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Sample GSM9088 Query DataSets for GSM9088
Status Public on Jan 20, 2004
Title c 2-1
Sample type RNA
 
Channel 1
Source name ID:c 2-1, 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 1620 18650 100 145 147 20 143 145 20 15 6 0 55 56 12 54 56 16 8 1 0 2.000 2.000 1.550 4.452 7.734 0.101 0.003 80 480 3 6 1.000 2 1 4 2 -50
2 4.965460e-02 1 1 2 1 1790 18570 100 22880 22216 3479 145 147 21 100 100 0 18806 18578 2409 54 58 17 100 100 0 1.212 1.191 1.202 1.198 0.174 1.172 0.955 80 489 41487 40595 0.278 22735 18752 22071 18524 0
3 1.193677e+00 1 1 3 1 1950 18670 80 771 823 410 146 146 19 100 100 0 295 310 133 52 54 13 100 100 0 2.572 2.624 2.640 2.583 0.814 2.578 0.878 52 329 868 935 1.363 625 243 677 258 0
4 -9.794550e-01 1 1 4 1 2130 18570 80 450 426 95 143 145 21 96 96 0 618 584 222 52 54 11 100 100 0 0.542 0.532 0.520 0.607 0.345 0.443 0.775 52 335 873 815 -0.883 307 566 283 532 0
5 -2.410777e-01 1 1 5 1 2280 18650 80 930 872 316 144 146 20 100 100 0 913 850 397 51 53 11 100 100 0 0.912 0.911 0.914 1.028 0.482 0.830 0.882 52 335 1648 1527 -0.133 786 862 728 799 0
6 1.410284e-01 1 1 6 1 2450 18560 80 511 542 175 146 146 19 100 100 0 357 378 152 52 54 12 100 100 0 1.197 1.215 1.209 1.295 0.491 1.136 0.868 52 340 670 722 0.259 365 305 396 326 0
7 6.052328e-01 1 1 7 1 2620 18660 80 386 398 115 145 145 20 100 98 0 186 185 64 54 55 12 96 94 0 1.826 1.931 1.912 2.232 1.068 1.679 0.763 52 334 373 384 0.868 241 132 253 131 0
8 -7.998121e-02 1 1 8 1 2770 18550 90 2267 2190 380 145 146 21 100 100 0 2058 2071 276 53 55 12 100 100 0 1.058 1.013 1.020 1.016 0.145 1.003 0.955 52 415 4127 4063 0.082 2122 2005 2045 2018 0
9 1.089355e+00 1 1 9 1 2930 18640 80 211 217 47 144 145 22 86 80 0 75 76 22 53 54 12 67 40 0 3.045 3.174 3.133 4.780 5.093 0.932 0.175 52 340 89 96 1.607 67 22 73 23 0
10 -1.747654e-01 1 1 10 1 3100 18560 90 882 869 110 143 144 21 100 100 0 811 814 95 53 56 13 100 100 0 0.975 0.954 0.936 0.962 0.153 0.946 0.909 52 407 1497 1487 -0.037 739 758 726 761 0
11 -2.383805e-01 1 1 11 1 3260 18640 80 375 383 72 143 148 26 100 100 0 287 294 75 54 55 12 100 100 0 0.996 1.000 1.052 1.076 0.407 0.882 0.746 52 321 465 480 -0.006 232 233 240 240 0
12 -5.041525e-01 1 1 12 1 3410 18550 130 470 434 184 154 184 101 76 64 0 342 388 293 57 64 27 78 65 0 1.109 0.846 0.762 2.851 6.227 0.639 0.586 120 778 601 611 0.149 316 285 280 331 0
13 -1.748631e-01 1 1 13 1 3600 18650 80 655 646 177 152 169 73 96 96 0 607 557 200 57 62 23 100 98 0 0.915 0.988 1.002 1.112 0.481 0.893 0.806 52 324 1053 994 -0.129 503 550 494 500 0
14 3.586299e-01 1 1 14 1 3750 18550 90 2435 2415 471 151 165 61 100 100 0 1705 1652 318 60 63 17 100 100 0 1.388 1.422 1.358 1.516 0.713 1.347 0.903 52 410 3929 3856 0.473 2284 1645 2264 1592 0
15 0 1 15 1 3910 18650 100 141 149 29 150 151 22 18 7 0 59 66 23 59 62 15 18 10 0 100000.000 -0.143 2.500 4.480 5.285 0.260 0.036 80 470 -9 6 16.610 -9 0 -1 7 -50
16 0 1 16 1 4080 18550 100 140 145 31 148 150 22 12 7 0 60 67 29 56 58 13 27 13 0 -2.000 -0.273 1.500 2.219 2.234 0.442 0.119 80 491 -4 8 Error -8 4 -3 11 -50
17 0 1 17 1 4240 18650 100 143 148 40 149 151 22 13 8 0 58 70 39 56 58 14 26 16 0 -3.000 -0.071 1.248 3.208 4.051 0.465 0.163 80 451 -4 13 Error -6 2 -1 14 -50
18 5.407918e-01 1 1 18 1 4410 18560 70 224 229 44 149 152 23 87 84 0 80 93 33 54 56 13 71 46 0 2.885 2.051 1.762 3.578 3.510 0.922 0.270 32 236 101 119 1.528 75 26 80 39 0
19 3.462228e-01 1 1 19 1 4570 18650 60 248 250 37 147 149 23 96 96 0 108 115 37 54 57 15 96 78 0 1.870 1.689 1.623 2.263 1.554 0.977 0.408 32 176 155 164 0.903 101 54 103 61 0
20 -1.574772e+00 1 1 20 1 4730 18550 90 818 809 227 148 150 20 100 100 0 1875 1983 615 53 56 14 100 100 0 0.368 0.342 0.330 0.348 0.091 0.335 0.889 52 420 2492 2591 -1.443 670 1822 661 1930 0

Total number of rows: 9568

Table truncated, full table size 1687 Kbytes.




Supplementary data files not provided
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