10x Genomics Support/Visium HD Spatial Gene Expression/Documentation/Sequencing/

Sequencing Requirements for Visium HD Spatial Gene Expression

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

Please note that Dual Index Kit TS, Set A (PN-1000251) is required for use with the Visium HD Spatial Gene Expression Solution.

Supported Sequencers:

  • Illumina® NovaSeq 6000
  • Illumina® NextSeq 2000

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

PhiX Spike-In Recommendations: 1%

Visium HD Spatial Gene Expression Libraries

Minimum Sequencing Depth: We recommend a minimum of 275 million read pairs per fully covered capture area with tissue. To calculate this, first estimate the % of capture area covered by the tissue section based upon the CytAssist image. Then use the following formula to calculate the recommended sequencing depth:

• Minimum sequencing depth = (275 million read pairs * fraction of capture area covered with tissue)

Example calculation for 60% tissue coverage: (275,000,000 * 0.60) = 165 million total read pairs for that sample

ReadRead 1i7 Indexi5 IndexRead 2
PurposeUMI, Spatial BarcodeSample IndexSample IndexInsert

** Shorter reads than indicated above can lead to decreased application performance, particularly for read 2 which is aligned to the reference. Sample index reads must not be shorter than indicated. Any read can be longer than recommended.

Document Type

Last Modified
January 23, 2024