Xenium In Situ Chemistry

High-performance in situ gene expression

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Close-up fluorescent image of FFPE human breast cancer tissue sample with labeled RNAs

Highly sensitive & specific padlock probe chemistry

Only commercial in situ platform to use a padlock probe rolling circle amplification chemistry. This powerful approach allows:

  • High sensitivity across a broad range of expression, including low expressing transcripts.
  • Recognition of short or highly degraded transcripts (i.e. FFPE) without requiring a large number of probes per gene.
  • Tunable sensitivity so that highly expressed transcripts can be included with minimal impact on performance.
  • The ability to distinguish between transcripts with high homology, such as isoforms.
  • Steps 1 & 2: Dual target recognition & hybridization

    Both probe arms must stably hybridize to their target. If only one arm hybridizes, the probe is unstable and will be washed off in the post hybridization wash. The padlock probes also contain a gene-specific barcode sequence that is used to generate a unique optical signature of each transcript.
  • Step 3: Probe ligation

    Only when both probe arms are stably hybridized to the target with a perfect match does proximal probe ligation occur. Partially bound or mis-matching probes are not ligated and cannot be amplified.
  • Step 4: Rolling circle amplification (RCA)

    Only ligated probes are amplified, enriching for true target recognition events and suppressing off-target events. The RCA approach creates a robust and strong signal allowing single probe detection.
  • On-instrument detection & decoding

    After the off-instrument chemistry workflow is completed the slides are loaded onto the Xenium Analyzer for transcript detection. The amplified products in the samples undergo successive rounds of fluorescent probe hybridization, imaging, and removal. An optical signature specific to each gene is generated, enabling identification of the target gene. Finally, a spatial map of the transcripts is built across the entire tissue section.

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The end-to-end Xenium platform

Xenium In Situ Analyzer

Simple design and interface plus fast run times and on-instrument analysis combine for world-class in situ profiling.

Xenium In Situ reagents and panels

Choose from a diverse menu of curated panels, customizable to fit your research needs.

Data visualization

Xenium Explorer provides off-instrument interactive visualization, simplified data QC, and exploration of subcellular readouts.

Dedicated team of spatial experts

Get the help you need from our expert support team, reachable by phone or email.

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