Spatial Transcriptomics

10X Genomics Xenium

The Xenium is an in situ spatial transcriptomics platform with subcellular resolution from 10x Genomics. This technology can map thousands of RNA targets within the same tissue section. These targets are defined by probe panels, which are pre-designed by 10x Genomics or can be custom ordered.

Technology

Both FFPE or fresh frozen sections can be analysed using the Xenium platform. After sample preparation, the Xenium workflow begins with probe panel hybridization. The Xenium platform uses padlock probes with gene-specific barcodes which undergo enzymatic amplification. Then, on the instrument, fluorophore-labelled oligo probes bind to these tags, and through successive imaging rounds an optical signature is generated for precise gene identification in situ. The onboard analysis software ensures that the data is viewable immediately after the run. The data can be processed with many third-party downstream analysis tools. .

Xenium

Xenium Slide

Probe ligation

Dual target recognition & hybridization

Rolling circle amplification (RCA)

Multimodal Segmentation

10X Visium HD and CytAssist

The Visium CytAssist is a compact instrument designed to simplify the Visium workflow by facilitating the transfer of transcriptomic probes from standard glass slides to Visium slides. This enables whole transcriptome spatial profiling insights across your entire tissue section.

CytAssist

Visium HD slide

Visium HD oligos

Technology

The LGTC offers the Visium HD workflow on the CytAssist platform. This workflow is compatible with either human or mouse FFPE sections. The input for this workflow is a 6.5 x 6.5 mm area of interest within the tissue section. The Visium HD technology uses pairs of probe sets covering the whole transcriptome. These probe pairs will hybridize to their complementary target RNA within the tissue section. After adding ligase, the hybridized probes will form a ligation product which will be released from the tissue slides and captured by the Visium HD slide using the CytAssist platform. The Visium HD slides contains a lawn of barcoded oligos spaced in a 2µm x 2µm grid. The captured spatial gene expression libraries are then sequenced using Illumina technology.

Questions?

Contact our specialized team to get tailor-made workflows that fit your research project.