Visium probe sets are bundled with the Space Ranger software. Both Space Ranger and individual probe sets can be downloaded here.
Probe Set Contents
-
19,405 gene_ids targeted by 55,538 probes.
- 346 (1.8%) of these genes (targeted by 351 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.
- 19,059 genes (targeted by 55,187 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 Mouse Transcriptome Probe Set v2.0 - Probe Set Reference CSV file
- Visium Mouse Transcriptome Probe Set v2.0 - BED file
- Visium Mouse Transcriptome Probe Set v2.0 - Probe Off-target CSV file
- Visium Mouse Transcriptome Probe Set v2.0 - 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 v2.0, Small PN-1000667