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Visium Spatial Gene Expression for FFPE: RNA-templated Ligation Probe Design

  • CG000437_TechNote_RTLProbeDesign_RevA.pdf

    Technical Note, CG000437


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The sequestration and degradation of RNA that occurs in formaldehyde fixed paraffin embedded (FFPE) tissues presents a major challenge to transcriptomic analyses. The Visium Spatial Gene Expression for FFPE assay overcomes traditional FFPE limitations by avoiding reliance on the polyA tail of transcripts or the need for extended reverse transcription and template switching. Instead, Visium Spatial Gene Expression for FFPE uses a highly specific RNA-templated ligation probe based strategy to assay protein-coding RNA expression across the whole transcriptome and map the expression of each transcript to its spatial location in the tissue. This Technical Note describes highly specific 10x Genomics probes for maximum capture efficiency from FFPE samples, for use in the Visium Spatial Gene Expression for FFPE assay.

Document Type
Technical Note

Last Modified
October 7, 2021