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Sample GSM132583 Query DataSets for GSM132583
Status Public on Nov 19, 2007
Title w1118 malpighian tubule 15 days set 2
Sample type RNA
 
Channel 1
Source name w1118 3 days malpighian tubule
Organism Drosophila melanogaster
Characteristics Drosophila w1118 male 3 days malpighian tubule
Extracted molecule polyA RNA
Extraction protocol Tissues or organs from four males of the same age were pooled together and used for each RNA sample preparation. Total RNA was extracted using miniRNA preparation kit (Zymo Research). RNA was then amplified as described in PMID: 12186645.
Label Cy5
Label protocol Two to four micrograms of amplified RNAs were labeled with fluorescent dye Cy5 and purified using the PowerScript labeling kit (Clontech)
 
Channel 2
Source name w1118 15 days malpighian tubule
Organism Drosophila melanogaster
Characteristics Drosophila w1118 male 15 days malpighian tubule
Extracted molecule polyA RNA
Extraction protocol Tissues or organs from four males of the same age were pooled together and used for each RNA sample preparation. Total RNA was extracted using miniRNA preparation kit (Zymo Research). RNA was then amplified as described in PMID: 12186645.
Label Cy3
Label protocol Two to four micrograms of amplified RNAs were labeled with fluorescent dye Cy3 and purified using the PowerScript labeling kit (Clontech)
 
 
Hybridization protocol Equal amount of sample and reference probes (one or two micrograms) were co-hybridized to microarrays at 42oC using cDNA Hyb Buffer (Full Moon Biosystems).
Scan protocol Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000B fluorescent scanner (Axon Instruments) and image intensity data were extracted and analyzed with GenePix Pro 6.0 analysis software (Axon Instruments).
Description w1118 15 days malpighian tubule
Data processing Raw microarray data were first processed by conducting within-slide normalization of signal intensities using the LOWESS curve-fitting method followed by between-slide scaling using Median Absolute Deviation method. Only genes with at most 4 missing values in the 10 time course samples for each tissue were included for further analysis. Remaining missing values were imputed using k-nearest neighbor algorithm.
 
Submission date Aug 29, 2006
Last update date Nov 21, 2006
Contact name Haruyoshi Yamaza
E-mail(s) yamazah@grc.nia.nih.gov
Phone 410-558-8450
Fax 410-558-8302
Organization name National Institute on Aging
Department Laboratory of Experimental Gerontology
Street address 6200 Seaforth Street
City Baltimore
State/province MD
ZIP/Postal code 21224
Country USA
 
Platform ID GPL4225
Series (1)
GSE6314 Temporal and Spatial Transcriptional Profiles of Aging in Drosophila

Data table header descriptions
ID_REF
Block the block number of the feature
Column the column number of the feature
Row the row number of the feature
Name the name of the feature derived from the Array List
Gene_symbol the accession number of the substance derived from the Array List
X the X-coordinate 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 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 µm of the feature-indicator
F635 Median median feature pixel intensity at 635 nm (Cy5)
F635 Mean mean feature pixel intensity at 635 nm (Cy5)
F635 SD the standard deviation of the feature pixel intensity at 635 nm (Cy5)
F635 CV the coefficient of variation of the feature pixel intensity at 635 nm (Cy5)
B635 all the background pixel intensities at 635nm
B635 Median the median local background intensity at 635 nm (Cy5)
B635 Mean the mean local background intensity at 635 (Cy5)
B635 SD the standard deviation of the local background intensity at 635 nm (Cy5)
B635 CV the coefficient of variation of the local background intensity at 635 nm (Cy5)
% > B635+1SD the percentage of feature pixels with intensities more than one standard deviation above the background intensity at 635 nm (Cy5)
% > B635+2SD the percentage of feature pixels with intensities more than two standard deviations above the background intensity at 635 nm (Cy5)
F635 % Sat. the percentage of feature pixels at 635 nm (Cy5) that are saturated
F532 Median median feature pixel intensity at 532 nm (Cy3)
F532 Mean mean feature pixel intensity at 532 nm (Cy3)
F532 SD the standard deviation of the feature pixel intensity at 532 nm (Cy3)
F532 CV the coefficient of variation of the feature pixel intensity at 532 nm (Cy3)
B532 all the background pixel intensities at 532nm
B532 Median the median local background intensity at 532 nm (Cy3)
B532 Mean the mean local background intensity at 532 (Cy3)
B532 SD the standard deviation of the local background intensity at 532 nm (Cy3)
B532 CV the coefficient of variation of the local background intensity at 532 nm (Cy3)
% > B532+1SD the percentage of feature pixels with intensities more than one standard deviation above the background intensity at 532 nm (Cy3)
% > B532+2SD the percentage of feature pixels with intensities more than two standard deviations above the background intensity at 532 nm (Cy3)
F532 % Sat. the percentage of feature pixels at 532 nm (Cy3) that are saturated
Ratio of Medians (635/532) the ratio of the median intensities of each feature for 635 nm (Cy5) and 532 nm (Cy3); with the median background intensity subtracted
Ratio of Means (635/532) the ratio of the arithmetic mean intensities of each feature for 635 nm (Cy5) and 532 nm (Cy3); with the median background intensity subtracted
Median of Ratios (635/532) the median of pixel-by-pixel ratios of pixel intensities for 635 nm (Cy5) and 532 nm (Cy3); with the median background intensity subtracted
Mean of Ratios (635/532) the geometric mean of the pixel-by-pixel ratios of pixel intensities for 635 nm (Cy5 and 532 nm (Cy3); with the median background intensity subtracted
Ratios SD (635/532) the standard deviation of the log of pixel intensity ratios for 635 nm (Cy5) and 532 nm (Cy3)
Rgn Ratio (635/532) the regression ratio for 635 nm (Cy5) and 532 nm (Cy3) (slope of the line of best fit (chi-square or minimum-of-squares method) through the set of pixels in a circle of diameter twice that of the feature-indicator of the current feature)
Rgn R2 (635/532) the coefficient of determination for the current regression value for 635 nm (Cy5) and 532 nm (Cy3)
F Pixels the total number of feature pixels
B Pixels the total number of local background pixels
Circularity uses a metric based on the variance of the distance of each boundary pixel to the centroid of the feature: 100 is most circular; 0 is most non-circular. Circular features are always 100; square features are always 79 (p/4*100).
Sum of Medians (635/532) the sum of the median intensities for 635 nm (Cy5) and 532 nm (Cy3); with the median background intensity at each wavelength subtracted
Sum of Means (635/532) the sum of the arithmetic mean intensities for 635 NM (Cy5) and 532 nm (Cy3); with the median background intensity at each wavelength subtracted
Log Ratio (635/532) log2 transform of the ratio of the medians for 635 nm (Cy5) and 532 nm (Cy3)
F635 Median - B635 the median feature pixel intensity at 635 nm (Cy5) with the background subtracted
F532 Median - B532 the median feature pixel intensity at 532 nm (Cy3) with the background subtracted
F635 Mean - B635 the mean feature pixel intensity at 635 nm (Cy5) with the background subtracted
F532 Mean - B532 the mean feature pixel intensity at 532 nm (Cy3) with the background subtracted
F635 Total Intensity the sum of feature pixel intensities at 635 nm (Cy5)
F532 Total Intensity the sum of feature pixel intensities at 532 nm (Cy3)
SNR 635 the signal-to-noise ratio at 635 nm (Cy5); defined by (Mean Foreground - Mean Background) / (Standard deviation of Background); that is: (F635 Mean - B635 Mean) / (B635 SD). The SNR is a key measure of the sensitivity of an image. If the background standard deviation is less than 1; its value is rounded to 0.5 for the purposes of calculating the SNR
SNR 532 the signal-to-noise ratio at 532 nm (Cy3); defined by (Mean Foreground - Mean Background) / (Standard deviation of Background); that is: (F532 Mean - B532 Mean) / (B532 SD). The SNR is a key measure of the sensitivity of an image. If the background standard deviation is less than 1; its value is rounded to 0.5 for the purposes of calculating the SNR
Flags a value of -100 means that this spot was bad. A value of -75 means that the ID for this spot is empty. A value of -50 means that this spot cannot be alighed during analysis. A value if 0 or larger than 0 means that this spot passed the flagging screen but may still fail other quality test
Normalize flag used to mark features to be used for normalization
Autoflag flag used to mark whether or not a good or bad flag was applied from the Flag Features dialog box
VALUE -[INV_VALUE]; normalized log (test/reference) ratio
INV_VALUE normalized log ratio

Data table
ID_REF Block Column Row Name Gene_symbol X Y Dia. F635 Median F635 Mean F635 SD F635 CV B635 B635 Median B635 Mean B635 SD B635 CV % > B635+1SD % > B635+2SD F635 % Sat. F532 Median F532 Mean F532 SD F532 CV B532 B532 Median B532 Mean B532 SD B532 CV % > B532+1SD % > B532+2SD F532 % Sat. Ratio of Medians (635/532) Ratio of Means (635/532) Median of Ratios (635/532) Mean of Ratios (635/532) Ratios SD (635/532) Rgn Ratio (635/532) Rgn R2 (635/532) F Pixels B Pixels Circularity Sum of Medians (635/532) Sum of Means (635/532) Log Ratio (635/532) F635 Median - B635 F532 Median - B532 F635 Mean - B635 F532 Mean - B532 F635 Total Intensity F532 Total Intensity SNR 635 SNR 532 Flags Normalize Autoflag VALUE INV_VALUE
1 1 1 1 CT30019 CG10711 1800 10830 150 159 173 83 47 154 154 164 72 43 20 8 0 276 281 56 19 259 259 260 46 17 26 11 0 0.294 0.864 1.178 1.526 3.824 7.038 0.012 156 890 100 22 41 -1.766 5 17 19 22 26958 43795 0.125 0.457 -50 0 0 null null
2 1 2 1 CT32994 CG13609 1980 10830 150 157 158 66 41 147 147 160 73 45 17 5 0 272 271 53 19 256 256 260 47 18 25 8 0 0.625 0.733 1.25 1.128 4.226 25.122 0.001 156 648 100 26 26 -0.678 10 16 11 15 24672 42231 -0.027 0.234 -50 0 0 null null
3 1 3 1 CT17698 CG5597 2160 10820 150 158 162 71 43 145 145 156 74 47 19 4 0 279 289 57 19 257 257 260 47 18 32 14 0 0.591 0.531 1.25 1.386 3.741 7.645 0.009 156 600 100 35 49 -0.759 13 22 17 32 25269 45006 0.081 0.617 -50 0 0 0.496523 -0.496522767
4 1 4 1 CT22043 CG7135 2340 10820 150 148 161 86 53 150 150 156 73 46 17 7 0 259 275 51 18 263 263 264 47 17 24 7 0 0.5 0.917 1.447 1.344 4.068 20.822 0.002 156 582 100 -6 23 -1 -2 -4 11 12 25184 42852 0.068 0.234 -50 0 0 null null
5 1 5 1 CT21320 CG6884 2520 10820 150 188 217 129 59 146 146 153 70 45 39 23 0 281 288 69 23 261 261 262 49 18 34 16 0 2.1 2.63 2.13 1.562 3.778 4.269 0.097 156 582 100 62 98 1.07 42 20 71 27 33925 44937 0.914 0.531 -50 0 0 -0.934275 0.934274846
6 1 6 1 CT13308 CG12234 2700 10820 150 167 174 75 43 155 155 161 73 45 23 7 0 271 278 57 20 253 253 256 46 17 32 14 0 0.667 0.76 1.485 1.247 5.051 13.006 0.003 156 712 100 30 44 -0.585 12 18 19 25 27090 43407 0.178 0.478 -50 0 0 null null
7 1 7 1 CT4012 CG1553 2930 10830 100 451 440 209 47 152 152 159 70 44 80 70 0 382 381 73 19 248 248 254 44 17 87 73 0 2.231 2.165 2.181 1.867 3.015 3.998 0.254 80 338 100 433 421 1.158 299 134 288 133 35232 30449 4.014 2.886 0 0 0 -0.43342 0.433419999
8 1 8 1 CT21344 CG6890 3060 10820 150 159 166 76 45 150 150 159 70 44 23 7 0 275 287 72 25 253 253 259 53 20 29 16 0 0.409 0.471 1.147 1.091 3.994 8.359 0.008 156 825 100 31 50 -1.29 9 22 16 34 25947 44727 0.1 0.528 -50 0 0 null null
9 1 9 1 CT38731 CG17514 3280 10820 90 630 649 218 33 152 152 160 65 40 98 96 0 648 644 116 18 256 256 257 45 17 100 100 0 1.219 1.281 1.291 1.194 1.726 1.538 0.701 52 332 100 870 885 0.286 478 392 497 388 33745 33473 7.523 8.6 0 0 0 0.697808 -0.697808476
10 1 10 1 CT14074 CG4297 3420 10820 150 175 183 80 43 152 152 161 71 44 25 9 0 276 279 58 20 257 257 257 44 17 32 10 0 1.211 1.409 1.181 1.193 3.592 10.453 0.006 156 775 100 42 53 0.276 23 19 31 22 28553 43458 0.31 0.5 -50 0 0 null null
11 1 11 1 CT21370 CG6905 3600 10820 150 186 207 107 51 149 149 157 70 44 37 19 0 279 285 65 22 257 257 258 44 17 32 17 0 1.682 2.071 1.552 1.539 3.723 4.527 0.06 156 602 100 59 86 0.75 37 22 58 28 32349 44452 0.714 0.614 -50 0 0 -0.627564 0.627564348
12 1 12 1 CT4054 CG3099 3780 10820 150 161 174 81 46 151 151 161 71 44 25 10 0 260 263 48 18 259 259 259 44 16 20 4 0 10 5.75 1.689 1.588 4.604 128.518 0 156 758 100 11 27 3.322 10 1 23 4 27083 41018 0.183 0.091 -50 0 0 null null
13 1 13 1 CT17720 CG9575 4000 10830 100 540 579 230 39 153 153 162 72 44 95 90 0 429 414 87 21 259 259 260 46 17 90 72 0 2.276 2.748 2.66 2.956 2.291 3.399 0.497 80 479 100 557 581 1.187 387 170 426 155 46352 33126 5.792 3.348 0 0 0 -0.375029 0.375029272
14 1 14 1 CT20678 CG6649 4180 10830 100 3264 3446 1423 41 140 140 157 84 53 100 100 0 1757 1804 761 42 251 251 256 42 16 95 95 0 2.074 2.129 2.165 2.414 2.249 2.209 0.807 80 325 100 4630 4859 1.053 3124 1506 3306 1553 275665 144335 39.155 36.857 0 0 0 null null
15 1 15 1 CT17736 CG5627 4320 10820 150 174 193 95 49 147 147 158 73 46 29 13 0 283 290 68 23 254 254 257 44 17 44 23 0 0.931 1.278 1.217 1.045 3.844 2.981 0.365 156 748 100 56 82 -0.103 27 29 46 36 30145 45230 0.479 0.75 -50 0 0 null null
16 1 16 1 CT17772 CG5695 4530 10820 90 1837 2054 819 39 154 154 182 140 76 100 100 0 1126 1162 316 27 255 255 264 60 22 100 100 0 1.932 2.095 2.149 2.061 1.354 2.299 0.844 52 375 100 2554 2807 0.95 1683 871 1900 907 106786 60426 13.371 14.967 0 0 0 0.308735 -0.308735062
17 1 17 1 CT7740 CG12132 4710 10830 90 493 499 158 31 162 162 186 133 71 86 63 0 624 613 113 18 261 261 266 58 21 98 98 0 0.912 0.957 0.958 0.896 1.864 1.134 0.535 52 332 100 694 689 -0.133 331 363 337 352 25967 31895 2.353 5.983 0 0 0 1.04893 -1.04893229
18 1 18 1 CT35117 CG12622 4860 10820 150 160 172 85 49 150 150 161 72 44 23 7 0 268 280 59 21 261 261 262 44 16 31 14 0 1.429 1.158 1.732 1.655 3.524 8.272 0.011 156 764 100 17 41 0.515 10 7 22 19 26834 43705 0.153 0.409 -50 0 0 null null
19 1 19 1 CT33707 CG14112 5040 10820 150 164 175 86 49 149 149 158 69 43 28 10 0 288 292 58 19 259 259 261 47 18 38 15 0 0.517 0.788 1.228 1.424 3.59 3.786 0.039 156 618 100 44 59 -0.951 15 29 26 33 27375 45556 0.246 0.66 -50 0 0 null null
20 1 20 1 CT26421 CG9269 5220 10820 150 161 171 75 43 154 154 160 67 41 21 8 0 275 280 59 21 259 259 263 47 17 26 10 0 0.438 0.81 1.279 1.359 4.655 -11.961 0.003 156 582 100 23 38 -1.193 7 16 17 21 26627 43710 0.164 0.362 -50 0 0 null null

Total number of rows: 17664

Table truncated, full table size 4292 Kbytes.




Supplementary data files not provided
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