ZFIN ID: ZDB-PUB-160725-21
Tomo-seq: A method to obtain genome-wide expression data with spatial resolution
Kruse, F., Junker, J.P., van Oudenaarden, A., Bakkers, J.
Date: 2016
Source: Methods in cell biology   135: 299-307 (Chapter)
Registered Authors: Bakkers, Jeroen
Keywords: Embryo, Gene expression, Patterning, RNA-seq, Zebrafish
MeSH Terms:
  • Animals
  • Embryonic Development/genetics*
  • Gene Expression Profiling/methods
  • Genome/genetics*
  • In Situ Hybridization/methods*
  • Sequence Analysis, RNA/methods*
  • Zebrafish/genetics
PubMed: 27443932 Full text @ Meth. Cell. Biol.
To improve our understanding of pattern formation during development and disease we heavily rely on the identification of novel regulators and pathways. While RNA sequencing yields genome-wide expression data that suit this purpose, it lacks spatial resolution. Such spatial resolution can be obtained by microscopy-based methods like in situ hybridization, but these fail to provide information on more than a few genes at a time. Here, we describe tomo-seq, a technique that combines the advantages of the above-mentioned approaches and provides genome-wide expression data with spatial information. The tomo-seq technique is based on cryosectioning of an embryo or tissue of interest and performing RNA-seq on individual sections. Using this method, we have generated genome-wide transcriptomics with high spatial resolution of the whole zebrafish embryo at various stages of development (Junker et al., 2014) and of adult zebrafish hearts after injury.