Details

Autor(en) / Beteiligte

• Junker, Jan Philipp
• Noël, Emily S.
• Guryev, Victor
• Peterson, Kevin A.
• Shah, Gopi
• Huisken, Jan
• McMahon, Andrew P.
• Berezikov, Eugene
• Bakkers, Jeroen
• van Oudenaarden, Alexander

Titel

Genome-wide RNA Tomography in the Zebrafish Embryo

Ist Teil von

• Cell, 2014-10, Vol.159 (3), p.662-675

Ort / Verlag

United States: Elsevier Inc

Erscheinungsjahr

2014

Quelle

MEDLINE

Beschreibungen/Notizen

• Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. Although genome-wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes, they are unable to yield spatially resolved information in embryos or tissues. Microscopy-based approaches, using in situ hybridization, for example, can provide spatial information about gene expression, but are limited to analyzing one or a few genes at a time. Here, we present a method where we combine traditional histological techniques with low-input RNA sequencing and mathematical image reconstruction to generate a high-resolution genome-wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. Importantly, our technique enables searching for genes that are expressed in specific spatial patterns without manual image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. [Display omitted] •A method for spatially resolved transcriptomics in 3D using standard lab equipment•Genome-wide resource of 3D zebrafish expression patterns at three embryonic stages•Identification of expression patterns, including genes with unknown function•Search for expression patterns without the need for annotation of anatomical terms An approach that combines histology with RNA sequencing and mathematical modeling allows for the construction of a genome-wide 3D atlas of gene expression in the developing zebrafish embryo.