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| Status |
Public on Nov 11, 2008 |
| Title |
A combinatorial code for pattern formation in Drosophila oogenesis |
| Organism |
Drosophila melanogaster |
| Experiment type |
Expression profiling by array
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| Summary |
Two-dimensional patterning of the follicular epithelium in Drosophila oogenesis is required for the formation of three-dimensional eggshell structures. Our analysis of a large number of published gene expression patterns in the follicle cells suggests that they follow a simple combinatorial code based on six spatial building blocks and the operations of union, difference, intersection, and addition. The building blocks are related to the distribution of inductive signals, provided by the highly conserved epidermal growth factor receptor and Decapentaplegic
(DPP) pathways. We demonstrate the validity of the code by testing it against a set of patterns obtained in a large-scale transcriptional profiling experiment. Using the proposed code, we distinguish 36 distinct patterns for 81 genes expressed in the follicular epithelium and characterize their joint dynamics over four stages of oogenesis. The proposed combinatorial
framework allows systematic analysis of the diversity and dynamics of two-dimensional transcriptional patterns and guides future studies of gene
regulation.
Keywords: EGFR, BMP, gain/loss-of-function
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| Overall design |
RNA was isolated from hand dissected, stage 9-10 egg chambers. Five genetic backgrounds were profiled including: wild type, EGFR gain of function, EGFR loss of function, BMP gain of function, and BMP loss of function. Three biological replicates were hybridized for each pathway perturbation. The samples were split across two rounds of hybridization. Each round of hybridizations included three biological replicates for wild type:
The first round included EGFR gof, EGFR lof, BMP gof, and wild type controls A1-A3 (GSM313514-16). For these 12 arrays the extraction, labeling, and hybridization steps were done in parallel.
The second round included the BMP lof and wild type controls B1-B3 (GSM313517-19). For these 6 arrays, the extraction, labeling, and hybridization steps were done in parallel.
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| Contributor(s) |
Yakoby N, Bristow CA, Gong D, Schafer X, Lembong J, Zartman JJ, Halfon MS, Schupbach T, Shvartsman S |
| Citation(s) |
19000837 |
| Submission date |
Aug 18, 2008 |
| Last update date |
Jul 06, 2016 |
| Contact name |
Stas Shvartsman |
| E-mail(s) |
stas@princeton.edu
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| Organization name |
Princeton University
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| Department |
Chemical Engineering and LSI Genomics
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| Street address |
Carl Icahn Lab
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| City |
Princeton |
| State/province |
NJ |
| ZIP/Postal code |
08544 |
| Country |
USA |
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| Platforms (1) |
| GPL72 |
[DrosGenome1] Affymetrix Drosophila Genome Array |
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| Samples (18)
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| GSM313517 |
egg chamber wildtype repB1 |
| GSM313518 |
egg chamber wildtype repB2 |
| GSM313519 |
egg chamber wildtype repB3 |
| GSM313520 |
egg chamber EGFR gain of function rep1 |
| GSM313521 |
egg chamber EGFR gain of function rep2 |
| GSM313522 |
egg chamber EGFR gain of function rep3 |
| GSM313523 |
egg chamber EGFR loss of function rep1 |
| GSM313524 |
egg chamber EGFR loss of function rep2 |
| GSM313525 |
egg chamber EGFR loss of function rep3 |
| GSM313526 |
egg chamber BMP gain of function rep1 |
| GSM313527 |
egg chamber BMP gain of function rep2 |
| GSM313528 |
egg chamber BMP gain of function rep3 |
| GSM313529 |
egg chamber BMP loss of function rep1 |
| GSM313530 |
egg chamber BMP loss of function rep2 |
| GSM313531 |
egg chamber BMP loss of function rep3 |
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| Relations |
| BioProject |
PRJNA112951 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE12477_RAW.tar |
29.5 Mb |
(http)(custom) |
TAR (of CEL) |
| Processed data included within Sample table |
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