RT Journal Article SR Electronic T1 The Drosophila Embryo at Single Cell Transcriptome Resolution JF bioRxiv FD Cold Spring Harbor Laboratory SP 117382 DO 10.1101/117382 A1 Nikos Karaiskos A1 Philipp Wahle A1 Jonathan Alles A1 Anastasiya Boltengagen A1 Salah Ayoub A1 Claudia Kipar A1 Christine Kocks A1 Nikolaus Rajewsky A1 Robert P. Zinzen YR 2017 UL http://biorxiv.org/content/early/2017/03/17/117382.abstract AB 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 blueprint’ 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.