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Sample GSM132271 Query DataSets for GSM132271
Status Public on Nov 19, 2007
Title w1118 accessory gland 45 days set 2
Sample type RNA
 
Channel 1
Source name w1118 3 days accessory gland
Organism Drosophila melanogaster
Characteristics Drosophila w1118 male 3 days accessory gland
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 45 days accessory gland
Organism Drosophila melanogaster
Characteristics Drosophila w1118 male 45 days accessory gland
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 45 days accessory gland
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 28, 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
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 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 1520 10670 150 165 169 77 45 154 154 168 166 98 3 0 0 263 273 53 19 263 263 265 48 18 25 5 0 100000 1.5 1.474 1.531 4.151 -378.141 0 156 910 100 11 25 16.61 11 0 15 10 26326 42638 0.006 0.167 -50 0 0 null null
2 1710 10680 150 157 167 78 46 156 156 162 77 47 19 3 0 276 288 65 22 269 269 271 48 17 31 14 0 0.143 0.579 1.248 1.18 3.79 10.663 0.004 156 703 100 8 30 -2.807 1 7 11 19 26106 44972 0.065 0.354 -50 0 0 null null
3 1890 10680 150 162 179 97 54 151 151 161 78 48 23 8 0 273 282 62 21 273 273 274 50 18 21 5 0 100000 3.111 1.187 1.386 4.645 48.599 0 156 629 100 11 37 16.61 11 0 28 9 27926 43951 0.231 0.16 -50 0 0 -1.64877 1.64876907
4 2070 10680 150 164 174 76 43 151 151 163 79 48 20 5 0 282 290 59 20 267 267 271 51 18 25 8 0 0.867 1 1.583 1.396 6.113 -301.031 0 156 582 100 28 46 -0.206 13 15 23 23 27178 45180 0.139 0.373 -50 0 0 null null
5 2250 10680 150 177 196 103 52 156 156 166 80 48 28 10 0 297 316 88 27 263 263 276 163 59 10 0 0 0.618 0.755 0.94 1.073 3.727 0.152 0.047 156 582 100 55 93 -0.695 21 34 40 53 30503 49228 0.375 0.245 -50 0 0 0.291111 -0.291110788
6 2430 10680 150 146 157 75 47 146 146 158 75 47 20 5 0 283 296 65 21 266 266 277 153 55 4 0 0 0 0.367 1.116 1.247 6.957 10.4 0.002 156 691 100 17 41 Error 0 17 11 30 24466 46177 -0.013 0.124 -50 0 0 null null
7 2630 10700 80 209 221 101 45 144 144 156 70 44 48 17 0 398 394 71 18 272 272 275 66 24 78 44 0 0.516 0.631 0.662 0.673 4.801 1.279 0.098 52 243 100 191 199 -0.955 65 126 77 122 11510 20472 0.929 1.803 0 0 0 1.18344 -1.183435886
8 2790 10680 150 158 187 307 164 146 146 156 71 45 19 5 0 286 298 73 24 264 264 271 58 21 28 12 0 0.545 1.206 0.952 1.13 4.91 108.797 0.001 156 762 100 34 75 -0.874 12 22 41 34 29149 46425 0.437 0.466 -50 0 0 null null
9 2980 10710 90 282 299 102 34 147 147 157 77 49 71 42 0 494 502 88 17 266 266 273 54 19 100 92 0 0.592 0.644 0.668 0.571 2.373 0.872 0.254 52 290 100 363 388 -0.756 135 228 152 236 15553 26117 1.844 4.241 0 0 0 0.729274 -0.7292739
10 3150 10690 150 179 194 101 52 145 145 159 77 48 32 14 0 297 309 80 25 264 264 269 55 20 36 14 0 1.03 1.089 1.714 1.747 4.293 3.83 0.032 156 659 100 67 94 0.043 34 33 49 45 30336 48180 0.455 0.727 -50 0 0 null null
11 3330 10690 150 160 175 111 63 162 162 173 83 47 16 2 0 298 309 61 19 267 267 269 50 18 39 17 0 -0.065 0.31 1.357 1.192 4.794 5.649 0.031 156 582 100 29 55 Error -2 31 13 42 27289 48162 0.024 0.8 -50 0 0 0.384492 -0.384491737
12 3510 10690 150 149 158 74 46 158 158 171 88 51 12 1 0 278 288 55 19 266 266 269 52 19 28 9 0 -0.75 0 1.571 1.455 4.715 5.752 0.022 156 582 100 3 22 Error -9 12 0 22 24669 44898 -0.148 0.365 -50 0 0 null null
13 3690 10690 150 195 209 105 50 154 154 166 95 57 30 12 0 312 333 107 32 265 265 269 48 17 48 33 0 0.872 0.809 0.994 0.939 3.533 2.164 0.07 156 668 100 88 123 -0.197 41 47 55 68 32611 51904 0.453 1.333 -50 0 0 0.710478 -0.710478264
14 3870 10710 90 1777 2118 998 47 155 155 210 343 163 100 96 0 1117 1320 582 44 272 272 301 197 65 100 94 0 1.92 1.873 1.988 1.909 1.869 2.285 0.559 52 290 100 2467 3011 0.941 1622 845 1963 1048 110111 68656 5.563 5.173 0 0 0 null null
15 4050 10690 150 162 169 83 49 155 155 178 206 115 0 0 0 300 311 70 22 266 266 324 1029 317 0 0 0 0.206 0.311 0.885 0.836 3.493 1.949 0.528 156 863 100 41 59 -2.28 7 34 14 45 26439 48463 -0.044 -0.013 -50 0 0 null null
16 4270 10720 80 257 296 136 45 151 151 160 68 42 67 46 0 461 461 104 22 261 261 266 46 17 90 86 0 0.53 0.725 0.842 0.675 2.762 3.506 0.07 52 256 100 306 345 -0.916 106 200 145 200 15416 23985 2 4.239 0 0 0 0.285365 -0.285364763
17 4410 10700 150 158 169 76 44 149 149 172 362 210 0 0 0 292 311 93 29 259 259 277 308 111 1 0 0 0.273 0.385 0.9 0.872 3.981 1.762 0.066 156 814 100 42 72 -1.874 9 33 20 52 26402 48479 -0.008 0.11 -50 0 0 0.511143 -0.511143065
18 4590 10700 150 149 155 77 49 150 150 174 390 224 0 0 0 298 304 64 21 259 259 280 332 118 0 0 0 -0.026 0.111 1.2 1.096 3.888 0.141 0.28 156 698 100 38 50 Error -1 39 5 45 24241 47371 -0.049 0.072 -50 0 0 null null
19 4770 10700 150 148 155 69 44 159 159 166 80 48 9 3 0 291 301 64 21 276 276 280 63 22 28 7 0 -0.733 -0.16 0.959 1.009 3.403 6.166 0.003 156 614 100 4 21 Error -11 15 -4 25 24143 46886 -0.137 0.333 -50 0 0 null null
20 4950 10700 150 158 170 74 43 155 155 165 76 46 17 5 0 276 284 62 21 274 274 278 58 20 20 6 0 1.5 1.5 0.723 0.858 3.812 23.094 0.001 156 582 100 5 25 0.585 3 2 15 10 26550 44239 0.066 0.103 -50 0 0 null null

Total number of rows: 17664

Table truncated, full table size 3871 Kbytes.




Supplementary data files not provided
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