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| Status |
Public on Sep 01, 2017 |
| Title |
The Drosophila Embryo at Single-Cell Transcriptome Resolution |
| Organisms |
Drosophila melanogaster; Drosophila virilis |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
By the onset of morphogenesis, Drosophila embryos consist of about 6000 cells that express distinct gene combinations. Here, we used single-cell sequencing of precisely staged embryos and devised DistMap, a computational mapping strategy to reconstruct the embryo and to predict spatial gene expression approaching single-cell resolution. We produce a virtual embryo with about 8000 expressed genes per cell. Our interactive “Drosophila-Virtual-Expression-eXplorer” (DVEX) database generates three-dimensional virtual in situ hybridizations and computes gene expression gradients. We used DVEX to uncover patterned expression of transcription factors and long noncoding RNAs, as well as signaling pathway components. Spatial regulation of Hippo signaling during early embryogenesis suggests a mechanism for establishing asynchronous cell proliferation. Our approach is suitable to generate transcriptomic blueprints for other complex tissues.
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| Overall design |
Single cell transcriptomics of the early Drosophila embryo were generated using Drop-seq
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| Contributor(s) |
Karaiskos N, Wahle P, Kocks C, Rajewsky N, Zinzen R |
| Citation(s) |
28860209 |
| |
| Submission date |
Feb 17, 2017 |
| Last update date |
Dec 09, 2019 |
| Contact name |
Nikos Karaiskos |
| E-mail(s) |
[email protected]
|
| Organization name |
Max Delbrück Center for Molecular Medicine
|
| Lab |
Systems Biology of Gene Regulatory Elements
|
| Street address |
Hannoversche Str. 28
|
| City |
Berlin |
| ZIP/Postal code |
10115 |
| Country |
Germany |
| |
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| Platforms (3) |
| GPL19132 |
Illumina NextSeq 500 (Drosophila melanogaster) |
| GPL20240 |
Illumina NextSeq 500 (Drosophila virilis) |
| GPL23079 |
Illumina NextSeq 500 (Drosophila melanogaster; Drosophila virilis) |
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| Samples (9)
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| Relations |
| BioProject |
PRJNA375756 |
| SRA |
SRP100163 |
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