Cell Ranger is designed to analyze single cell datasets generated by the 10x Genomics Chromium platform.
| Library Combination | CR v10.0 | CR v9.0 | CR v8.0 | CR v7.2 and lower |
|---|---|---|---|---|
| Universal 3' Gene Expression v4 | - | |||
| Universal 3' Gene Expression v4 + Antibody Capture | - | |||
| Universal 3' Gene Expression v4 + CRISPR Guide Capture | - | - |
The Chromium GEM-X Universal 3' Gene Expression v4 chemistry does not support the following:
- Cell multiplexing (CellPlex): As a result, Cell Ranger cannot process this analysis combination.
- CRISPR Guide Capture: Although unsupported by GEM-X, analysis for this feature is enabled in Cell Ranger v9.0.
- High-throughput (HT) assays: There is no
SC3Pv4HTequivalent toSC3Pv3HT. - OCM does not support multi-species analysis. For example, human and mouse samples cannot be loaded on different wells of the same OCM chip.
- Hashing with Antibody Capture in combination with OCM.
| Library Combination | CR v10.0 | CR v9.0 | CR v8.0 | CR v7.2 |
|---|---|---|---|---|
| Universal 3' Gene Expression v2 | ||||
| Universal 3' Gene Expression v3 | ||||
| Universal 3' Gene Expression v3 + Antibody Capture | ||||
| Universal 3' Gene Expression v3 + CRISPR Screening Expression | ||||
| Universal 3' Antibody Capture only | ||||
| 3' LT (Low Throughput) | - | - | - | |
| 3' HT (High Throughput) |
| Library Combination | CR v10.0 | CR v9.0 | CR v8.0 | CR v7.2 and lower |
|---|---|---|---|---|
| Universal 5' Gene Expression v3 | - | |||
| Universal 5' Gene Expression v3 + V(D)J | - | |||
| Universal 5' Gene Expression v3 + Antibody Capture | - | |||
| Universal 5' Gene Expression v3 + Antibody Capture + V(D)J | - | |||
| Universal 5' Gene Expression v3 + Antibody Capture + CRISPR | - | |||
| Universal 5' Gene Expression v3 + CRISPR | - | |||
| Universal 5' Gene Expression v3 + V(D)J + CRISPR | - | |||
| Universal 5' Gene Expression v3 + Antibody Capture + V(D)J + CRISPR | - |
- GEM-X Single Cell Immune Profiling v3 chemistry does not support 5' Gene Expression v3 + V(D)J + Antigen Capture. However, Cell Ranger v8.0 can process 5' Gene Expression + V(D)J libraries + Antigen Capture generated using Next GEM v2 chemistry.
- Analysis of GEM-X Universal 5' VDJ libraries (Singleplex and Multiplex) without an accompanying Gene Expression library is enabled but unsupported.
- High-throughput (HT) is not an available option for GEM-X assays. There is no
SC3Pv4HTequivalent toSC3Pv3HT. - OCM does not support multi-species analysis. For example, human and mouse samples cannot be loaded on different wells of the same OCM chip.
- Hashing with Antibody Capture is disabled for OCM.
| Library Combination | CR v10.0 | CR v9.0 | CR v8.0 | CR v7.2 |
|---|---|---|---|---|
| Universal 5' Gene Expression | ||||
| Universal 5' V(D)J | ||||
| Universal 5' Gene Expression + V(D)J | ||||
| Universal 5' Gene Expression + Antibody Capture | ||||
| Universal 5' Gene Expression + Antibody Capture + V(D)J | ||||
| V(D) J + Antibody Capture | ||||
| Universal 5' Antibody Capture only | ||||
| Targeted Gene Expression | - | - | - | - |
| 5' HT (High Throughput) | ||||
| Universal 5' Gene Expression + CRISPR | ||||
| Universal 5' Gene Expression + CRISPR + Antibody Capture | ||||
| Universal 5' Gene Expression + CRISPR + V(D)J | ||||
| Universal 5' Gene Expression + Antigen Capture + V(D)J ± Antibody Capture |
| Library Combination | CR v10.0 | CR v9.0 | CR v8.0 | CR v7.2 |
|---|---|---|---|---|
| Flex v2 Gene Expression | - | - | - | |
| Flex v2 Gene Expression + Antibody Capture | - | - | - | |
| Flex v2 Gene Expression + CRISPR | - | - | - | |
| Flex v2 Gene Expression + CRISPR + Antibody Capture | - | - | - | |
| Flex v1 Gene Expression | ||||
| Flex v1 Gene Expression + Antibody Capture | ||||
| Flex v1 Gene Expression + CRISPR | - | |||
| Flex v1 Gene Expression + CRISPR + Antibody Capture | - |
| Multiplexing Solution | Technology | Product | CR Version |
|---|---|---|---|
| On-chip multiplexing (OCM) | GEM-X | Universal 5' and Universal 3' | v9.0 and later |
| Cell multiplexing or CellPlex | Next GEM | Universal 3' only | v6.0 and later |
| Hashing with Antibody Capture* | Next GEM, GEM-X | Universal 5' and Universal 3' | v9.0 and later |
| Probe-based multiplexing with Flex v1 | Next GEM, GEM-X | Flex v1 | v7.0 and later |
| Probe-based multiplexing with Flex v2 | GEM-X | Flex v2 | v10.0 and later |
Combining two or more multiplexing solutions in Cell Ranger is disabled and unsupported. Hashing with Antibody Capture is enabled but unsupported.