Question: What workflows and reagent kits are compatible with the Next GEM Single Cell 3’ v3.1 LT assay?
Answer: The following workflows and reagent kits are compatible with the LT product:
- 3’ gene expression (dual index)
- Feature Barcode technology for cell surface protein analysis
- Dual Index Kit TT Set A
The following workflows and reagent kits are not compatible with the LT product:
- Chromium Connect
- Single Index Kit T Set A
The following workflows and reagent kits are not supported with the LT product:
- CellPlex
- Feature Barcode technology for CRISPR screens
- Targeted gene expression
LT with CellPlex:
- While it is theoretically possible, it is not supported, tested or recommended to use LT with Feature Barcoding with CellPlex. Cell Ranger will not run data that has been multiplexed with the LT chemistry.
- Additionally, using the CellPlex product with the LT kit is not practical given the higher multiplet rate and lower cell recovery.
LT with Feature Barcode technology for CRISPR screens:
- While it is theoretically possible, it is not supported, tested or recommended to use LT for CRISPR screens, as they typically require a higher cell load in order to validate the experimental design of the study. The nature of the LT product (with a lower number of cells, higher multiplet rate and lower cell recovery rate) means that it is not an ideal product to use for optimizing or conducting these types of experiments.
LT with Targeted Gene Expression:
- While compatible without workflow modifications, it is not supported or recommended to use LT with Targeted Gene Expression assays. The Cell Ranger 6.1 pipeline is capable of analyzing Targeted Gene Expression from LT datasets, but prior Cell Ranger pipeline releases are not compatible.
Products: Single Cell Gene Expression