Spatial Omics Solutions for Plant Research

Spatial Omics Solutions for Plant Research

The study of specific tissue structural domains and their interactions is essential for a comprehensive understanding of the function of biological systems, including a wide variety of plant species. Plant tissues and cells face many special challenges compared to mammalian tissues, including plant cell walls, vesicles, chloroplasts, and secondary metabolites. These features require different manipulation procedures and often need to be optimized for species or tissue specificity.

Functional aspects of plant growth, development, biochemistry, and physiology are also ultimately derived from underlying gene expression programs that are actively regulated in different organs and tissues. Specific molecular conditions exist at every morphological level throughout the organism, organ, tissue, and cell. Therefore spatial resolution, high resolution, and high throughput analysis of plant tissues are essential.

How we provide spatial omics solutions in plant research

CD Genomics offers an integrated solution of spatial transcriptomics combined with histological imaging and RNA sequencing to simultaneously quantify and localize gene expression in plant tissues. We do this by placing frozen sections on arrays coated with reverse transcription oligonucleotide (dT) primers that have unique positional barcodes. The protocol we provide has been validated and applied in a wide range of herbaceous and woody plant model systems, including Arabidopsis thaliana, Populus tremula, and Picea abies.

Spatially resolved transcriptome profiling in plants.Figure 1. Spatially resolved transcriptome profiling in plants. (Giacomello, S., et al., 2017)

General analysis procedure

  • Slice fixation. Use less intense fixation to prevent irreversible attachment.
  • Staining and permeabilization. Stain to preserve and visualize plant morphology and structure, and image. Enzymatic permeabilization is performed for each tissue type.
  • Local capture of mRNA and reverse transcription. The capture of secondary metabolites is an additional step during permeabilization and cDNA synthesis.
  • Tissue Removal. Use an enzyme mixture to degrade tissue sections without interfering with the captured gene expression information.
  • Release mRNA-cDNA hybrids. Perform library preparation and sequencing.
  • Combine tissue section morphology with barcoded gene expression data. Provide spatially resolved transcriptomics data for spatial gene expression studies.

We do it better

CD Genomics offers an integrated solution that enables high-throughput and spatially resolved transcriptomics analysis in plant tissues. It has the distinct advantages of high biological technical reproducibility, high specificity, accuracy, and low false-positive rate. We can directly detect gene expression in tissue sections while preserving histological information, enabling its application to a broader range of species. You can derive accurate gene expression patterns using the optimized spatial transcriptomics protocols we provide. Combined with the corresponding morphological information, you can link gene expression profiles to cellular and developmental processes in plant tissues to address a wider range of botanical research questions.


  1. Giacomello, S., et al., (2017). "Spatially resolved transcriptome profiling in model plant species." Nature Plants. 3, 17061.
For research use only, not intended for any clinical use.

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