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Sample GSM132586 Query DataSets for GSM132586
Status Public on Nov 19, 2007
Title w1118 malpighian tubule 30 days set 1
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 30 days malpighian tubule
Organism Drosophila melanogaster
Characteristics Drosophila w1118 male 30 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 30 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 1550 10630 150 160 170 72 42 148 148 158 76 48 21 5 0 284 296 62 20 281 281 284 59 20 22 8 0 4 1.467 1.386 1.307 4.111 14.656 0.001 156 910 100 15 37 2 12 3 22 15 26555 46107 0.158 0.203 -50 0 0 null null
2 1 2 1 CT32994 CG13609 1740 10630 150 163 164 79 48 152 152 170 110 64 10 1 0 307 316 59 18 289 289 296 67 22 25 5 0 0.611 0.444 1.057 1.118 3.933 -24.944 0.001 156 695 100 29 39 -0.71 11 18 12 27 25587 49298 -0.055 0.299 -50 0 0 null null
3 1 3 1 CT17698 CG5597 1920 10630 150 152 167 85 50 149 149 161 91 56 14 4 0 291 302 68 22 288 288 294 61 20 19 6 0 1 1.286 1.085 1.177 4.258 11.825 0.002 156 619 100 6 32 0 3 3 18 14 25976 47076 0.066 0.131 -50 0 0 -1.66422 1.664220485
4 1 4 1 CT22043 CG7135 2100 10630 150 161 166 67 40 150 150 157 70 44 21 3 0 298 305 64 20 283 283 285 47 16 32 8 0 0.733 0.727 1.287 1.273 4.146 6.149 0.01 156 726 100 26 38 -0.447 11 15 16 22 25834 47638 0.129 0.426 -50 0 0 null null
5 1 5 1 CT21320 CG6884 2330 10630 80 231 246 109 44 138 138 154 78 50 53 28 0 416 416 74 17 286 286 290 47 16 88 69 0 0.715 0.831 1.021 0.849 3.037 1.571 0.096 52 247 100 223 238 -0.483 93 130 108 130 12812 21610 1.179 2.681 0 0 0 0.728271 -0.728271386
6 1 6 1 CT13308 CG12234 2460 10630 150 162 170 75 44 145 145 156 72 46 25 7 0 307 314 62 19 279 279 281 47 16 36 15 0 0.607 0.714 0.978 1.16 3.662 21.609 0.001 156 869 100 45 60 -0.72 17 28 25 35 26471 49008 0.194 0.702 -50 0 0 null null
7 1 7 1 CT4012 CG1553 2670 10630 100 266 276 111 40 148 148 153 67 43 68 42 0 383 390 89 22 282 282 282 50 17 72 50 0 1.168 1.185 1.258 1.314 4.176 1.791 0.152 80 365 100 219 236 0.224 118 101 128 108 22104 31194 1.836 2.16 0 0 0 0.0194371 -0.019437125
8 1 8 1 CT21344 CG6890 2820 10630 150 155 167 73 43 152 152 157 72 45 18 5 0 312 311 66 21 278 278 280 52 18 37 14 0 0.088 0.455 1.345 1.299 3.665 8.112 0.004 156 795 100 37 48 -3.503 3 34 15 33 25991 48588 0.139 0.596 -50 0 0 null null
9 1 9 1 CT38731 CG17514 3030 10630 90 560 603 250 41 147 147 157 74 47 96 94 0 535 540 126 23 275 275 277 47 16 96 94 0 1.588 1.721 1.885 1.731 1.766 1.911 0.614 52 336 100 673 721 0.668 413 260 456 265 31353 28095 6.027 5.596 0 0 0 -0.19304 0.193039774
10 1 10 1 CT14074 CG4297 3180 10630 150 164 175 88 50 149 149 159 77 48 21 8 0 282 291 64 21 271 271 274 48 17 28 12 0 1.364 1.3 1.366 1.589 4.073 31.074 0.001 156 793 100 26 46 0.447 15 11 26 20 27272 45366 0.208 0.354 -50 0 0 null null
11 1 11 1 CT21370 CG6905 3360 10630 150 160 183 92 50 151 151 160 74 46 28 10 0 305 312 67 21 272 272 274 48 17 43 17 0 0.273 0.8 1.298 1.209 3.479 3.204 0.066 156 602 100 42 72 -1.874 9 33 32 40 28511 48727 0.311 0.792 -50 0 0 1.40753 -1.40752559
12 1 12 1 CT4054 CG3099 3540 10630 150 160 174 77 44 151 151 158 70 44 26 7 0 297 294 52 17 274 274 277 49 17 28 5 0 0.391 1.15 1.377 1.286 4.656 -23.176 0.001 156 678 100 32 43 -1.354 9 23 23 20 27087 45904 0.229 0.347 -50 0 0 null null
13 1 13 1 CT17720 CG9575 3730 10630 80 386 408 119 29 143 143 159 76 47 96 84 0 530 528 92 17 282 282 282 52 18 100 98 0 0.98 1.077 1.144 1.012 1.993 1.403 0.455 52 302 100 491 511 -0.029 243 248 265 246 21226 27479 3.276 4.731 0 0 0 0.437223 -0.437222853
14 1 14 1 CT20678 CG6649 3940 10630 100 2784 2960 1475 49 141 141 151 71 47 100 98 0 2836 3321 1690 50 272 272 277 94 33 96 96 0 1.031 0.925 0.937 1.024 1.884 0.937 0.909 80 377 100 5207 5868 0.044 2643 2564 2819 3049 236821 265659 39.563 32.383 0 0 0 null null
15 1 15 1 CT17736 CG5627 4080 10630 150 174 190 113 59 143 143 158 84 53 23 8 0 297 338 219 64 277 277 278 49 17 39 21 0 1.55 0.77 0.8 0.788 3.76 1.01 0.85 156 730 100 51 108 0.632 31 20 47 61 29680 52666 0.381 1.224 -50 0 0 null null
16 1 16 1 CT17772 CG5695 4290 10630 100 1420 1483 630 42 145 145 161 81 50 100 98 0 1122 1105 374 33 279 279 284 79 27 96 96 0 1.512 1.62 1.523 1.597 1.607 1.68 0.819 80 452 100 2118 2164 0.597 1275 843 1338 826 118622 88410 16.321 10.392 0 0 0 -0.0061218 0.006121803
17 1 17 1 CT7740 CG12132 4480 10630 100 534 550 250 45 149 149 159 69 43 92 86 0 532 557 178 31 276 276 283 83 29 87 66 0 1.504 1.427 1.505 1.398 2.303 1.487 0.646 80 362 100 641 682 0.589 385 256 401 281 43964 44585 5.667 3.301 0 0 0 -0.123097 0.123096837
18 1 18 1 CT35117 CG12622 4620 10630 150 166 169 75 44 151 151 161 71 44 23 3 0 291 299 67 22 275 275 280 47 16 34 16 0 0.938 0.75 1.056 1.104 4.34 4.447 0.026 156 716 100 31 42 -0.093 15 16 18 24 26392 46588 0.113 0.404 -50 0 0 null null
19 1 19 1 CT33707 CG14112 4800 10630 150 161 164 75 45 150 150 161 72 44 16 5 0 299 307 66 21 276 276 281 67 23 25 7 0 0.478 0.452 1.074 1.102 3.945 9.571 0.004 156 602 100 34 45 -1.064 11 23 14 31 25591 47901 0.042 0.388 -50 0 0 null null
20 1 20 1 CT26421 CG9269 4980 10630 150 157 163 74 45 152 152 159 69 43 22 6 0 274 281 55 19 275 275 279 64 22 14 2 0 -5 1.833 1.394 1.357 4.231 26.356 0.001 156 702 100 4 17 Error 5 -1 11 6 25430 43791 0.058 0.031 -50 0 0 null null

Total number of rows: 17664

Table truncated, full table size 4314 Kbytes.




Supplementary data files not provided
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