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Sample GSM9080 Query DataSets for GSM9080
Status Public on Jan 20, 2004
Title db/m 6-4
Sample type RNA
 
Channel 1
Source name ID:6-4, Genotype=(C57BKsJ) Lepr db/m, 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 1640 17240 100 381 390 69 410 421 74 6 2 0 168 173 32 177 184 36 11 2 0 3.222 5.000 2.567 3.742 4.417 0.702 0.118 80 462 -38 -24 1.688 -29 -9 -20 -4 -50
2 9.977779e-02 1 1 2 1 1800 17140 110 25418 25279 4659 434 477 274 100 100 0 17556 17636 2853 187 200 64 100 100 0 1.438 1.424 1.442 1.425 0.163 1.421 0.966 80 562 42353 42294 0.524 24984 17369 24845 17449 0
3 -1.301723e-01 1 1 3 1 1970 17250 110 2473 2459 591 435 451 106 100 98 0 2052 2155 656 190 195 35 100 100 0 1.095 1.030 1.071 1.046 0.161 0.992 0.958 80 501 3900 3989 0.130 2038 1862 2024 1965 0
4 0 1 4 1 2140 17150 110 326 313 79 396 410 73 1 0 0 1319 1240 317 184 189 42 98 98 0 -0.062 -0.079 0.036 0.625 1.556 -0.060 0.143 80 541 1065 973 Error -70 1135 -83 1056 0
5 -5.155479e-01 1 1 5 1 2290 17230 110 2859 2764 625 420 429 73 100 98 0 3287 3180 751 188 193 33 100 100 0 0.787 0.783 0.781 0.781 0.139 0.765 0.959 80 509 5538 5336 -0.346 2439 3099 2344 2992 0
6 -5.464562e-01 1 1 6 1 2470 17150 100 1008 1000 343 410 424 80 92 88 0 1287 1200 527 173 177 37 98 98 0 0.537 0.574 0.561 0.669 0.614 0.561 0.868 80 519 1712 1617 -0.898 598 1114 590 1027 0
7 3.034016e-01 1 1 7 1 2650 17240 90 658 634 142 435 446 78 88 71 0 448 434 97 174 183 41 96 94 0 0.814 0.765 0.787 1.015 1.109 0.762 0.533 52 373 497 459 -0.297 223 274 199 260 0
8 -3.821574e-01 1 1 8 1 2800 17150 110 3694 3473 1349 444 453 76 96 92 0 3814 3514 1438 174 180 34 96 96 0 0.893 0.907 0.913 1.196 2.333 0.887 0.959 80 562 6890 6369 -0.163 3250 3640 3029 3340 0
9 1.274430e-01 1 1 9 1 2960 17250 70 670 636 158 498 501 64 81 65 0 447 423 103 190 201 51 87 84 0 0.669 0.592 0.805 4.916 18.113 0.756 0.510 32 236 429 371 -0.579 172 257 138 233 0
10 -4.291608e-01 1 1 10 1 3120 17150 110 2161 2086 466 509 514 67 98 98 0 2209 2186 485 176 180 34 100 100 0 0.813 0.785 0.783 0.772 0.130 0.791 0.957 80 591 3685 3587 -0.299 1652 2033 1577 2010 0
11 -7.408387e-02 1 1 11 1 3300 17240 100 855 817 186 546 562 92 87 80 0 633 607 160 188 192 38 98 96 0 0.694 0.647 0.711 0.789 0.488 0.658 0.706 80 420 754 690 -0.526 309 445 271 419 0
12 -1.160326e+00 1 1 12 1 3430 17130 110 774 741 165 497 506 98 85 73 0 1068 1025 221 176 183 37 100 100 0 0.311 0.287 0.325 0.312 0.113 0.317 0.613 80 523 1169 1093 -1.687 277 892 244 849 0
13 -4.118425e-01 1 1 13 1 3590 17230 100 1008 951 323 469 475 68 83 80 0 1081 992 337 175 180 29 100 100 0 0.595 0.590 0.630 0.598 0.229 0.624 0.810 80 439 1445 1299 -0.749 539 906 482 817 0
14 1.357172e-01 1 1 14 1 3760 17130 100 4498 4310 1026 449 469 168 100 100 0 2986 2915 672 168 176 42 100 100 0 1.437 1.406 1.418 1.406 0.191 1.385 0.963 80 491 6867 6608 0.523 4049 2818 3861 2747 0
15 6.980553e-01 1 1 15 1 3920 17230 110 2973 2741 943 445 452 64 96 93 0 1424 1326 448 170 173 25 96 95 0 2.016 1.986 2.010 2.418 2.295 1.928 0.929 80 467 3782 3452 1.011 2528 1254 2296 1156 0
16 1.724795e-01 1 1 16 1 4080 17120 110 1592 1480 377 432 452 115 95 92 0 1189 1108 291 169 172 28 97 97 0 1.137 1.116 1.146 1.161 0.390 1.095 0.895 80 559 2180 1987 0.186 1160 1020 1048 939 0
17 7.632058e-01 1 1 17 1 4250 17220 100 978 933 206 438 452 102 91 87 0 563 531 109 170 175 31 100 98 0 1.374 1.371 1.409 1.447 0.437 1.291 0.815 80 469 933 856 0.458 540 393 495 361 0
18 2.400469e-01 1 1 18 1 4420 17130 100 602 569 125 428 441 105 70 25 0 376 367 88 166 171 32 95 92 0 0.829 0.701 0.803 0.847 0.493 0.712 0.469 80 484 384 342 -0.271 174 210 141 201 0
19 0 1 19 1 4580 17220 100 346 334 79 435 448 85 1 0 0 212 211 43 167 173 39 55 22 0 -1.978 -2.295 4.056 6.759 6.981 -0.070 0.001 80 460 -44 -57 Error -89 45 -101 44 -50
20 -1.754964e+00 1 1 20 1 4740 17130 100 2105 2014 433 426 437 79 100 100 0 5873 5734 1283 163 168 30 100 100 0 0.294 0.285 0.291 0.283 0.049 0.281 0.954 80 487 7389 7159 -1.766 1679 5710 1588 5571 0

Total number of rows: 9568

Table truncated, full table size 1775 Kbytes.




Supplementary data files not provided
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