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Sample GSM73411 Query DataSets for GSM73411
Status Public on Sep 20, 2006
Title GOF_stage13_replicate4
Sample type RNA
 
Channel 1
Source name stage13 embryo wt
Organism Drosophila melanogaster
Characteristics pooled wildtypcontrol from Bloomington stock B5446 and Gal4-driver MZ1060
Extracted molecule polyA RNA
Label Cy3
 
Channel 2
Source name stage13 embryo ectopic expression
Organism Drosophila melanogaster
Characteristics ectopic expression of glial cells missing with the Gal4-driver MZ1060
Extracted molecule polyA RNA
Label Cy5
 
 
Description Cy5/Cy3 labeled RNA was co-hybridized onto a QMT Amino (Quantifoil) glass slide. For wt control we pooled mRNA from UAS-gcm stock B5446 and Gal4-line MZ1060 in equal amounts.
Sample collection:
Embryo samples from the MZ1060 x B5446, B5446 and MZ1060 were collected in parallel as one-hour egg lays at 25°C, which were allowed to develop to the desired stage at 29°C.
First total RNA was isolated from all samples using the Rneasy Kit and then mRNA was isolated using the Oligotex Kit (both Qiagen,Hilden,Germany)
Microarray hybridization:
At least four independent experiments were performed for each of the 8 different stages
(embryonic stage 9 to 16) in competitive hybridizations against the pooled wildtype control of the same stage.
At least one dye swap was included in each of the repetitions.
We used the indirect labeling method, with 4,5µg random hexamer primer and 0,75µg Poly-dT primer ( both Invitrogen, Karlsruhe, Germany) added to 1µg mRNA.
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 over night.
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 5.0; 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.
Data processing Genepix 5.0/MChips software
 
Submission date Sep 07, 2005
Last update date Sep 19, 2006
Contact name Angela Becker
E-mail(s) angibeck@gmx.de
Organization name University of Mainz
Department Institute of Genetics
Lab AG Technau
Street address Becherweg 32
City Mainz
ZIP/Postal code 55099
Country Germany
 
Platform ID GPL517
Series (1)
GSE3257 Time course microarray approach comparing the ectopic expression and loss-of-function of gcm to wildtype

Data table header descriptions
ID_REF
MChips_ID MChips_ID for inhouse datawarehouse system
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 pixel intensity of feature for Cy3 channel
F532 Mean Mean pixel intensity of feature for Cy3 channel
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)
F632 Median - B632
F532 Median - B532
F632 Mean - B632
F532 Mean - B532
Sum of Medians (632/532)
Sum of Means (632/532)
F Pixels
B Pixels
VALUE log2 ratio (log2 of ratio of Ratio of Means (632/532) Not normalized!

Data table
ID_REF MChips_ID 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) F632 Median - B632 F532 Median - B532 F632 Mean - B632 F532 Mean - B532 Sum of Medians (632/532) Sum of Means (632/532) F Pixels B Pixels VALUE
1 01_61_03_12 4880 5250 100 1349 1380 437 1482 1522 425 10 3 0 299 359 309 471 498 373 8 0 0 0.773 0.911 1.078 1.126 4.440 4.607 0.008 -133 -172 -102 -112 -305 -214 80 380 -0.371
2 01_61_05_12 5010 5250 100 1433 1454 434 1500 1515 431 13 2 0 528 562 398 480 516 406 20 3 0 -1.396 -0.561 1.319 1.186 4.093 1.219 0.028 -67 48 -46 82 -19 36 80 284 0
3 01_61_07_12 5150 5250 100 1320 1385 463 1429 1435 413 15 3 0 201 296 316 410 453 391 8 1 0 0.522 0.386 1.116 1.351 3.777 10.746 0.002 -109 -209 -44 -114 -318 -158 80 258 -0.938
4 01_61_09_12 5280 5250 100 1303 1371 418 1397 1403 381 17 3 0 334 401 406 480 494 357 15 2 0 0.644 0.329 0.777 0.937 2.968 0.151 0.000 -94 -146 -26 -79 -240 -105 80 303 -0.635
5 01_61_11_12 5410 5260 50 2503 2580 987 1582 1598 465 66 50 0 901 984 565 511 507 337 50 33 0 2.362 2.110 1.924 1.801 3.479 3.504 0.130 921 390 998 473 1311 1471 12 93 1.240
6 01_61_13_12 5540 5280 80 7308 6804 2757 1704 1763 524 94 86 0 2647 2491 1348 466 516 403 80 78 0 2.569 2.519 2.471 2.671 2.101 2.483 0.791 5604 2181 5100 2025 7785 7125 52 209 1.361
7 01_61_15_12 5670 5250 80 13053 12663 5113 1665 1795 578 100 98 0 5838 5529 2567 509 551 409 94 92 0 2.137 2.191 2.255 2.362 1.353 2.136 0.940 11388 5329 10998 5020 16717 16018 52 231 1.096
8 01_61_01_24 5790 5260 70 10540 10836 5193 1671 2122 1545 96 84 0 5095 4706 2455 802 879 798 84 78 0 2.066 2.348 2.347 2.609 1.623 2.215 0.912 8869 4293 9165 3904 13162 13069 32 182 1.047
9 01_61_03_24 5950 5260 100 1396 1436 456 1447 1633 1164 1 0 0 514 535 361 647 734 618 2 0 0 0.383 0.098 1.708 1.569 3.918 125.604 0.000 -51 -133 -11 -112 -184 -123 80 336 -1.385
10 01_61_05_24 6080 5260 100 1426 1507 435 1560 1573 460 11 2 0 720 789 478 823 819 430 17 3 0 1.301 1.559 0.844 0.737 2.910 3.361 0.000 -134 -103 -53 -34 -237 -87 80 303 0.380
11 01_61_07_24 6210 5260 100 1474 1497 426 1536 1560 445 10 3 0 903 980 498 910 909 459 21 7 0 8.857 -0.557 0.968 0.811 5.111 0.002 0.000 -62 -7 -39 70 -69 31 80 280 3.147
12 01_61_09_24 6350 5260 100 1658 1634 435 1469 1499 440 25 5 0 831 846 485 848 878 460 15 3 0 -11.118 -82.500 0.775 0.985 5.052 0.551 0.032 189 -17 165 -2 172 163 80 262 0
13 01_61_11_24 6480 5260 100 1600 1656 485 1495 1551 433 25 10 0 991 1028 500 808 831 424 36 11 0 0.574 0.732 0.685 0.599 4.925 0.136 0.000 105 183 161 220 288 381 80 254 -0.801
14 01_61_13_24 6610 5260 100 1527 1505 441 1524 1567 459 16 2 0 896 976 435 887 953 462 21 2 0 0.333 -0.213 1.182 1.216 3.823 2.018 0.013 3 9 -19 89 12 70 80 268 -1.586
15 01_61_15_24 6750 5270 100 1861 2034 756 1605 1642 479 35 17 0 1283 1284 475 1059 1129 475 25 5 0 1.143 1.907 1.101 1.273 4.934 4.896 0.025 256 224 429 225 480 654 80 251 0.193
16 01_62_01_12 6880 5270 100 1487 1471 437 1559 1564 444 10 1 0 548 597 422 807 835 479 6 0 0 0.278 0.419 0.987 0.993 6.290 0.265 0.007 -72 -259 -88 -210 -331 -298 80 262 -1.847
17 01_62_03_12 7020 5270 100 1574 1531 379 1563 1610 474 10 0 0 726 801 401 702 701 412 27 2 0 0.458 -0.323 0.869 0.684 5.795 0.168 0.001 11 24 -32 99 35 67 80 278 -1.127
18 01_62_05_12 7150 5270 100 1509 1540 436 1609 1638 466 13 0 0 616 672 424 672 702 449 17 1 0 1.786 100.000.000 0.974 0.956 3.563 1.898 0.018 -100 -56 -69 0 -156 -69 80 270 0.837
19 01_62_07_12 7280 5270 100 1448 1438 506 1516 1545 409 15 5 0 486 526 377 713 720 435 8 0 0 0.300 0.417 1.180 1.058 3.335 3.479 0.012 -68 -227 -78 -187 -295 -265 80 246 -1.737
20 01_62_09_12 7420 5270 100 1457 1435 403 1462 1489 450 13 0 0 688 737 426 1155 6912 13079 0 0 0 0.011 0.065 0.623 0.552 3.782 0.017 0.034 -5 -467 -27 -418 -472 -445 80 296 -6.506

Total number of rows: 47616

Table truncated, full table size 8586 Kbytes.




Supplementary data files not provided
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