Question: Is Barcode Enabled Antigen Mapping (BEAM) compatible with cell hashing?
Answer: Cell hashing is theoretically compatible with BEAM, but is untested and not officially supported.
BEAM is compatible with Cell Surface Protein labeling (TotalSeq-C). We officially support labeling a cell sample with BEAM Assemblies and TotalSeq-C antibodies, sorting the sample to collect antigen-specific cells, and loading the sample onto its own well of a chip. We have tested this with TotalSeq-C antibodies to label cell surface markers for immune cell populations (such as. CD19, CD8, CD3, CD14). See our User Guides for BEAM + TotalSeq-C labeling and library preparation:
- CG000595 - BEAM Reagent Assembly, Sample Labeling, and Flow Sorting (includes optional TotalSeq-C labeling)
- CG000592 - BEAM & Cell Surface Protein library preparation (5’ v2 assay)
- CG000594 - BEAM & Cell Surface Protein library preparation (5’ HT v2 assay)
However, we have not specifically tested TotalSeq-C cell hashing antibodies. It is theoretically possible to label cell samples with BEAM Assemblies and cell hashing antibodies, sort each sample to collect antigen-specific cells, and then pool multiple sorted samples for loading onto one well of a chip. However, this is not officially supported by 10x Genomics. We have not validated this internally and cannot guarantee assay performance.
We have performed limited internal testing of cell hashing with the 5’ Gene Expression & V(D)J assay (without BEAM). Although this is not officially supported, general suggestions can be found here: Can I perform Cell Hashing in the 5' workflow?
Given that cell hashing is not officially supported by 10x Genomics, workaround solutions or third party tools would be needed for analyzing BEAM + cell hashing data. We have a suggested workaround solution for analyzing 5’ cell hashing data, but we have not specifically tested this with BEAM datasets. See this article: I have multiplexed multiple samples in 5'GEX with TCR/BCR libraries. Can I use Cell Ranger to demultiplex the samples?
Note on alternative multiplexing strategies:
It may theoretically be possible to label cell samples with BEAM Assemblies prepared from different BEAM Conjugates (eg. BEAM Conjugate 1 for Sample 1, BEAM Conjugate 2 for Sample 2), sort to collect antigen-positive cells, and then pool the sorted samples together to load onto one well of a chip. However, this is untested and unsupported. Custom data analysis tools may be required, given that the Cell Ranger BEAM data analysis pipeline was not designed to demultiplex data based on the BEAM Conjugate of the parent sample.
Products: Single Cell Immune Profiling, Barcode Enabled Antigen Mapping (BEAM)