Genome-wide RNA Tomography in the zebrafish embryo

TY - JOUR

T1 - Genome-wide RNA Tomography in the zebrafish embryo

AU - Junker, Jan Philipp

AU - Noël, Emily S

AU - Guryev, Victor

AU - Peterson, Kevin A

AU - Shah, Gopi

AU - Huisken, Jan

AU - McMahon, Andrew P

AU - Berezikov, Eugene

AU - Bakkers, Jeroen

AU - van Oudenaarden, Alexander

PY - 2014/10/23

Y1 - 2014/10/23

N2 - 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.

AB - 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.

U2 - 10.1016/j.cell.2014.09.038

DO - 10.1016/j.cell.2014.09.038

M3 - Article

C2 - 25417113

SN - 0092-8674

VL - 159

SP - 662

EP - 675

JO - Cell

JF - Cell

IS - 3

ER -