The human and mouse probe sets are bundled with the Space Ranger software. The rat probe set must be downloaded separately, and will be bundled in a future Space Ranger release. Space Ranger and all individual probe sets can be downloaded here.
Visium Rat Transcriptome Probe Set v2.0 is a reference for use with the probes in Visium Rat Transcriptome Probe Kit v2, Small PN-1001123
Visium Rat Transcriptome Probe Set v2.0 is a reference for use with the probes in Visium Rat Transcriptome Probe Kit v2, Small PN-1001123
Probe Set Contents
- 22,311 genes targeted by 62,506 probes.
- 882 (4.0%) of these genes (targeted by 2,212 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.
- 21,429 genes (targeted by 60,294 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 mRatBN7.2-2024-A reference transcriptome was used to design this probe set.
The gene_id information is included in the probe set reference CSV file.
Accompanying Probe Set Files
- Visium Rat Transcriptome Probe Set v2.0 - Probe Set Reference CSV file
- Visium Rat Transcriptome Probe Set v2.0 - BED file
- Visium Rat Transcriptome Probe Set v2.0 - Probe Off-target CSV file
- Visium Rat 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 Rat Transcriptome Probe Kit v2, Small PN-1001123