RNA Tomography for Spatially Resolved Transcriptomics (Tomo-Seq)

  • Karoline Holler
  • Jan Philipp JunkerEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1920)


Embryonic development is heavily dependent on temporally and spatially restricted gene expression. Spatially resolved measurements of gene expression are therefore crucial for identifying novel regulators and the understanding of their function. However, in situ methods do not resolve global gene expression, and sequencing-based methods usually do not provide spatial information. Here, we describe tomo-seq, a method that combines classical histological sectioning of embryos or tissues with a highly sensitive RNA-sequencing technique. Application of tomo-seq to zebrafish embryos allows reconstructing the spatial gene expression of thousands of genes.

Key words

mRNA sequencing Local gene expression Spatial transcriptomics Developmental patterning Gene expression mapping Morphogen gradients 


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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Berlin Institute for Medical Systems Biology, MDC BerlinBerlinGermany

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