NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM9172 Query DataSets for GSM9172
Status Public on Jan 20, 2004
Title db/db 10-1
Sample type RNA
 
Channel 1
Source name ID:10-1, 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 18, 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 1760 18730 100 91 92 21 93 104 48 1 0 0 125 125 19 129 135 33 1 0 0 0.500 0.250 1.000 1.739 1.935 0.674 0.227 80 402 -6 -5 -1.000 -2 -4 -1 -4 -50
2 -0.0776836965 1 1 2 1 1930 18650 90 20270 19932 3344 93 99 45 100 100 0 16319 15813 2072 132 135 22 100 100 0 1.246 1.265 1.257 1.264 0.122 1.264 0.970 52 414 36364 35520 0.318 20177 16187 19839 15681 0
3 0.7966996796 1 1 3 1 2110 18740 60 1621 1635 893 95 99 22 100 100 0 1087 1025 504 134 138 29 100 100 0 1.601 1.728 1.822 2.125 1.518 1.616 0.848 32 176 2479 2431 0.679 1526 953 1540 891 0
4 -3.8726004024 1 1 4 1 2260 18650 80 150 157 46 96 99 23 80 59 0 1265 1249 287 129 132 23 100 100 0 0.048 0.054 0.050 0.061 0.043 0.049 0.374 52 340 1190 1181 -4.395 54 1136 61 1120 0
5 0.1243578867 1 1 5 1 2420 18730 70 1383 1587 931 105 108 24 100 100 0 1645 1488 711 137 141 29 100 100 0 0.847 1.097 1.062 1.040 0.357 1.126 0.912 32 236 2786 2833 -0.239 1278 1508 1482 1351 0
6 -0.2288360949 1 1 6 1 2590 18640 70 1012 1232 697 111 124 64 100 100 0 1362 1446 777 144 151 38 100 100 0 0.740 0.861 0.849 0.919 0.320 0.840 0.920 32 228 2119 2423 -0.435 901 1218 1121 1302 0
7 0.8653006720 1 1 7 1 2750 18710 150 144 262 237 111 121 52 42 35 0 192 268 187 139 146 36 57 43 0 0.623 1.171 1.108 1.370 1.414 1.129 0.812 156 901 86 280 -0.684 33 53 151 129 0
8 -0.3485024972 1 1 8 1 2920 18640 90 2909 2619 1023 112 117 28 100 100 0 3385 2991 989 141 144 28 100 100 0 0.862 0.880 0.859 0.857 0.222 0.887 0.950 52 389 6041 5357 -0.214 2797 3244 2507 2850 0
9 0 1 9 1 3110 18730 60 127 156 98 121 123 30 31 15 0 249 384 493 151 155 30 81 75 0 0.061 0.150 0.313 1.052 2.592 0.173 0.642 32 176 104 268 -4.030 6 98 35 233 0
10 -0.4247083165 1 1 10 1 3240 18640 90 1301 1262 305 110 113 26 100 100 0 1682 1673 299 134 137 29 100 100 0 0.769 0.749 0.757 0.746 0.152 0.763 0.934 52 408 2739 2691 -0.378 1191 1548 1152 1539 0
11 0.2294750220 1 1 11 1 3410 18730 70 516 547 167 103 106 23 100 100 0 550 563 124 125 127 21 100 100 0 0.972 1.014 0.995 1.064 0.424 0.885 0.741 32 236 838 882 -0.041 413 425 444 438 0
12 -2.0243419683 1 1 12 1 3570 18630 70 357 358 71 108 111 23 100 100 0 1246 1212 242 124 127 30 100 100 0 0.222 0.230 0.227 0.234 0.065 0.214 0.862 32 230 1371 1338 -2.172 249 1122 250 1088 0
13 -0.1171656399 1 1 13 1 3730 18730 70 1361 1332 334 114 116 28 100 100 0 1444 1439 242 120 122 24 100 100 0 0.942 0.923 0.915 0.919 0.157 0.912 0.921 32 236 2571 2537 -0.086 1247 1324 1218 1319 0
14 0.6949038831 1 1 14 1 3900 18630 90 4340 4014 1213 110 114 27 100 100 0 2384 2302 440 117 122 27 100 100 0 1.866 1.787 1.755 1.767 0.384 1.763 0.928 52 417 6497 6089 0.900 4230 2267 3904 2185 0
15 0.0431855641 1 1 15 1 4060 18720 80 1593 1467 449 105 110 25 100 100 0 1568 1436 373 117 120 30 100 100 0 1.025 1.033 1.030 1.043 0.273 1.026 0.933 52 340 2939 2681 0.036 1488 1451 1362 1319 0
16 -0.1324515038 1 1 16 1 4230 18630 80 1392 1318 318 108 113 30 100 100 0 1442 1440 244 117 121 29 100 100 0 0.969 0.915 0.924 0.913 0.196 0.922 0.946 52 330 2609 2533 -0.045 1284 1325 1210 1323 0
17 0 1 17 1 4390 18720 100 127 138 47 109 112 25 45 23 0 137 150 49 114 118 26 43 18 0 0.783 0.806 1.143 2.741 6.898 0.559 0.335 80 498 41 65 -0.354 18 23 29 36 -50
18 0.3633012505 1 1 18 1 4540 18620 70 324 324 108 112 116 31 96 93 0 364 350 125 120 123 27 100 93 0 0.869 0.922 0.916 1.127 0.808 0.857 0.755 32 230 456 442 -0.203 212 244 212 230 0
19 -1.9425270872 1 1 19 1 4720 18720 90 118 124 35 106 110 25 38 21 0 237 228 46 114 117 23 98 92 0 0.098 0.158 0.350 0.491 0.403 0.089 0.026 52 417 135 132 -3.358 12 123 18 114 0
20 -2.0024969705 1 1 20 1 4880 18630 80 1774 1950 997 107 111 26 100 100 0 6184 6613 3239 116 118 25 100 100 0 0.275 0.284 0.282 0.286 0.080 0.284 0.960 52 332 7735 8340 -1.864 1667 6068 1843 6497 0

Total number of rows: 9568

Table truncated, full table size 1801 Kbytes.




Supplementary data files not provided
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap