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The Drosophila embryo at single cell transcriptome resolution

Item Type:Preprint
Title:The Drosophila embryo at single cell transcriptome resolution
Creators Name:Karaiskos, N. and Wahle, P. and Alles, J. and Boltengagen, A. and Ayoub, S. and Kipar, C. and Kocks, C. and Rajewsky, N. and Zinzen, R.P.
Abstract:Drosophila is a premier model system for understanding the molecular mechanisms of development. By the onset of morphogenesis, ~6000 cells express distinct gene combinations according to embryonic position. Despite extensive mRNA in situ screens, combinatorial gene expression within individual cells is largely unknown. Therefore, it is difficult to comprehensively identify the coding and non-coding transcripts that drive patterning and to decipher the molecular basis of cellular identity. Here, we single-cell sequence precisely staged embryos, measuring >3100 genes per cell. We produce a ‘transcriptomic lueprint’ of development - a virtual embryo where 3D locations of sequenced cells are confidently identified. Our “Drosophila -Virtual-Expression-eXplorer” performs virtual in situ hybridizations and computes expression gradients. Using DVEX, we predict spatial expression and discover patterned lncRNAs. DEVX is sensitive enough to detect subtle evolutionary changes in expression patterns between Drosophila species. We believe DVEX is a prototype for powerful single cell studies in complex tissues.
Publisher:Cold Spring Harbor Laboratory Press
Article Number:117382
Date:17 March 2017
Official Publication:https://doi.org/10.1101/117382
Related to:
https://edoc.mdc-berlin.de/16746/Final version

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