Visium probe sets are bundled with the Space Ranger software. Both Space Ranger and individual probe sets can be downloaded here.
Probe Set Contents
-
20,551 gene_ids targeted by 20,873 probes.
- 1,086 (5.3%) of these gene_ids (targeted by 1,110 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.
- 19,465 gene_ids (targeted by 19,763 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 [email protected] 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 v1.0 - Probe Set Reference CSV file
- Visium Mouse Transcriptome Probe Set v1.0 - BED file
- Visium Mouse Transcriptome Probe Set v1.0 - Probe Off-target CSV file
- Visium Mouse Transcriptome Probe Set v1.0 - 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, Large PN-1000366
- Visium Mouse Transcriptome Probe Kit, Small PN-1000365