Fixed RNA Profiling has been renamed Flex. All future updates, documentation, and support will reference Flex.
Cell Ranger v9.0 supports analysis of GEM-X 3’ and 5’ on-chip multiplexing (OCM) libraries
Cell Surface Protein libraries are also referred to as Antibody Capture libraries, and both terms are used interchangeably in 10x Genomics documentation.
| Library Combination | CR 9.0 | CR 8.0 | CR 7.2 and lower |
|---|---|---|---|
| 3’ Gene Expression v4 | - | ||
| 3’ Gene Expression v4 + Antibody Capture | - | ||
| 3' Gene Expression v4 + CRISPR Guide Capture | - | - |
The Chromium GEM-X Single Cell 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 9.0 | CR 8.0 | CR 7.2 | CR 7.1 | CR 7.0 | CR 6.1 | CR 6.0 | CR 5.0 | CR 4.0 | CR 3.1 | CR 3.0 | CR 2.2 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 3’ Gene Expression v2 | ||||||||||||
| 3’ Gene Expression v3 | - | |||||||||||
| 3’ Gene Expression v3 + Antibody Capture | - | |||||||||||
| 3’ Gene Expression v3 + CRISPR Screening Expression | - | |||||||||||
| 3’ Antibody Capture only | - | - | ||||||||||
| 3’ Targeted Gene Expression | - | - | - | - | - | - | ||||||
| 3’ LT (Low Throughput) | - | - | - | - | - | - | - | - | ||||
| 3’ HT (High Throughput) | - | - | - | - | - | - |
| Library Combination | CR 9.0 | CR 8.0 | CR 7.2 and lower |
|---|---|---|---|
| 5’ Gene Expression v3 | - | ||
| 5’ Gene Expression v3 + V(D)J | - | ||
| 5’ Gene Expression v3 + Antibody Capture | - | ||
| 5’ Gene Expression v3 + Antibody Capture + V(D)J | - | ||
| 5’ Gene Expression v3 + Antibody Capture + CRISPR | - | ||
| 5’ Gene Expression v3 + CRISPR | - | ||
| 5’ Gene Expression v3 + V(D)J + CRISPR | - | ||
| 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 5’ VDJ libraries 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 9.0 | CR 8.0 | CR 7.2 | CR 7.1 | CR 7.0 | CR 6.1 | CR 6.0 | CR 5.0 | CR 4.0 | CR 3.1 | CR 3.0 | CR 2.2 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 5’ Gene Expression | ||||||||||||
| 5’ V(D)J | ||||||||||||
| 5’ Gene Expression + V(D)J | ||||||||||||
| 5’ Gene Expression + Antibody Capture | - | |||||||||||
| 5’ Gene Expression + Antibody Capture + V(D)J | - | |||||||||||
| V(D) J + Antibody Capture | - | |||||||||||
| 5’ Antibody Capture only | - | - | ||||||||||
| 5’ Targeted Gene Expression | - | - | - | - | - | - | ||||||
| 5’ HT (High Throughput) | - | - | - | - | - | - | - | |||||
| 5’ Gene Expression + CRISPR | - | - | - | - | - | - | - | |||||
| 5’ Gene Expression + CRISPR + Antibody Capture | - | - | - | - | - | - | - | |||||
| 5’ Gene Expression + CRISPR + V(D)J | - | - | - | - | - | - | - | |||||
| 5’ Gene Expression + Antigen Capture + V(D)J ± Antibody Capture | - | - | - | - | - | - | - | - |
| Library Combination | CR 9.0* | CR 8.0 | CR 7.2 | CR 7.1 | CR 7.0 |
|---|---|---|---|---|---|
| Gene expression | |||||
| Gene expression + Antibody Capture | |||||
| Gene expression + CRISPR | - | - | - | ||
| Gene expression + CRISPR + Antibody Capture | - | - | - |
*Cell Ranger v9.0 supports GEM-X Flex libraries
| Multiplexing Solution | Technology | Product | Cell Ranger Version |
|---|---|---|---|
| On-chip multiplexing (OCM) | GEM-X | 5’ and 3’ | v9.0 and later |
| Cell multiplexing or CellPlex | Next GEM | 3’ only | v6.0 and later |
| Hashing with Antibody Capture* | Next GEM, GEM-X | 5’ and 3’ | v9.0 and later |
| Probe-based multiplexing with Flex | Next GEM, GEM-X | Flex | v7.0 and later |
Combining two or more multiplexing solutions in Cell Ranger is disabled and unsupported. Hashing with Antibody Capture is enabled but unsupported.