Both Cell Ranger and individual probe sets can be downloaded on the Cell Ranger Downloads page. Rat probe sets will be bundled in a future version of Cell Ranger.
Probe set contents
- 22,309 genes targeted by 62,468 probes.
- 882 (4.0%) of these genes (targeted by 2,190 probes) are excluded by default.
- 21,427 genes (targeted by 60,278 probes) are present in the final filtered output.
- The mRatBN7.2 reference transcriptome was used to design this probe set (reference is available on the Cell Ranger downloads page; see reference build steps here).
The gene_id information is included in the probe set reference CSV file.
Accompanying probe set files
- Chromium Rat Transcriptome Probe Set v2.0 - Probe Set Reference CSV file
- Chromium Rat Transcriptome Probe Set v2.0 - BED file
- Chromium Rat Transcriptome Probe Set v2.0 - Probe Off-target CSV file
- Chromium Rat Transcriptome Probe Set v2.0 - Metadata TSV file
For details on the file formats, see the probe set file descriptions page.
Check this page to find the compatible Cell Ranger version(s) for each probe set version.