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Sample GSM10928 Query DataSets for GSM10928
Status Public on Dec 31, 2003
Title Larval_c
Sample type RNA
 
Channel 1
Source name total RNA from larvae 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
1 900 1020 100 39982 34716 12775 2183 2190 687 98 98 0 65535 55251 20523 1395 1728 1655 97 93 76 0.589 0.604 0.616 0.681 2.259 0.544 0.744 80 393 101939 86389 -0.763 37799 64140 32533 53856 -75 -0.727379545
2 1040 1020 100 1442 1471 700 1874 1903 544 7 2 0 1078 1217 613 1221 1377 1320 2 0 0 3.021 100.75 1.272 1.582 3.48 13.231 0.002 80 264 -575 -407 1.595 -432 -143 -403 -4 -75 6.654636029
3 1180 1020 100 1403 1439 619 1704 1751 568 7 1 0 1145 1168 539 1158 1214 531 16 5 0 23.154 -26.5 0.966 1.1 3.582 2.006 0.03 80 257 -314 -255 4.533 -301 -13 -265 10 -75 4.727920455
4 1320 1020 100 1525 1469 685 1656 1715 574 15 2 0 933 971 498 1175 1258 730 3 0 0 0.541 0.917 1.425 1.341 3.859 0.318 0.286 80 252 -373 -391 -0.885 -131 -242 -187 -204 -75 -0.125006361
5 1460 1020 100 1912 2825 2248 1675 1746 571 36 25 0 1555 2172 1627 1205 1283 734 36 21 0 0.677 1.189 0.95 0.826 3.711 1.512 0.471 80 254 587 2117 -0.562 237 350 1150 967 -75 0.249748715
6 1600 1010 100 2693 3147 1660 1706 1791 685 58 38 0 1752 2407 1661 1243 1302 523 50 35 0 1.939 1.238 1.136 1.286 3.649 1.103 0.386 80 260 1496 2605 0.955 987 509 1441 1164 -75 0.308011315
7 1740 1010 100 4684 10358 10366 1701 1768 688 90 75 0 3609 7907 7742 1181 1256 536 90 80 0 1.229 1.287 1.169 1.193 2.894 1.544 0.588 80 252 5411 15383 0.297 2983 2428 8657 6726 -75 0.364012054
8 1880 1010 100 13955 23798 23087 1625 1816 1053 91 78 16 5477 18842 22013 1160 1352 1072 81 65 10 2.856 1.254 1.402 1.747 2.858 1.128 0.669 80 259 16647 39855 1.514 12330 4317 22173 17682 -75 0.326537348
9 2020 1010 100 1441 1491 478 1606 1758 1049 1 0 0 1086 1181 583 1106 1311 1077 3 2 0 8.25 -1.533 0.994 0.957 3.944 0.361 0.147 80 249 -185 -40 3.044 -165 -20 -115 75 -50 0.616357697
10 2160 1010 100 1546 1564 587 1619 1656 506 17 2 0 1148 1165 507 1134 1193 472 21 5 0 -5.214 -1.774 0.872 1.251 5.078 1.768 0.025 80 258 -59 -24 Error -73 14 -55 31 -50 0.82700601
11 2300 1010 100 1448 1446 722 1648 1727 549 17 3 0 1116 1186 526 1111 1173 478 20 7 0 -40 -2.693 1.651 1.615 3.423 3.608 0.014 80 260 -195 -127 Error -200 5 -202 75 -50 1.42921423
12 2440 1010 100 1723 1702 579 1500 1589 597 26 3 0 1362 1606 741 1128 1193 582 36 21 0 0.953 0.423 0.7 0.914 4.28 0.471 0.057 80 291 457 680 -0.069 223 234 202 478 -50 -1.241270432
13 2560 990 60 2414 2653 878 1448 1547 617 78 43 0 1787 1888 682 1087 1100 549 71 28 0 1.38 1.504 1.108 1.195 2.535 2.029 0.07 32 116 1666 2006 0.465 966 700 1205 801 0 0.588804567
14 2720 1000 100 1115 1185 638 1617 1705 700 3 1 0 859 1008 571 1088 1401 3753 0 0 0 2.192 5.4 1.589 1.263 3.995 0.046 0.201 80 310 -731 -512 1.132 -502 -229 -432 -80 -50 2.432959407
15 2860 1000 100 1494 1683 1128 1649 1689 573 27 13 0 1256 1342 602 1075 1188 598 26 8 0 -0.856 0.127 2.066 1.685 4.149 1.668 0.106 80 252 26 301 Error -155 181 34 267 -50 -2.977099598
16 3000 1000 100 1724 1732 497 1739 1768 596 11 2 0 1325 1365 500 1286 1324 608 15 3 0 -0.385 -0.089 1.333 1.165 4.308 0.849 0.012 80 258 24 72 Error -15 39 -7 79 -50 -3.490050854
17 3140 1000 100 1917 1923 643 1968 1984 551 17 5 0 1446 1472 489 1439 1489 557 15 2 0 -7.286 -1.364 1.17 1 3.664 2.018 0.01 80 257 -44 -12 Error -51 7 -45 33 -50 0.447843644
18 3280 1000 100 2401 2393 631 2194 2271 717 17 2 0 1697 1708 574 1597 1647 566 16 3 0 2.07 1.793 1.047 1.516 3.923 0.004 0 80 262 307 310 1.05 207 100 199 111 -50 0.842375488
19 3420 1000 100 2354 2359 623 1974 2163 738 28 5 0 1701 1744 582 1505 1579 663 21 3 0 1.939 1.611 0.962 0.865 3.544 3.15 0.005 80 241 576 624 0.955 380 196 385 239 -50 0.687956494
20 3560 1000 100 2030 2016 629 1845 1913 573 23 5 0 1351 1406 503 1431 1496 628 11 1 0 -2.312 -6.84 1.378 0.858 4.132 0.009 0 80 237 105 146 Error 185 -80 171 -25 -50 2.773996325

Total number of rows: 47616

Table truncated, full table size 8644 Kbytes.




Supplementary data files not provided
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