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| Status |
Public on Jul 06, 2005 |
| Title |
wesle-affy-droso-91201 |
| Organism |
Drosophila melanogaster |
| Experiment type |
Expression profiling by array
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| Summary |
Neurogenesis in all animals is dependent on the function of different Notch receptors and their ligands. Drosophila is an excellent system to understand the principles and mechanisms governing this conserved process. Since the different Notch receptors and their ligands are expressed and function in the same cells, or overlapping stages of neurogenesis, and since there is extensive feedback regulation between them, it is very difficult to identify the target genes of each receptor or ligand in vivo. We have developed an excellent model system based on Drosophila cultured Schneider (S2) cells that faithfully represents in vivo activities. We propose microarray analysis with this system to identify the suite of putative target genes that are independently regulated by each protein in our study. We also expect to gather information about the signaling pathways used by the different receptors and their ligands, and develop hypotheses for testing during neurogenesis in vivo. These efforts will contribute significantly towards achieving the Specific Objectives of the grant parent (R01 NS043122, ‘Different Notch Receptors in Drosophila Development’).
To determine the sets of genes regulated by NFull, NDCterm, and Delta through microarray analyses of RNA extracted from S2 cells expressing these proteins that were treated or not treated with S2 cells expressing their ligand or receptor.
Neurogenesis in Drosophila initiates within clusters of cells that have acquired the potential to become neuronal cells. The action of the full-length Notch receptor, NFull, and the ligand Delta make the majority of these cells to differentiate the epidermis. The action of a truncated Notch receptor, NDCterm, and Delta make the remaining cells to differentiate the nervous system. We have recently shown that Delta also has activities independent of Notch receptors that promote neurogenesis. We will test the hypothesis that NFull would promote expression of epidermal differentiation genes while NDCterm and Delta that would promote expression of neuronal differentiation genes. We will also test the hypothesis that genes regulated by NDCterm and Delta would be the same or would complement each other’s activities.
We request the Microarray Consortium to process our samples and help us analyze the data. We will select a set of genes for validation by northern blotting or QPCR on similar samples of RNA from S2 cells and in vivo materials. We have available in the lab fly stocks carrying mutants (nulls) alleles or inducible transgenes for all the proteins used in this microarray experiment. Funds from the parent grant will be used for these in vitro and in vivo validation experiments. This project proposal is a part of the Supplementary Proposal approved by NIH/NINDS. Project proposals covering other parts, the effects on secreted ligands of Scabrous and Wingless, will be submitted when we have ready the RNAs from these experiments.
Keywords: other
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| Overall design |
S2 cells or S2 cell lines expressing NFull, NDCterm, Delta, and Delta lacking the intracellular domain (DlDI) were mixed and allowed to interact for 45 minutes. RNAs were extracted from these samples and quantified. Six RNA samples were extracted from the following treatments (the cell types mixed are separated by a slash).
(1) S2-NFull/S2; (2) S2-NFull/S2-Dl; (3) S2/S2; (4) S2/S2-Dl; (5) S-NFull/S2-DlDI; (6) S2/S2- DlDI; (7) S2/S2-NDCterm; (8) S2- NDCterm /S2-Dl.
Two independent samples were pooled to yield triplicates for each treatment. Genes responding to the activities of different proteins can be identified using the following contrasts or comparisons. Contrasts/comparison is indicated by versus (vs).
1. Genes responding to NFull treated with Delta: [S2-NFull/S2 vs S2-NFull/S2-Dl] - [S2/S2 vs S2-Dl]- [S2/S2-NFull vs S2-NFull/S2-DlDI] - [S2/S2 vs S2/S2- DlDI]
2. Genes responding to NDCterm treated with Delta: [S2-NDCterm/S2 vs S2-NDCterm/S2-Dl] - [S2/S2 vs S2/S2-Dl]
3. Genes responding to Delta: [S2/S2-Dl vs S2/S2] - [S2/S2 vs S2/S2- DlDI]
4. Genes responding to Delta treated with NFull: [S2-NFull/S2-Dl vs S2-NFull/S2- DlDI] - [S2/S2 vs S2/S2- DlDI] -[S2/S2-Dl vs S2/S2]
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| Contributor(s) |
Wesley CS |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| Submission date |
Jul 01, 2005 |
| Last update date |
Aug 28, 2018 |
| Contact name |
Winnie Liang |
| E-mail(s) |
wliang@tgen.org
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| Organization name |
Translational Genomics
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| Street address |
445 N. Fifth Street
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| City |
Phoenix |
| State/province |
AZ |
| ZIP/Postal code |
85012 |
| Country |
USA |
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| Platforms (1) |
| GPL1322 |
[Drosophila_2] Affymetrix Drosophila Genome 2.0 Array |
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| Samples (24)
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| GSM53388 |
Late Embryonic tissue, epidermal: S2/S2-DI-I_3_e1_le1 |
| GSM53389 |
Late Embryonic tissue, epidermal: S2-NdCterm/S2-DI_2_e1_le1 - 1 |
| GSM53390 |
Late Embryonic tissue, epidermal: S2/S2-DI_2_e1_le1 |
| GSM53391 |
Late Embryonic tissue, epidermal: S2-NdCterm/S2-DI_3_e1_le1 |
| GSM53392 |
Late Embryonic tissue, epidermal: S2-NFull/S2-DI-I_1_e1_le1 - 1 |
| GSM53393 |
Late Embryonic tissue, epidermal: S2/S2_1_e1_le1 |
| GSM53394 |
Late Embryonic tissue, epidermal: S2-NdCterm/S2-DI_1_e1_le1 |
| GSM53395 |
Late Embryonic tissue, epidermal: S2/S2-NdCterm_1_e1_le1 |
| GSM53396 |
Late Embryonic tissue, epidermal: S2/S2_3_e1_le1 |
| GSM53397 |
Late Embryonic tissue, epidermal: S2-NFull/S2_3_e1_le1 |
| GSM53398 |
Late Embryonic tissue, epidermal: S2/S2-DI-I_2_e1_le1 |
| GSM53399 |
Late Embryonic tissue, epidermal: S2-NFull/S2_1_e1_le1 - 1 |
| GSM53400 |
Late Embryonic tissue, epidermal: S2-NFull/S2-DI-I_2_e1_le1 - 1 |
| GSM53401 |
Late Embryonic tissue, epidermal: S2/S2-D1_1_e1_le1 |
| GSM53402 |
Late Embryonic tissue, epidermal: S2-NFull/S2-DI_2_e1_le1 |
| GSM53403 |
Late Embryonic tissue, epidermal: S2/S2_2_e1_le1 |
| GSM53404 |
Late Embryonic tissue, epidermal: S2/S2-NdCterm_3_e1_le1 |
| GSM53405 |
Late Embryonic tissue, epidermal: S2-NFull/S2-DI-I_3_e1_le1 - 1 |
| GSM53406 |
Late Embryonic tissue, epidermal: S2/S2-DI_3_e1_le1 |
| GSM53407 |
Late Embryonic tissue, epidermal: S2-NdCterm/S2-DI_2_e1_le1 - 2 |
| GSM53408 |
Late Embryonic tissue, epidermal: S2-NFull/S2_1_e1_le1 - 2 |
| GSM53409 |
Late Embryonic tissue, epidermal: S2-NFull/S2-DI-I_1_e1_le1 - 2 |
| GSM53410 |
Late Embryonic tissue, epidermal: S2-NFull/S2-DI-I_2_e1_le1 - 2 |
| GSM53411 |
Late Embryonic tissue, epidermal: S2-NFull/S2-DI-I_3_e1_le1 - 2 |
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| Relations |
| BioProject |
PRJNA92527 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE2863_RAW.tar |
75.7 Mb |
(http)(custom) |
TAR (of CEL) |
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