PUBLICATION
Tomo-seq: A method to obtain genome-wide expression data with spatial resolution
- Authors
- Kruse, F., Junker, J.P., van Oudenaarden, A., Bakkers, J.
- ID
- ZDB-PUB-160725-21
- 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.
Citation
Kruse, F., Junker, J.P., van Oudenaarden, A., Bakkers, J. (2016) Tomo-seq: A method to obtain genome-wide expression data with spatial resolution. Methods in cell biology. 135:299-307.
Abstract
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.
Genes / Markers
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Orthology
Engineered Foreign Genes
Mapping