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Sample GSM9085 Query DataSets for GSM9085
Status Public on Jan 20, 2004
Title c 4-5
Sample type RNA
 
Channel 1
Source name ID:c 4-5, 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 1710 18440 100 218 221 30 206 216 48 12 1 0 81 84 20 80 92 45 3 0 0 12.000 3.750 1.578 3.543 6.303 0.170 0.013 80 455 13 19 3.585 12 1 15 4 -50
2 3.583921e-01 1 1 2 1 1870 18360 130 36225 30936 12828 282 349 192 100 100 0 29298 25408 10567 156 222 174 100 100 0 1.233 1.214 1.214 1.255 0.392 1.198 0.974 120 709 65085 55906 0.303 35943 29142 30654 25252 0
3 1.506594e+00 1 1 3 1 2040 18450 90 1684 1593 630 239 252 60 100 100 0 875 837 419 113 132 64 100 94 0 1.896 1.870 2.005 2.179 0.849 1.700 0.923 52 395 2207 2078 0.923 1445 762 1354 724 0
4 -2.103481e+00 1 1 4 1 2200 18350 80 537 524 100 228 228 29 100 100 0 1327 1375 431 98 102 24 100 100 0 0.251 0.232 0.241 0.254 0.118 0.212 0.801 52 331 1538 1573 -1.992 309 1229 296 1277 0
5 -3.328814e-02 1 1 5 1 2360 18430 80 2045 2127 675 224 229 33 100 100 0 2619 2745 1148 103 108 27 100 100 0 0.724 0.720 0.702 0.782 0.227 0.665 0.943 52 339 4337 4545 -0.466 1821 2516 1903 2642 0
6 -7.011016e-02 1 1 6 1 2520 18350 70 1092 1093 280 217 222 40 100 100 0 1220 1268 384 93 100 36 100 100 0 0.776 0.746 0.760 0.771 0.184 0.697 0.912 32 236 2002 2051 -0.365 875 1127 876 1175 0
7 1.140154e+00 1 1 7 1 2710 18440 80 810 825 237 214 217 34 98 98 0 471 468 205 86 91 32 100 94 0 1.548 1.599 1.656 1.969 1.200 1.345 0.864 52 323 981 993 0.63 596 385 611 382 0
8 -1.603306e-01 1 1 8 1 2850 18350 110 3222 3009 853 230 248 78 100 100 0 4343 4158 1176 105 116 49 100 100 0 0.706 0.686 0.681 0.691 0.139 0.677 0.969 80 534 7230 6832 -0.502 2992 4238 2779 4053 0
9 0 1 9 1 3020 18440 100 354 352 46 275 299 85 45 1 0 154 164 41 136 151 55 21 6 0 4.389 2.750 2.071 5.702 11.252 0.828 0.308 80 447 97 105 2.134 79 18 77 28 -50
10 -2.424865e-01 1 1 10 1 3190 18340 90 1775 1765 243 256 258 37 100 100 0 2508 2471 440 121 126 38 100 100 0 0.636 0.642 0.656 0.662 0.137 0.608 0.933 52 407 3906 3859 -0.652 1519 2387 1509 2350 0
11 -3.987284e-02 1 1 11 1 3350 18420 80 754 769 104 228 231 36 100 100 0 809 792 133 106 111 32 100 100 0 0.748 0.789 0.785 0.800 0.138 0.768 0.931 52 334 1229 1227 -0.418 526 703 541 686 0
12 -1.118752e+00 1 1 12 1 3510 18340 100 761 722 199 225 228 34 100 98 0 1467 1327 425 106 113 36 100 100 0 0.394 0.407 0.401 0.408 0.113 0.406 0.921 80 521 1897 1718 -1.344 536 1361 497 1221 0
13 -8.363241e-02 1 1 13 1 3680 18440 60 1319 1305 132 214 217 29 100 100 0 1620 1600 286 101 103 27 100 100 0 0.727 0.728 0.720 0.757 0.184 0.687 0.938 32 176 2624 2590 -0.459 1105 1519 1091 1499 0
14 6.601179e-01 1 1 14 1 3840 18340 100 4789 4107 1715 218 221 29 100 100 0 4149 3592 1517 91 95 23 100 100 0 1.126 1.111 1.121 1.202 0.676 1.091 0.959 80 495 8629 7390 0.172 4571 4058 3889 3501 0
15 0 1 15 1 4000 18430 100 208 210 32 210 213 31 13 5 0 77 82 20 82 86 23 12 2 0 0.400 0.000 2.000 3.018 3.177 0.288 0.038 80 430 -7 0 -1.322 -2 -5 0 0 -50
16 0 1 16 1 4160 18330 100 195 195 27 214 213 30 0 0 0 78 80 18 78 81 18 13 5 0 100000.000 -9.500 1.856 3.361 5.046 0.149 0.008 80 477 -19 -17 16.61 -19 0 -19 2 -50
17 0 1 17 1 4330 18430 100 207 213 34 211 211 31 20 3 0 80 82 20 76 79 19 20 8 0 -1.000 0.333 2.375 5.002 9.445 0.155 0.009 80 460 0 8 Error -4 4 2 6 -50
18 1.036239e+00 1 1 18 1 4500 18340 70 362 378 85 195 198 27 100 96 0 175 181 54 76 78 18 93 93 0 1.687 1.743 1.827 2.030 1.039 1.405 0.747 32 236 266 288 0.754 167 99 183 105 0
19 6.318399e-01 1 1 19 1 4650 18440 60 288 292 47 202 204 30 96 75 0 134 139 39 80 81 21 84 65 0 1.593 1.525 1.700 2.286 2.336 0.782 0.288 32 170 140 149 0.671 86 54 90 59 0
20 -1.908496e+00 1 1 20 1 4810 18340 80 1712 1695 571 201 205 33 100 100 0 6215 6254 2173 79 82 24 100 100 0 0.246 0.242 0.237 0.244 0.058 0.237 0.939 52 334 7647 7669 -2.022 1511 6136 1494 6175 0

Total number of rows: 9568

Table truncated, full table size 1746 Kbytes.




Supplementary data files not provided
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