00 1 1 20 1 4890 18870 90 843 860 217 128 129 22 100 100 0 2247 2200 834 51 53 13 100 100 0 0.326 0.341 0.335 0.491 0.741 0.302 0.882 52 412 2911 2881 -1.619 715 2196 732 2149 0

Total number of rows: 9568

Table truncated, full table size 1704 Kbytes.




Supplementary data files not provided
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