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Sample GSM132590 Query DataSets for GSM132590
Status Public on Nov 19, 2007
Title w1118 malpighian tubule 60 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 60 days malpighian tubule
Organism Drosophila melanogaster
Characteristics Drosophila w1118 male 60 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 60 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 1720 10660 150 158 177 93 52 155 155 164 77 46 19 8 0 296 305 66 21 282 282 284 48 16 26 12 0 0.214 0.957 1.222 1.361 4.766 5.844 0.017 156 880 100 17 45 -2.222 3 14 22 23 27534 47616 0.169 0.438 -50 0 0 null null
2 1 2 1 CT32994 CG13609 1900 10660 150 164 178 81 45 156 156 183 229 125 1 0 0 302 317 112 35 282 282 292 102 34 13 2 0 0.4 0.629 1.168 1.202 3.977 1.289 0.021 156 659 100 28 57 -1.322 8 20 22 35 27699 49428 -0.022 0.245 -50 0 0 null null
3 1 3 1 CT17698 CG5597 2080 10660 150 181 189 89 47 166 166 179 151 84 7 1 0 308 313 65 20 282 282 292 100 34 12 1 0 0.577 0.742 1.263 1.316 3.915 5.405 0.02 156 601 100 41 54 -0.794 15 26 23 31 29507 48826 0.066 0.21 -50 0 0 1.00063 -1.000631349
4 1 4 1 CT22043 CG7135 2260 10660 150 162 168 75 44 156 156 164 72 43 18 7 0 292 300 55 18 282 282 285 46 16 28 10 0 0.6 0.667 1.371 1.35 3.335 19.161 0.002 156 582 100 16 30 -0.737 6 10 12 18 26212 46793 0.056 0.326 -50 0 0 null null
5 1 5 1 CT21320 CG6884 2440 10660 150 176 211 137 64 157 157 167 79 47 32 18 0 305 318 88 27 280 280 283 52 18 35 19 0 0.76 1.421 1.757 1.524 3.644 2.594 0.201 156 582 100 44 92 -0.396 19 25 54 38 32927 49671 0.557 0.673 -50 0 0 0.671417 -0.671417374
6 1 6 1 CT13308 CG12234 2620 10660 150 174 186 79 42 156 156 165 82 49 25 5 0 287 302 72 23 273 273 277 50 18 27 13 0 1.286 1.034 1.189 1.058 4.494 3.33 0.058 156 726 100 32 59 0.363 18 14 30 29 29043 47119 0.256 0.5 -50 0 0 null null
7 1 7 1 CT4012 CG1553 2850 10650 90 408 432 178 41 161 161 172 80 46 86 71 0 469 471 76 16 272 272 274 48 17 100 88 0 1.254 1.362 1.206 1.17 2.505 2.129 0.337 52 305 100 444 470 0.326 247 197 271 199 22489 24490 3.25 4.104 0 0 0 0.662137 -0.662136788
8 1 8 1 CT21344 CG6890 2980 10660 150 164 170 81 47 154 154 165 78 47 21 4 0 293 301 70 23 272 272 278 54 19 28 12 0 0.476 0.552 1.5 1.481 3.906 3.327 0.045 156 850 100 31 45 -1.07 10 21 16 29 26551 46932 0.064 0.426 -50 0 0 null null
9 1 9 1 CT38731 CG17514 3200 10640 90 1251 1422 631 44 151 151 165 80 48 100 100 0 768 848 256 30 269 269 276 58 21 100 100 0 2.204 2.195 2.322 2.113 1.753 2.619 0.675 52 333 100 1599 1850 1.14 1100 499 1271 579 73952 44094 15.713 9.862 0 0 0 0.118419 -0.118419097
10 1 10 1 CT14074 CG4297 3340 10660 150 180 196 95 48 151 151 163 74 45 31 11 0 287 297 63 21 269 269 273 48 17 30 10 0 1.611 1.607 1.395 1.248 4.401 5.949 0.028 156 762 100 47 73 0.688 29 18 45 28 30576 46384 0.446 0.5 -50 0 0 null null
11 1 11 1 CT21370 CG6905 3520 10660 150 209 218 115 52 155 155 167 78 46 38 19 0 291 527 2775 526 267 267 274 49 17 40 20 0 2.25 0.242 1.595 1.516 3.602 -0.001 0 156 611 100 78 323 1.17 54 24 63 260 34030 82156 0.654 5.163 -50 0 0 -0.687936 0.687936175
12 1 12 1 CT4054 CG3099 3710 10650 150 165 175 76 43 153 153 164 74 45 19 7 0 288 287 53 18 269 269 272 49 18 26 7 0 0.632 1.222 1.282 1.289 3.46 9.952 0.006 156 760 100 31 40 -0.663 12 19 22 18 27288 44738 0.149 0.306 -50 0 0 null null
13 1 13 1 CT17720 CG9575 3920 10650 90 647 631 179 28 156 156 165 73 44 100 96 0 522 520 83 15 272 272 272 45 16 100 100 0 1.964 1.915 1.998 1.869 1.578 2.35 0.605 52 395 100 741 723 0.974 491 250 475 248 32799 27035 6.384 5.511 0 0 0 0.130382 -0.130382239
14 1 14 1 CT20678 CG6649 4110 10640 90 5886 7185 3457 48 157 157 172 81 47 100 100 0 2210 2561 1011 39 268 268 271 53 19 100 100 0 2.95 3.065 2.788 3.003 1.495 3.407 0.751 52 397 100 7671 9321 1.561 5729 1942 7028 2293 373620 133175 86.58 43.208 0 0 0 null null
15 1 15 1 CT17736 CG5627 4290 10640 90 305 295 99 33 154 154 165 78 47 69 46 0 377 374 66 17 267 267 271 65 23 78 36 0 1.373 1.318 1.458 1.256 4.144 1.793 0.096 52 383 100 261 248 0.457 151 110 141 107 15357 19449 1.667 1.585 0 0 0 null null
16 1 16 1 CT17772 CG5695 4460 10640 90 2577 2805 945 33 154 154 164 83 50 100 100 0 1288 1399 428 30 267 267 273 71 26 100 100 0 2.373 2.342 2.436 2.354 1.357 2.622 0.799 52 385 100 3444 3783 1.247 2423 1021 2651 1132 145840 72759 31.819 15.859 0 0 0 0.117496 -0.117495632
17 1 17 1 CT7740 CG12132 4650 10650 90 1094 1137 348 30 163 163 171 79 46 100 100 0 688 719 148 20 261 261 266 65 24 100 98 0 2.18 2.127 2.116 2.094 1.547 1.006 0.143 52 320 100 1358 1432 1.125 931 427 974 458 59128 37395 12.228 6.969 0 0 0 0.108202 -0.108202207
18 1 18 1 CT35117 CG12622 4790 10650 150 171 183 92 50 147 147 158 70 44 30 16 0 281 292 62 21 262 262 264 45 17 34 14 0 1.263 1.2 1.769 1.751 3.753 0.02 0.004 156 816 100 43 66 0.337 24 19 36 30 28478 45486 0.357 0.622 -50 0 0 null null
19 1 19 1 CT33707 CG14112 4970 10650 150 179 192 94 48 152 152 162 75 46 29 10 0 293 303 69 22 263 263 264 45 17 41 21 0 0.9 1 1.253 1.217 4.058 4.221 0.035 156 696 100 57 80 -0.152 27 30 40 40 30006 47237 0.4 0.867 -50 0 0 null null
20 1 20 1 CT26421 CG9269 5150 10650 150 166 173 81 46 158 158 165 71 43 22 8 0 281 287 57 19 266 266 268 46 17 28 13 0 0.533 0.714 1.649 1.62 3.921 6.86 0.017 156 730 100 23 36 -0.907 8 15 15 21 26948 44845 0.113 0.413 -50 0 0 null null

Total number of rows: 17664

Table truncated, full table size 4298 Kbytes.




Supplementary data files not provided
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