The Visium Spatial Gene Expression for FFPE 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 Spatial Gene Expression for FFPE Solution.
- Illumina® NovaSeq
- Illumina® NextSeq 500/550
- Illumina® NextSeq 2000
- Illumina® MiSeq*
- Illumina® iSeq 100*
Dual-Indexed Sequencing Run: Visium Spatial Gene Expression for FFPE 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 for FFPE Libraries
Minimum Sequencing Depth: We recommend a minimum of 25k read pairs per spot covered with tissue. To calculate this, first estimate the % of capture area covered by the tissue section based upon the tissue 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 25,000 read pairs/spot
Example calculation for 60% tissue coverage: (0.60 x 5,000 total spots) x 25,000 read pairs/spot = 75 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.
|Read||Read 1||i7 Index||i5 Index||Read 2|
|Purpose||Spatial Barcode, UMI||Sample Index||Sample Index||Insert|
** 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.