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Sample GSM132563 Query DataSets for GSM132563
Status Public on Nov 19, 2007
Title w1118 brain 15 days set 2
Sample type RNA
 
Channel 1
Source Name w1118 3 days brain
Organism(s) Drosophila melanogaster
Characteristics Drosophila w1118 male 3 days brain
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 brain
Organism(s) Drosophila melanogaster
Characteristics Drosophila w1118 male 15 days brain
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 brain
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
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 1690 10730 150 170 179 79 44 161 161 173 120 69 10 0 0 191 191 41 21 179 179 182 37 20 23 8 0 0.75 1.5 2.095 2.01 3.904 -708.731 0 156 860 100 21 30 -0.415 9 12 18 12 27894 29811 0.05 0.243 -50 0 0 null null
2 1 2 1 CT32994 CG13609 1870 10730 150 157 177 84 47 154 154 164 73 44 27 8 0 192 197 50 25 179 179 181 36 19 32 14 0 0.231 1.278 1.321 1.464 3.081 22.967 0.003 156 696 100 16 41 -2.115 3 13 23 18 27557 30658 0.178 0.444 -50 0 0 null null
3 1 3 1 CT17698 CG5597 2050 10730 150 158 164 67 40 147 147 157 71 45 22 3 0 193 197 45 22 177 177 179 36 20 32 12 0 0.688 0.85 1.412 1.519 4.412 11.584 0.009 156 748 100 27 37 -0.541 11 16 17 20 25656 30670 0.099 0.5 -50 0 0 -0.0147429 0.014742929
4 1 4 1 CT22043 CG7135 2230 10730 150 180 183 80 43 155 155 164 74 45 25 5 0 199 212 105 49 179 179 182 36 19 37 19 0 1.25 0.848 1.678 1.57 4.147 27.546 0 156 711 100 45 61 0.322 25 20 28 33 28521 33050 0.257 0.833 -50 0 0 null null
5 1 5 1 CT21320 CG6884 2410 10730 150 195 214 113 52 155 155 163 76 46 39 19 0 206 238 86 36 180 180 183 36 19 42 31 0 1.538 1.017 1.35 1.485 3.46 2.494 0.148 156 618 100 66 117 0.621 40 26 59 58 33375 37050 0.671 1.528 -50 0 0 -0.727942 0.727942433
6 1 6 1 CT13308 CG12234 2590 10730 150 165 170 78 45 153 153 161 78 48 18 5 0 189 196 48 24 175 175 181 39 21 30 12 0 0.857 0.81 1.719 1.735 4.833 -93.364 0 156 576 100 26 38 -0.222 12 14 17 21 26496 30533 0.115 0.385 -50 0 0 null null
7 1 7 1 CT4012 CG1553 2770 10730 150 165 173 72 41 148 148 154 76 49 25 5 0 208 214 60 28 178 178 183 41 22 42 23 0 0.567 0.694 1.091 1.068 3.367 6.281 0.018 156 594 100 47 61 -0.819 17 30 25 36 26985 33436 0.25 0.756 -50 0 0 0.662689 -0.66268914
8 1 8 1 CT21344 CG6890 2950 10730 150 156 161 73 45 153 153 159 73 45 14 3 0 200 200 48 24 183 183 185 38 20 28 11 0 0.176 0.471 1 1.063 3.793 76.029 0 156 682 100 20 25 -2.503 3 17 8 17 25106 31184 0.027 0.395 -50 0 0 null null
9 1 9 1 CT38731 CG17514 3100 10720 90 405 432 167 38 154 154 158 70 44 94 73 0 562 601 175 29 185 185 185 37 20 100 100 0 0.666 0.668 0.596 0.572 2.342 0.732 0.492 52 316 100 628 694 -0.587 251 377 278 416 22483 31232 3.914 11.243 0 0 0 0.444204 -0.444204462
10 1 10 1 CT14074 CG4297 3300 10730 150 160 169 78 46 156 156 162 73 45 19 7 0 194 199 44 22 181 181 183 36 19 28 11 0 0.308 0.722 2.194 1.992 5.154 101.88 0 156 820 100 17 31 -1.7 4 13 13 18 26441 31076 0.096 0.444 -50 0 0 null null
11 1 11 1 CT21370 CG6905 3480 10730 150 162 169 77 45 159 159 163 71 43 19 5 0 214 232 75 32 185 185 189 38 20 45 32 0 0.103 0.213 1.181 1.263 6.116 4.241 0.015 156 720 100 32 57 -3.273 3 29 10 47 26365 36131 0.085 1.132 -50 0 0 2.56906 -2.569055813
12 1 12 1 CT4054 CG3099 3660 10730 150 154 168 75 44 157 157 165 72 43 19 5 0 195 201 41 20 186 186 188 39 20 26 7 0 -0.333 0.733 2.233 2.013 4.617 -47.776 0.001 156 766 100 6 26 Error -3 9 11 15 26275 31324 0.042 0.333 -50 0 0 null null
13 1 13 1 CT17720 CG9575 3830 10730 90 350 378 132 34 153 153 163 72 44 88 71 0 449 462 88 19 189 189 189 38 20 100 100 0 0.758 0.824 0.809 0.747 1.789 0.963 0.455 52 366 100 457 498 -0.4 197 260 225 273 19649 24011 2.986 7.184 0 0 0 0.224502 -0.224501742
14 1 14 1 CT20678 CG6649 4010 10730 90 669 759 345 45 153 153 158 68 43 100 98 0 457 498 168 33 187 187 188 42 22 100 98 0 1.911 1.949 1.883 1.929 1.519 2.107 0.586 52 376 100 786 917 0.934 516 270 606 311 39443 25900 8.838 7.381 0 0 0 null null
15 1 15 1 CT17736 CG5627 4180 10730 80 324 314 98 31 148 148 155 68 43 82 61 0 403 411 83 20 193 193 191 38 19 100 96 0 0.838 0.761 0.841 0.631 3.018 0.908 0.292 52 321 100 386 384 -0.255 176 210 166 218 16302 21353 2.338 5.789 0 0 0 null null
16 1 16 1 CT17772 CG5695 4370 10730 90 470 504 223 44 149 149 158 71 44 98 80 0 511 542 131 24 196 196 197 52 26 100 100 0 1.019 1.026 0.923 0.9 1.746 1.211 0.609 52 396 100 636 701 0.027 321 315 355 346 26195 28176 4.873 6.635 0 0 0 -0.166462 0.166461646
17 1 17 1 CT7740 CG12132 4560 10730 150 206 210 78 37 160 160 169 73 43 35 9 0 221 239 73 30 199 199 208 184 88 5 0 0 2.091 1.25 1.309 1.125 3.954 6.913 0.014 156 786 100 68 90 1.064 46 22 50 40 32713 37311 0.562 0.168 -50 0 0 -1.17231 1.172313151
18 1 18 1 CT35117 CG12622 4740 10730 150 164 180 75 41 155 155 163 72 44 24 7 0 212 219 50 22 198 198 212 224 105 0 0 0 0.643 1.19 1.377 1.478 3.456 0.008 0 156 700 100 23 46 -0.637 9 14 25 21 28015 34210 0.236 0.031 -50 0 0 null null
19 1 19 1 CT33707 CG14112 4920 10730 150 167 175 75 42 154 154 161 70 43 24 8 0 203 209 58 27 187 187 195 118 60 5 0 0 0.813 0.955 1.733 1.372 4.493 85.931 0 156 695 100 29 43 -0.3 13 16 21 22 27303 32627 0.2 0.119 -50 0 0 null null
20 1 20 1 CT26421 CG9269 5100 10730 150 147 156 72 46 155 155 161 71 44 14 5 0 189 208 239 114 184 184 191 131 68 0 0 0 -1.6 0.042 1.847 1.785 4.392 -0.026 0.001 156 700 100 -3 25 Error -8 5 1 24 24260 32426 -0.07 0.13 -50 0 0 null null

Total number of rows: 17664

Table truncated, full table size 4274 Kbytes.




Supplementary data files not provided
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