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Sample GSM132593 Query DataSets for GSM132593
Status Public on Nov 19, 2007
Title w1118 fat 15 days set 1
Sample type RNA
 
Channel 1
Source name w1118 3 days fat
Organism Drosophila melanogaster
Characteristics Drosophila w1118 male 3 days fat
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 fat
Organism Drosophila melanogaster
Characteristics Drosophila w1118 male 15 days fat
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 fat
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 1930 10990 150 113 121 60 49 110 110 121 62 51 18 6 0 118 121 37 30 115 115 118 37 31 19 5 0 1 1.833 1.679 1.848 4.436 68.767 0 156 832 100 6 17 0 3 3 11 6 18905 18892 0 0.081 -50 0 0 null null
2 1 2 1 CT32994 CG13609 2110 10990 150 107 118 62 52 115 115 123 63 51 16 5 0 123 124 36 29 112 112 115 34 29 24 7 0 -0.727 0.25 2 1.666 3.818 26.378 0.001 156 576 100 3 15 Error -8 11 3 12 18479 19288 -0.079 0.265 -50 0 0 null null
3 1 3 1 CT17698 CG5597 2290 10990 150 126 134 68 50 120 120 124 60 48 21 5 0 117 118 33 27 109 109 113 33 29 22 4 0 0.75 1.556 1.706 1.882 4.415 75.71 0 156 581 100 14 23 -0.415 6 8 14 9 20890 18485 0.167 0.152 -50 0 0 0.0615014 -0.061501442
4 1 4 1 CT22043 CG7135 2470 11000 150 112 120 66 55 115 115 122 57 46 19 5 0 122 131 51 38 111 111 115 35 30 28 9 0 -0.273 0.25 1.75 1.656 5.398 4.618 0.029 156 560 100 8 25 Error -3 11 5 20 18680 20496 -0.035 0.457 -50 0 0 null null
5 1 5 1 CT21320 CG6884 2650 11000 150 117 122 63 51 115 115 122 59 48 21 5 0 118 120 40 33 111 111 116 37 31 18 7 0 0.286 0.778 2.111 1.715 4.32 33.785 0.001 156 564 100 9 16 -1.807 2 7 7 9 18995 18754 0 0.108 -50 0 0 0.979373 -0.97937345
6 1 6 1 CT13308 CG12234 2820 11000 150 127 128 61 47 120 120 125 59 47 19 7 0 125 128 42 32 113 113 118 34 28 26 12 0 0.583 0.533 1.482 1.663 3.867 16.886 0.003 156 570 100 19 23 -0.778 7 12 8 15 20015 20024 0.051 0.294 -50 0 0 null null
7 1 7 1 CT4012 CG1553 3000 11000 150 114 125 60 48 113 113 123 62 50 18 7 0 115 119 39 32 116 116 119 35 29 19 5 0 -1 4 1.624 1.35 4.956 36.419 0.001 156 739 100 0 15 Error 1 -1 12 3 19550 18527 0.032 0 -50 0 0 1.04 -1.04
8 1 8 1 CT21344 CG6890 3240 11020 80 141 160 88 55 105 105 116 64 55 34 21 0 229 246 72 29 113 113 119 33 27 94 84 0 0.31 0.414 0.455 0.472 3.245 1.032 0.033 52 215 100 152 188 -1.688 36 116 55 133 8327 12776 0.688 3.848 0 0 0 null null
9 1 9 1 CT38731 CG17514 3360 11000 150 121 126 64 50 111 111 119 62 52 19 8 0 124 124 34 27 115 115 118 34 28 21 3 0 1.111 1.667 1.914 1.971 3.611 26.448 0.002 156 704 100 19 24 0.152 10 9 15 9 19650 19304 0.113 0.176 -50 0 0 -0.339654 0.339653564
10 1 10 1 CT14074 CG4297 3540 11000 150 118 125 60 48 110 110 119 60 50 17 7 0 124 129 47 36 114 114 116 34 29 26 9 0 0.8 1 1.5 1.553 3.871 9.524 0.008 156 711 100 18 30 -0.322 8 10 15 15 19571 20177 0.1 0.382 -50 0 0 null null
11 1 11 1 CT21370 CG6905 3720 11000 150 112 121 58 47 114 114 121 61 50 18 3 0 113 118 33 27 114 114 116 34 29 16 4 0 2 1.75 1.633 1.957 4.009 52.74 0 156 642 100 -3 11 1 -2 -1 7 4 18812 18412 0 0.059 -50 0 0 -0.78 0.78
12 1 12 1 CT4054 CG3099 3900 11000 150 118 137 88 64 116 116 125 65 52 19 8 0 122 154 112 72 113 113 119 50 42 21 11 0 0.222 0.512 1.244 1.259 4.203 0.682 0.277 156 582 100 11 62 -2.17 2 9 21 41 21387 24046 0.185 0.7 -50 0 0 null null
13 1 13 1 CT17720 CG9575 4080 11000 150 115 124 69 55 119 119 127 66 51 16 7 0 119 126 44 34 113 113 120 52 43 12 3 0 -0.667 0.385 1.369 1.232 4.454 1.525 0.172 156 576 100 2 18 Error -4 6 5 13 19333 19626 -0.045 0.115 -50 0 0 0.38 -0.38
14 1 14 1 CT20678 CG6649 4260 11000 150 115 124 56 45 120 120 126 63 50 13 3 0 124 121 36 29 114 114 118 45 38 12 1 0 -0.5 0.571 1.7 1.735 3.618 7.259 0.004 156 576 100 5 11 Error -5 10 4 7 19311 18869 -0.032 0.067 -50 0 0 null null
15 1 15 1 CT17736 CG5627 4440 11000 150 114 139 91 65 113 113 126 65 51 25 10 0 124 181 206 113 115 115 124 74 59 10 8 0 0.111 0.394 1.591 1.551 4.787 0.353 0.337 156 622 100 10 92 -3.17 1 9 26 66 21609 28228 0.2 0.77 -50 0 0 null null
16 1 16 1 CT17772 CG5695 4620 11010 150 125 137 71 51 110 110 124 66 53 21 8 0 122 138 65 47 114 114 122 68 55 17 8 0 1.875 1.125 1.016 1.14 4.434 0.573 0.232 156 676 100 23 51 0.907 15 8 27 24 21354 21596 0.197 0.235 -50 0 0 -1.0246 1.024603838
17 1 17 1 CT7740 CG12132 4790 11010 150 103 108 53 49 117 117 128 63 49 10 1 0 122 120 38 31 115 115 117 34 29 19 5 0 -2 -1.8 1.42 1.196 3.77 7.145 0.02 156 618 100 -7 -4 Error -14 7 -9 5 16920 18711 -0.317 0.088 -50 0 0 0.32 -0.32
18 1 18 1 CT35117 CG12622 4970 11010 150 123 125 59 47 120 120 128 62 48 16 3 0 119 121 36 29 114 114 115 34 29 21 3 0 0.6 0.714 1.722 1.813 3.367 -53.338 0.001 156 592 100 8 12 -0.737 3 5 5 7 19577 18819 -0.048 0.176 -50 0 0 null null
19 1 19 1 CT33707 CG14112 5150 11010 150 119 124 61 49 112 112 119 56 47 23 5 0 115 589 4137 702 110 110 113 34 30 23 4 0 1.4 0.025 1.911 1.45 5.612 0 0 156 684 100 12 491 0.485 7 5 12 479 19404 91823 0.089 14 -50 0 0 null null
20 1 20 1 CT26421 CG9269 5330 11010 150 111 118 57 48 113 113 120 59 49 17 3 0 124 126 36 28 113 113 118 43 36 17 3 0 -0.182 0.385 1.704 1.286 4.073 30.894 0.001 156 642 100 9 18 Error -2 11 5 13 18429 19636 -0.034 0.186 -50 0 0 null null

Total number of rows: 17664

Table truncated, full table size 4238 Kbytes.




Supplementary data files not provided
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