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Sample GSM9072 Query DataSets for GSM9072
Status Public on Jan 20, 2004
Title db/db 13-1
Sample type RNA
 
Channel 1
Source name ID:13-1, Genotype=(C57BKsJ) Lepr db/db, 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 2230 16570 100 56 59 15 57 61 15 17 3 0 106 108 16 107 107 15 13 3 0 1.000 2.000 1.250 2.604 4.982 0.085 0.006 80 463 -2 3 0.000 -1 -1 2 1 -50
2 4.743382e-01 1 1 2 1 2410 16470 120 21751 21482 7704 58 60 16 100 100 0 10040 9951 3683 99 99 16 100 100 0 2.182 2.175 2.175 2.250 0.563 2.148 0.988 120 606 31634 31276 1.126 21693 9941 21424 9852 0
3 4.463528e-01 1 1 3 1 2580 16570 120 1875 2025 1078 56 58 14 100 99 0 1278 1407 801 96 98 18 99 99 0 1.539 1.502 1.522 1.734 0.922 1.419 0.958 120 423 3001 3280 0.622 1819 1182 1969 1311 0
4 -3.820181e+00 1 1 4 1 2740 16470 110 124 125 26 56 60 16 98 92 0 1243 1228 245 100 101 18 100 100 0 0.059 0.061 0.061 0.061 0.022 0.054 0.640 80 485 1211 1197 -4.071 68 1143 69 1128 0
5 -9.527188e-02 1 1 5 1 2890 16560 120 2542 2341 951 59 62 17 100 100 0 2300 2141 817 106 107 18 100 100 0 1.132 1.121 1.118 1.202 0.520 1.099 0.944 120 487 4677 4317 0.179 2483 2194 2282 2035 0
6 -5.103826e-01 1 1 6 1 3040 16490 90 863 875 348 62 88 119 100 96 0 1177 1195 428 110 131 106 100 100 0 0.751 0.749 0.753 0.753 0.169 0.782 0.954 52 352 1868 1898 -0.414 801 1067 813 1085 0
7 5.225754e-01 1 1 7 1 3200 16570 90 384 365 144 64 88 113 88 71 0 381 379 106 112 128 99 90 75 0 1.190 1.127 1.089 1.209 0.600 1.114 0.817 52 376 589 568 0.250 320 269 301 267 0
8 4.538901e-02 1 1 8 1 3400 16470 110 4461 4394 651 58 65 39 100 100 0 3297 3280 525 97 105 67 100 100 0 1.376 1.362 1.359 1.370 0.117 1.360 0.983 80 593 7603 7519 0.460 4403 3200 4336 3183 0
9 4.686630e-01 1 1 9 1 3540 16570 80 325 328 127 57 61 25 98 98 0 360 351 137 95 99 40 94 84 0 1.011 1.059 1.029 1.301 0.909 0.928 0.838 52 322 533 527 0.016 268 265 271 256 0
10 -8.865873e-02 1 1 10 1 3720 16470 110 2210 2177 431 55 58 19 100 100 0 2028 2012 401 94 95 27 100 100 0 1.114 1.106 1.104 1.116 0.139 1.090 0.975 80 547 4089 4040 0.156 2155 1934 2122 1918 0
11 -5.636256e-01 1 1 11 1 3870 16560 100 369 352 106 64 68 18 100 100 0 639 606 165 112 114 18 100 100 0 0.579 0.583 0.575 0.601 0.174 0.591 0.898 80 397 832 782 -0.789 305 527 288 494 0
12 -2.057223e+00 1 1 12 1 4030 16460 110 197 199 46 61 64 18 100 98 0 810 788 168 102 104 19 100 100 0 0.192 0.201 0.192 0.201 0.049 0.203 0.872 80 533 844 824 -2.380 136 708 138 686 0
13 -4.057622e-01 1 1 13 1 4200 16540 110 798 750 278 65 71 46 96 96 0 1030 983 338 103 107 38 97 95 0 0.791 0.778 0.768 0.927 1.208 0.771 0.914 80 482 1660 1565 -0.339 733 927 685 880 0
14 7.024927e-01 1 1 14 1 4350 16450 110 5523 5239 1732 66 72 44 100 100 0 2715 2549 870 103 109 36 100 100 0 2.089 2.115 2.128 2.239 0.518 2.078 0.975 80 553 8069 7619 1.063 5457 2612 5173 2446 0
15 -3.232003e-01 1 1 15 1 4530 16540 110 1002 947 319 69 77 32 97 97 0 1249 1148 376 113 116 22 96 96 0 0.821 0.848 0.843 0.880 0.380 0.832 0.956 80 541 2069 1913 -0.284 933 1136 878 1035 0
16 -2.265996e-01 1 1 16 1 4690 16450 110 866 809 266 69 76 31 98 97 0 1024 954 299 115 119 26 97 95 0 0.877 0.882 0.884 1.020 0.675 0.881 0.967 80 535 1706 1579 -0.190 797 909 740 839 0
17 8.258585e-01 1 1 17 1 4860 16550 120 568 546 217 66 70 22 98 96 0 459 443 169 124 126 21 93 93 0 1.499 1.505 1.465 1.735 1.059 1.374 0.908 120 507 837 799 0.584 502 335 480 319 0
18 4.938802e-01 1 1 18 1 5020 16460 110 401 393 85 69 71 18 100 100 0 425 413 72 125 126 18 100 100 0 1.107 1.125 1.128 1.149 0.270 1.091 0.901 80 523 632 612 0.146 332 300 324 288 0
19 1.629149e-01 1 1 19 1 5190 16550 100 166 164 51 71 73 17 90 86 0 289 263 73 128 129 17 91 87 0 0.590 0.689 0.585 0.739 0.494 0.563 0.671 80 425 256 228 -0.761 95 161 93 135 0
20 -1.487896e+00 1 1 20 1 5350 16470 110 2675 2496 662 69 72 23 100 100 0 5583 5223 1365 124 125 18 100 100 0 0.477 0.476 0.476 0.479 0.054 0.473 0.980 80 524 8065 7526 -1.067 2606 5459 2427 5099 0

Total number of rows: 9568

Table truncated, full table size 1772 Kbytes.




Supplementary data files not provided
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