NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM10921 Query DataSets for GSM10921
Status Public on Dec 31, 2003
Title embryo_8_12_b
Sample type RNA
 
Channel 1
Source name total RNA from embryo 8-12 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
1 780 880 100 351 3276 4178 126 422 1415 38 36 0 486 19581 28527 65 2241 11242 32 30 23 0.534 0.161 0.221 0.382 3.337 0.144 0.905 80 387 646 22666 -0.904 225 421 3150 19516 -75 -2.634867407
2 920 880 100 87 484 1461 117 527 1657 3 3 0 474 7940 19143 73 3095 13148 11 11 7 -0.075 0.047 0.186 0.29 8.116 0.107 0.7 80 279 371 8234 Error -30 401 367 7867 -75 -4.411195433
3 1060 880 100 18 84 133 66 159 208 8 3 0 102 270 836 65 144 196 23 11 0 -1.297 0.088 1.015 1.005 3.045 0.018 0.006 80 257 -11 223 Error -48 37 18 205 -75 -3.506352666
4 1200 880 100 29 97 137 33 127 174 21 6 0 100 156 177 66 147 190 21 6 0 -0.118 0.711 0.508 0.733 4.684 0.525 0.023 80 274 30 154 Error -4 34 64 90 -75 -0.492078535
5 1340 880 100 81 364 701 86 209 344 20 11 0 98 173 197 73 152 189 28 12 0 -0.2 2.78 1.667 2.126 2.84 3.706 0.314 80 274 20 378 Error -5 25 278 100 -75 1.475084883
6 1480 880 100 157 473 710 139 271 395 26 17 0 65 175 246 75 161 222 20 11 0 -1.8 3.34 1.932 2.03 4.874 3.749 0.166 80 274 8 434 Error 18 -10 334 100 -75 1.739848103
7 1620 880 100 622 6087 9648 145 257 370 55 47 0 199 1624 2992 48 158 325 41 27 0 3.159 3.77 3.073 3.041 3.937 3.583 0.763 80 268 628 7518 1.659 477 151 5942 1576 -75 1.914564523
8 1760 870 100 599 12674 22298 128 670 2992 30 26 7 279 2896 5929 31 306 1220 20 18 0 1.899 4.379 4.173 3.946 4.094 3.913 0.821 80 273 719 15411 0.925 471 248 12546 2865 -75 2.13060145
9 1900 870 100 379 930 1868 169 680 3023 5 3 0 236 512 1132 46 288 1212 10 3 0 1.105 1.633 1.384 1.413 4.644 3.277 0.771 80 266 400 1227 0.144 210 190 761 466 -50 0.707524791
10 2040 870 100 151 170 154 184 247 232 7 0 0 91 120 127 29 113 161 25 6 0 -0.532 -0.154 1.605 1.48 4.646 2.311 0.021 80 266 29 77 Error -33 62 -14 91 -50 -2.698997744
11 2180 870 100 79 126 164 167 235 226 3 3 0 97 146 174 50 113 150 27 10 0 -1.872 -0.427 2.15 1.449 3.792 9.46 0.001 80 266 -41 55 Error -88 47 -41 96 -50 -1.227692025
12 2320 870 100 365 500 442 160 252 303 41 28 0 123 209 259 91 161 201 28 15 0 6.406 2.881 1.768 1.798 3.191 3.522 0.141 80 320 237 458 2.679 205 32 340 118 -50 1.52656966
13 2490 870 90 1494 1566 565 158 271 328 98 90 0 522 584 345 121 176 214 78 46 0 3.332 3.041 3.02 3.047 2.605 4.199 0.173 52 237 1737 1871 1.736 1336 401 1408 463 0 1.604545816
14 2600 870 100 265 340 311 172 237 258 33 12 0 104 155 173 88 149 185 23 6 0 5.813 2.507 1.678 1.898 3.684 0.01 0 80 309 109 235 2.539 93 16 168 67 -50 1.325961996
15 2780 850 70 845 868 362 180 229 235 90 71 0 371 374 256 91 137 164 59 43 0 2.375 2.431 2.509 2.495 3.124 4.671 0.091 32 151 945 971 1.248 665 280 688 283 0 1.281549893
16 2880 870 100 224 284 276 220 290 270 16 5 0 104 172 206 53 120 157 31 17 0 0.078 0.538 1.613 1.537 3.848 0.001 0 80 295 55 183 -3.672 4 51 64 119 -50 -0.894321922
17 3020 870 100 304 369 304 344 405 312 13 6 0 110 140 157 72 140 166 23 6 0 -1.053 0.368 2.848 2.133 4.835 75.475 0 80 280 -2 93 Error -40 38 25 68 -50 -1.442222329
18 3160 870 100 431 421 281 354 422 308 12 6 0 79 126 159 63 150 200 12 6 0 4.813 1.063 2.921 2.144 3.481 0.052 0.002 80 339 93 130 2.267 77 16 67 63 -50 0.088141597
19 3300 870 100 413 467 302 324 384 287 28 6 0 70 137 174 62 145 205 17 8 0 11.125 1.907 2.081 1.822 4.611 0.047 0.003 80 290 97 218 3.476 89 8 143 75 -50 0.931304844
20 3440 870 100 363 416 277 312 361 273 25 7 0 77 176 250 80 143 168 27 13 0 -17 1.083 1.481 1.348 3.758 133.659 0 80 255 48 200 Error 51 -3 104 96 -50 0.115033243

Total number of rows: 47616

Table truncated, full table size 8360 Kbytes.




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