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Sample GSM10937 Query DataSets for GSM10937
Status Public on Dec 31, 2003
Title Pupal3_c
Sample type RNA
 
Channel 1
Source name total RNA from pupal 3 labeled with Cy3 (532 nm)
Organism Drosophila melanogaster
Extracted molecule total RNA
 
Channel 2
Source name total RNA from embryo 0-4 h labeled with Cy5 (632 nm)
Organism Drosophila melanogaster
Extracted molecule total RNA
 
 
Description Cy5/Cy3 labeled RNA was co-hybridized onto a QMT Amino (Quantifoil) glass slide. Embryo 0-4 h was used as common reference control.
Sample collection:
Embryo samples were collected as four-hour egg lays, which were allowed to develop for the desired interval
and then snap frozen in liquid nitrogen.
The different larval stages as well as the different pupal stages were handpicked and separately snap frozen.
Adults were collected as male and female flies and also snap frozen. Total RNA was isolated from all samples
using the Trizol reagent (Invitrogen, Karlsruhe, Germany).
Microarray hybridization:
At least three independent experiments were performed for each of the 8 different stages
(embryonic stage 4-8h, embryonic stage 8-12h, embryonic stage 12-16h, pooled larval stage, pupal stage 1, pupal stage 2,
pupal stage 3 and adult stage) in competitive hybridizations against the common control,
which was a sample made from RNA isolated from embryonic stage 0-4h. At least one dye swap was included in each of the repetitions.
We used the indirect labeling method, with 9µg random hexamer primer (Invitrogen, Karlsruhe, Germany) added to 20µg total RNA.
For hybridization, the labeled cDNAs were taken up in SlideHyb buffer #1 (Ambion, Woodward, USA), denatured at 95°C for 5min,
and applied to the array. Hybridization was performed in appropriate chambers (TeleChem) in a waterbath at 55°C for 16h.
The hybridized glass slides were scanned on a ScanArray 5000 (Perkin Elmer, Wellesley, USA) using the ScanArray software (Version 3.1).
The resulting images (TIFF format, 16-bit grayscale) for each channel - Cy5 (632nm) and Cy3 (532nm) - were analyzed
further with the GenePix software (Version 4.0; Axon Instruments, Union City, USA).
As each microarray contains two replicates for each gene, we used the standard deviation (SD)
of their dye-ratio (Cy5/Cy3) to filter for reproducible hybridizations. Only if at least 30% of all genes on the array
had a SD of log(632/532) of less than 1/3 between the replicates was the microarray included for further analysis.
 
Submission date Oct 02, 2003
Last update date Oct 28, 2005
Contact name Boris Beckmann
E-mail(s) b.beckmann@dkfz.de
Phone +49-6221-424679
Organization name Deutsches Krebsforschungszentrum
Department Funktionelle Genomanalyse
Street address Im Neuenheimer Feld 580
City Heidelberg
ZIP/Postal code 69121
Country Germany
 
Platform ID GPL517
Series (1)
GSE695 Drosophila melanogaster transcriptome life cycle

Data table header descriptions
ID_REF
X X-coordinate of the center of the feature-indicator associated with the feature, where (0,0) is the top left of the image
Y Y-coordinate of the center of the feature-indicator associated with the feature, where (0,0) is the top left of the image
Dia. Diameter in µm of the feature-indicator
F632 Median Median pixel intensity of feature for Cy5 channel
F632 Mean Mean pixel intensity of feature for Cy5 channel
F632 SD
B632 Median
B632 Mean
B632 SD
% > B632+1SD
% > B632+2SD
F632 % Sat.
F532 Median Median feature pixel intensity at wavelength #2 (532 nm, Cy3)
F532 Mean Mean feature pixel intensity at wavelength #2 (532 nm, Cy3)
F532 SD
B532 Median
B532 Mean
B532 SD
% > B532+1SD
% > B532+2SD
F532 % Sat.
Ratio of Medians (632/532)
Ratio of Means (632/532)
Median of Ratios (632/532)
Mean of Ratios (632/532)
Ratios SD (632/532)
Rgn Ratio (632/532)
Rgn R² (632/532)
F Pixels
B Pixels
Sum of Medians
Sum of Means
Log Ratio (632/532)
F632 Median - B632
F532 Median - B532
F632 Mean - B632
F532 Mean - B532
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 aligned during analysis. A value of 0 or larger than 0 means that this spot passed the flagging screen but may still fail other quality tests.
VALUE log2 ratio (log2 ratio of Ratio of Means(632/532) Not normalized!

Data table
ID_REF X Y Dia. F632 Median F632 Mean F632 SD B632 Median B632 Mean B632 SD % > B632+1SD % > B632+2SD F632 % Sat. F532 Median F532 Mean F532 SD B532 Median B532 Mean B532 SD % > B532+1SD % > B532+2SD F532 % Sat. Ratio of Medians (632/532) Ratio of Means (632/532) Median of Ratios (632/532) Mean of Ratios (632/532) Ratios SD (632/532) Rgn Ratio (632/532) Rgn R² (632/532) F Pixels B Pixels Sum of Medians Sum of Means Log Ratio (632/532) F632 Median - B632 F532 Median - B532 F632 Mean - B632 F532 Mean - B532 Flags VALUE
1 910 1160 100 10460 8378 10061 0 120 456 67 61 0 65535 35885 31585 218 1789 9054 57 55 51 0.16 0.235 0.211 0.25 2.363 0.192 0.573 80 380 75777 44045 -2.643 10460 65317 8378 35667 -75 -2.089267338
2 1050 1160 100 0 82 164 0 129 492 6 0 0 367 552 593 261 2089 9869 0 0 0 0 0.282 0.765 0.546 5.762 0.02 0.18 80 318 106 373 Error 0 106 82 291 -75 -1.826232932
3 1190 1160 100 0 94 164 0 72 164 22 8 0 472 564 491 295 405 427 35 11 0 0 0.349 0.333 0.37 4.124 0.026 0.003 80 330 177 363 Error 0 177 94 269 -75 -1.518701058
4 1330 1160 100 0 86 166 0 66 140 21 12 0 329 488 517 244 353 410 25 12 0 0 0.352 0.602 0.465 3.625 0.008 0 80 278 85 330 Error 0 85 86 244 -75 -1.506352666
5 1470 1160 100 0 903 2318 0 57 144 38 33 0 393 1000 1862 225 343 411 38 27 0 0 1.165 0.796 1.044 4.36 1.324 0.414 80 266 168 1678 Error 0 168 903 775 -75 0.220329955
6 1610 1160 100 129 487 721 0 64 134 50 38 0 487 753 844 188 337 427 46 25 0 0.431 0.862 0.944 1.075 4.991 0.281 0.133 80 266 428 1052 -1.213 129 299 487 565 -75 -0.214240226
7 1750 1160 100 41 1345 3390 0 142 754 17 15 0 387 1216 2324 210 437 975 17 11 0 0.232 1.337 0.942 0.771 6.052 1.609 0.546 80 266 218 2351 -2.11 41 177 1345 1006 -75 0.418999465
8 1890 1160 100 931 7776 11178 0 302 1604 41 33 0 929 5145 8258 187 544 1381 36 30 0 1.255 1.568 1.381 1.617 4.389 1.462 0.659 80 266 1673 12734 0.327 931 742 7776 4958 -75 0.648925559
9 2030 1160 100 0 137 252 0 228 1409 0 0 0 423 513 484 199 469 1055 10 1 0 0 0.436 0.438 0.505 4.333 0.167 0.041 80 275 224 451 Error 0 224 137 314 -50 -1.19759996
10 2170 1150 100 0 65 164 0 96 203 12 6 0 200 314 363 209 361 449 17 3 0 0 0.619 0.63 0.78 3.6 27.806 0.002 80 377 -9 170 Error 0 -9 65 105 -50 -0.691988685
11 2330 1140 60 21 165 267 0 70 149 34 18 0 807 940 599 199 367 436 59 40 0 0.035 0.223 0.325 0.339 2.488 0.088 0.053 32 127 629 906 -4.856 21 608 165 741 0 -2.164884385
12 2450 1150 100 8 135 241 0 74 153 28 15 0 441 598 469 264 369 383 40 18 0 0.045 0.404 0.472 0.426 7.284 0.063 0.011 80 360 185 469 -4.468 8 177 135 334 -50 -1.307572802
13 2600 1160 50 0 169 265 0 75 138 33 25 0 1125 1059 460 449 634 1030 16 0 0 0 0.277 0.508 0.947 8.843 0.038 0.007 12 99 676 779 Error 0 676 169 610 0 -1.852042119
14 2730 1150 100 2 100 208 0 83 174 16 11 0 426 484 398 303 473 696 11 1 0 0.016 0.552 0.271 0.317 4.223 0.057 0.025 80 392 125 281 -5.943 2 123 100 181 -50 -0.857259828
15 2870 1170 70 137 211 249 0 66 126 50 34 0 841 987 585 328 515 564 46 18 0 0.267 0.32 0.616 0.691 2.735 0.061 0.032 32 158 650 870 -1.905 137 513 211 659 0 -1.64385619
16 3010 1150 100 0 72 163 0 79 151 15 7 0 135 284 388 225 374 451 16 3 0 0 1.22 0.83 0.856 10.093 0.022 0.003 80 308 -90 131 Error 0 -90 72 59 -50 0.286881148
17 3150 1150 100 0 89 147 0 85 169 20 8 0 198 299 367 214 338 399 12 6 0 0 1.047 0.537 0.645 5.167 28.691 0.005 80 286 -16 174 Error 0 -16 89 85 -50 0.066261442
18 3290 1140 100 0 117 241 0 104 189 17 8 0 148 302 366 206 331 396 18 7 0 0 1.219 0.531 0.491 6.619 11.469 0.013 80 326 -58 213 Error 0 -58 117 96 -50 0.285698126
19 3430 1140 100 73 157 219 0 111 208 28 11 0 190 340 412 213 315 376 23 8 0 -3.174 1.236 0.445 0.57 3.907 58.294 0 80 286 50 284 Error 73 -23 157 127 -50 0.305678743
20 3570 1140 100 0 97 175 2 121 226 13 7 0 108 238 332 216 312 356 13 6 0 0.019 4.318 0.059 0.076 5.655 0.126 0.031 80 258 -110 117 -5.755 -2 -108 95 22 -50 2.110363243

Total number of rows: 47616

Table truncated, full table size 8155 Kbytes.




Supplementary data files not provided
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