Visium probe sets are bundled with the Space Ranger software. Both Space Ranger and individual probe sets can be downloaded here.

Visium Human Transcriptome Probe Set v2.1 is an updated reference for use with the probes in Visium Human Transcriptome Probe Kit v2, Small PN-1000466

Probe Set Contents

18,530 genes targeted by 54,018 probes.
- 398 (2.1%) of these genes (targeted by 499 probes) are excluded by default due to predicted off-target activity to a different gene. See the probe filter section of the Space Ranger algorithms overview for more details.
- 18,132 genes (targeted by 53,519 probes) are present in the final filtered output.
- Some reagent lots may include a small number of probes whose ID includes the prefix DEPRECATED and are always excluded from analysis. Please contact support@10xgenomics.com with any questions.

The gene_id information is included in the probe set reference CSV file.

Accompanying Probe Set Files

Visium Human Transcriptome Probe Set v2.1 - Probe Set Reference CSV file
Visium Human Transcriptome Probe Set v2.1 - BED file
Visium Human Transcriptome Probe Set v2.1 - Probe Off-target CSV file
Visium Human Transcriptome Probe Set v2.1 - Probe Set Metadata TSV file

These files are downloadable from the software downloads section.

For details on the file formats, see the probe set file descriptions.

Associated Part Numbers

Visium Human Transcriptome Probe Kit v2, Small PN-1000466