NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM10923 Query DataSets for GSM10923
Status Public on Dec 31, 2003
Title embryo_12_16_a
Sample type RNA
 
Channel 1
Source name total RNA from embryo 12-16 h 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
1 790 890 100 8526 8512 2814 344 417 355 98 98 0 65535 55781 20701 120 191 256 98 97 76 0.125 0.147 0.144 0.172 2.231 0.12 0.75 80 388 73597 63829 -2.999 8182 65415 8168 55661 -75 -2.76611194
2 930 890 100 190 269 264 303 426 475 6 0 0 295 518 772 83 178 282 43 21 0 -0.533 -0.078 1.17 0.803 7.199 0.161 0.042 80 254 99 401 Error -113 212 -34 435 -75 -3.680382066
3 1070 890 100 269 339 288 303 444 554 10 0 0 155 182 184 77 165 265 17 2 0 -0.436 0.343 1.425 1.355 3.38 12.191 0.012 80 265 44 141 Error -34 78 36 105 -75 -1.543719518
4 1210 890 100 237 296 270 332 399 386 8 2 0 94 166 200 65 139 188 26 10 0 -3.276 -0.356 2.662 2.062 3.769 0.05 0.002 80 274 -66 65 Error -95 29 -36 101 -75 -1.490050854
5 1350 890 100 1192 2550 2794 347 452 496 56 48 0 416 769 878 52 126 176 68 51 0 2.321 3.073 2.868 2.368 3.12 3.952 0.602 80 274 1209 2920 1.215 845 364 2203 717 -75 1.619647767
6 1490 890 100 1668 2675 2252 344 443 445 80 61 0 635 851 844 59 125 163 68 60 0 2.299 2.943 2.923 3.022 2.94 3.644 0.532 80 274 1900 3123 1.201 1324 576 2331 792 -75 1.557287542
7 1630 890 100 8563 19669 22551 298 408 370 97 92 13 1238 4967 6904 37 110 161 83 76 0 6.882 3.929 4.659 5.208 2.569 3.738 0.802 80 268 9466 24301 2.783 8265 1201 19371 4930 -75 1.974162168
8 1770 880 100 23111 29623 27071 355 634 1626 77 66 23 4869 9095 9875 54 158 255 86 73 0 4.726 3.237 2.819 3.767 2.613 3.525 0.674 80 273 27571 38309 2.241 22756 4815 29268 9041 -75 1.694657366
9 1910 880 100 592 737 791 432 682 1599 2 1 0 108 198 252 63 168 256 22 7 0 3.556 2.259 2.287 2.332 2.804 14.45 0.16 80 280 205 440 1.83 160 45 305 135 -50 1.175684271
10 2050 880 100 355 469 493 419 509 405 13 6 0 98 200 241 79 159 207 28 11 0 -3.368 0.413 2.899 2.417 7.357 10.284 0.016 80 322 -45 171 Error -64 19 50 121 -50 -1.275786313
11 2190 880 100 328 394 458 330 395 300 18 7 0 104 156 167 78 159 214 17 5 0 -0.077 0.821 2.329 2.305 4.504 0.019 0.001 80 279 24 142 Error -2 26 64 78 -50 -0.284545873
12 2330 880 100 658 723 354 423 482 373 36 13 0 310 366 308 91 181 235 48 25 0 1.073 1.091 1.243 1.25 4.324 9.532 0.004 80 286 454 575 0.102 235 219 300 275 -50 0.125651102
13 2470 880 100 833 830 495 525 589 423 41 13 0 431 442 304 126 190 216 58 36 0 1.01 0.965 1.558 1.524 3.935 6.241 0.045 80 350 613 621 0.014 308 305 305 316 -50 -0.051399153
14 2610 880 100 342 437 368 470 502 337 16 3 0 141 219 241 127 184 215 30 12 0 -9.143 -0.359 1.898 1.807 4.175 9.661 0.011 80 343 -114 59 Error -128 14 -33 92 -50 -1.477944251
15 2760 850 50 926 897 430 551 586 337 58 25 0 532 485 238 142 217 264 58 16 0 0.962 1.009 1.022 1.34 4.427 28.902 0.002 12 69 765 689 -0.057 375 390 346 343 0 0.012926174
16 2890 880 100 363 421 335 361 429 323 22 6 0 24 145 231 63 159 227 20 5 0 -0.051 0.732 2.449 1.838 3.399 4.497 0.032 80 313 -37 142 Error 2 -39 60 82 -50 -0.450084446
17 3030 880 100 433 512 342 430 475 355 18 3 0 73 118 171 55 144 202 13 2 0 0.167 1.302 2.848 2.43 4.213 0.008 0 80 280 21 145 -2.585 3 18 82 63 -50 0.380729449
18 3170 880 100 552 590 388 516 582 475 13 3 0 26 135 217 94 172 218 17 6 0 -0.529 1.805 2.957 1.619 4.985 72.375 0.001 80 320 -32 115 Error 36 -68 74 41 -50 0.851998837
19 3310 880 100 570 601 396 462 504 336 21 8 0 42 114 155 106 148 178 13 3 0 -1.687 17.375 2.043 2.115 4.698 0.051 0.009 80 295 44 147 Error 108 -64 139 8 -50 4.118941073
20 3450 880 100 500 551 348 420 481 309 31 10 0 95 159 187 31 115 166 32 16 0 1.25 1.023 2.76 2.541 3.019 38.431 0.001 80 277 144 259 0.322 80 64 131 128 -50 0.032806145

Total number of rows: 47616

Table truncated, full table size 8456 Kbytes.




Supplementary data files not provided
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap