PUBLICATION

Genome-wide RNA Tomography in the Zebrafish Embryo

Authors
Junker, J.P., Noël, E.S., Guryev, V., Peterson, K.A., Shah, G., Huisken, J., McMahon, A.P., Berezikov, E., Bakkers, J., van Oudenaarden, A.
ID
ZDB-PUB-141125-5
Date
2014
Source
Cell   159: 662-75 (Journal)
Registered Authors
Bakkers, Jeroen, Guryev, Victor, Huisken, Jan, McMahon, Andrew, Noël, Emily
Keywords
none
Datasets
GEO:GSE59873
MeSH Terms
  • Animals
  • Embryo, Nonmammalian/metabolism*
  • Gene Expression Profiling*
  • Imaging, Three-Dimensional
  • Sequence Analysis, RNA*
  • Tomography/methods*
  • Zebrafish/embryology*
PubMed
25417113 Full text @ Cell
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.
Genes / Markers
Figures
Show all Figures
Expression
Phenotype
Mutation and Transgenics
Human Disease / Model Data
Sequence Targeting Reagents
Fish
Antibodies
Orthology
Engineered Foreign Genes
Mapping
Errata and Notes