Visium probe sets are bundled with the Space Ranger software. Both Space Ranger and individual probe sets can be downloaded here.
Visium Mouse Transcriptome Probe Set v2.1 is an updated reference for use with the probes in Visium Mouse Transcriptome Probe Kit v2, Small PN-1000667
Visium Mouse Transcriptome Probe Set v2.1 is an updated reference for use with the probes in Visium Mouse Transcriptome Probe Kit v2, Small PN-1000667
Probe Set Contents
- 19,403 gene_ids targeted by 55,538 probes.
- 333 of these genes (targeted by 360 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.
- 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 Mouse Transcriptome Probe Set v2.1 - Probe Set Reference CSV file
- Visium Mouse Transcriptome Probe Set v2.1 - BED file
- Visium Mouse Transcriptome Probe Set v2.1 - Probe Off-target CSV file
- Visium Mouse 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 Mouse Transcriptome Probe Kit v2, Small PN-1000667