Probe sets are bundled with the Cell Ranger software. Both Cell Ranger and individual probe sets can be downloaded on the Cell Ranger Downloads page.
Probe set contents
-
19,403 genes targeted by 55,479 probes
- 333 (1.7%) of these genes (targeted by 360 probes) are excluded by default
- 19,070 genes (targeted by 55,119 probes) are present in the final filtered output
The gene_id information is included in the probe set reference CSV file.
Accompanying probe set files
The Mouse Probe Set v1.1.0 differs in two gene names when compared to the GRCm39-2024-A transcriptome reference. These discrepancies have been resolved in Mouse Probe Set v1.1.1.
- Chromium Mouse Transcriptome Probe Set v1.1.1 - Probe Set Reference CSV file
- Chromium Mouse Transcriptome Probe Set v1.1.1 - BED file
- Chromium Mouse Transcriptome Probe Set v1.1.1 - Probe Off-target CSV file
- Chromium Mouse Transcriptome Probe Set v1.1.1 - Metadata TSV file
These files can be downloaded from the software downloads section and the probe set file descriptions page.
For details on the file formats, see the probe set file descriptions page.
Check this page to find the compatible Cell Ranger version for each probe sets version.