Spatial transcriptomics

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Gain deeper insights into tissue structure and organization by adding spatial information to your genomics data. By showing which expression profiles occur where, spatial transcriptomics enables you to create detailed maps of healthy and diseased tissue based on mRNA sequence data.

Spatial transcriptomics icon

Many transcriptome studies greatly benefit from spatial information. Macrogen Europe’s spatial transcriptomics service uses 10x Genomics Visium technology to help you create precise mRNA expression maps of your tissue slides.

Our service works as follows: You send us your blocks of formalin-fixed, paraffin-embedded (FFPE) tissue. We will use 10x Visium technology to barcode the mRNA present on the slide in a location-specific manner. We then prepare the libraries and sequence the samples – with the barcodes ensuring that each sequence can be traced back to a location on the slide.

This technology enables you to get an unprecedented view of the organization of complex tissues by combining histology with spatial mRNA sequencing data. It can also deliver unique data on disease progression, for example the way in which new mutations appear and organize in cancer tissue.

Library preparation kits

  • 10x Genomics Visium

Sequencing platforms

  • Illumina: NovaSeq 6000, HiSeq

Data analysis

  • Cell clustering and classification
  • Analysis of spatially variable features
  • Finding the top expressed cluster biomarkers
  • Finding differentially expressed genes (DEGs) between two groups for each cluster
  • Functional annotations