title: Genome-wide RNA Tomography in the zebrafish embryo.
abstract: 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.
authors.affiliation: Hubrecht Institute, KNAW and University Medical Center Utrecht, Cancer Genomics Netherlands, 3584 CT Utrecht, the Netherlands.
authors.forename: Jan Philipp
authors.initials: JP
authors.lastname: Junker
authors.affiliation: Hubrecht Institute, KNAW and University Medical Center Utrecht, Cancer Genomics Netherlands, 3584 CT Utrecht, the Netherlands.
authors.forename: Emily S
authors.initials: ES
authors.lastname: Noël
authors.affiliation: European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, 9713 AV Groningen, the Netherlands.
authors.forename: Victor
authors.initials: V
authors.lastname: Guryev
authors.affiliation: Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of Southern California Keck School of Medicine, Los Angeles, CA 90089, USA.
authors.forename: Kevin A
authors.initials: KA
authors.lastname: Peterson
authors.affiliation: Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany.
authors.forename: Gopi
authors.initials: G
authors.lastname: Shah
authors.affiliation: Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany.
authors.forename: Jan
authors.initials: J
authors.lastname: Huisken
authors.affiliation: Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of Southern California Keck School of Medicine, Los Angeles, CA 90089, USA.
authors.forename: Andrew P
authors.initials: AP
authors.lastname: McMahon
authors.affiliation: European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, 9713 AV Groningen, the Netherlands; Skolkovo Institute of Science and Technology (Skoltech), Novaya Street 100, Skolkovo Moscow Region 143025, Russia.
authors.forename: Eugene
authors.initials: E
authors.lastname: Berezikov
authors.affiliation: Hubrecht Institute, KNAW and University Medical Center Utrecht, Cancer Genomics Netherlands, 3584 CT Utrecht, the Netherlands.
authors.forename: Jeroen
authors.initials: J
authors.lastname: Bakkers
authors.affiliation: Hubrecht Institute, KNAW and University Medical Center Utrecht, Cancer Genomics Netherlands, 3584 CT Utrecht, the Netherlands; Skolkovo Institute of Science and Technology (Skoltech), Novaya Street 100, Skolkovo Moscow Region 143025, Russia. Electronic address: a.vanoudenaarden@hubrecht.eu.
authors.forename: Alexander
authors.initials: A
authors.lastname: van Oudenaarden
mesh_terms: D000818:Animals; D004625:Embryo, Nonmammalian / Q000378:metabolism*; D020869:Gene Expression Profiling; D021621:Imaging, Three-Dimensional; D017423:Sequence Analysis, RNA; D014054:Tomography / Q000379:methods*; D015027:Zebrafish / Q000196:embryology*