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Sequencing Requirements for Visium Spatial Gene Expression

Sequencing Requirements for Visium Spatial Gene Expression

The Visium Spatial Gene Expression Solution produces spatially barcoded, Illumina® sequencer-ready libraries.

Please note that Dual Index Kit TT, Set A (PN-1000215) is required for use with the Visium Spatial Gene Expression Solution.

Supported Sequencers:

  • Illumina® NovaSeq 6000
  • Illumina® HiSeq 3000/4000
  • Illumina® HiSeq 2500 (Rapid Run and High Output)
  • Illumina® NextSeq 2000
  • Illumina® NextSeq 500/550
  • Illumina® MiSeq*
  • Illumina® iSeq 100*

Dual-Indexed Sequencing Run: Visium Spatial Gene Expression libraries are dual-indexed. We do not recommend sequencing these libraries with a single-index configuration.

PhiX Spike-In Recommendations: 1%

* Recommended for library QC only

Visium Spatial Gene Expression Libraries

Minimum Sequencing Depth: We recommend a minimum of 50k read pairs per spot covered with tissue. To calculate this, first estimate the % of capture area covered by the tissue section based upon the H&E brightfield image. Then use the following formula to calculate the recommended sequencing depth:

• Total sequencing depth = (Coverage Area x total spots on the Capture Area) x 50,000 read pairs/spot

Example calculation for 60% tissue coverage: (0.60 x 5,000 total spots) x 50,000 read pairs/spot = 150 million total read pairs for that sample

Additional guidelines for estimating the number of spots covered: Determining number of spots covered with tissue may be performed visually or by using the Visium Manual Alignment Wizard in Loupe Browser for a more accurate measurement.

ReadRead 1i7 Indexi5 IndexRead 2
PurposeSpatial Barcode, UMISample IndexSample IndexInsert

** Shorter reads than indicated above can lead to decreased application performance. Sample index reads must not be shorter than indicated. Any read can be longer than recommended.

Document Type

Last Modified
August 2, 2023