Thorough understanding of complex model systems requires the characterisation of processes in different cell types of an organism. This can be achieved with high-throughput spatial transcriptomics at a large scale. However, for plant model systems this is still challenging as suitable transcriptomics methods are sparsely available. Researchers at the John Innes Centre have developed GaST-seq (Grid-assisted, Spatial Transcriptome sequencing), an easy to adopt, micro-scale spatial-transcriptomics workflow that allows to study expression profiles across small areas of plant tissue at a fraction of the cost of existing sequencing-based methods.
The researchers compare the GaST-seq method with widely used library preparation methods (Illumina TruSeq). In spatial experiments they show that the GaST-seq method is sensitive enough to identify expression differences across a plant organ. They further assess the spatial transcriptome response of Arabidopsis thaliana leaves exposed to the bacterial molecule flagellin-22, and show that with eukaryotic (Albugo laibachii) infection both host and pathogen spatial transcriptomes are obtained.
Overview of the GaST-seq workflow
a tissue sections of approximately 1 mm2 size are mechanically extracted (e.g. a cross-section of a leaf) and after mRNA extraction (b) prepared into uniquely barcoded Illumina sequencing libraries. After c Illumina sequencing d transcript specific, spatial expression data can be assessed and analysed