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.
Compatible Sequencers:
- Illumina® NovaSeq 6000
- Illumina® NextSeq 2000
- Illumina® NovaSeq X Series
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: The minimum sequencing depth for Visium HD 6.5 mm is 275 million read pairs per fully-covered Capture Area. The recommended minimum sequencing depth was chosen because it achieved >50% sequencing saturation for >50% formalin fixed, paraffin embedded (FFPE) tissues tested at 10x Genomics. To achieve >50% saturation for >50% of fresh frozen (FF) tissues tested by 10x Genomics, 700 million read pairs per fully-covered Capture Area were required. To achieve >50% saturation for >50% of the Fixed Frozen (FxF) tissues tested by 10x Genomics, 500 million read pairs per fully-covered Capture Area were required. Please refer to the Visium HD Spatial Gene Expression Reagent Kits User Guide (CG001679) “Sequencing Depth” section for additional information.
The minimum sequencing depth for Visium HD, 11 mm is 825 million read pairs per fully-covered Capture Area for FFPE, 2.1 B+ read pairs per fully-covered 11 mm Capture Area for Fresh Frozen, and 1.5 B+ reads pairs per fully-covered 11 mm Capture Area for Fixed Frozen tissue types.
10x Genomics recommends calculating the minimum sequencing depth for libraries by multiplying the percentage of the Capture Area covered by tissue by 275 million read pairs for 6.5 mm slides and 825 million for 11 mm Visium HD slides for FFPE samples. For example, a 6.5 mm Capture Area that is 50% covered tissue would require at least 137 million read pairs (0.50 X 275,000,000).