Question: Is 5’ CRISPR compatible with Cell Hashing?
Answer: 5’ CRISPR is compatible with our 5’ v2 chemistry (including 5' HT v2) and 5' v3 chemistry, allowing for cell capture of up to 10,000 cells for the standard assay and 30,000 cells for HT. In addition, 5’ CRISPR is compatible with Cell Surface Protein (TotalSeq-C).
Although cell hashing is not officially supported by 10x Genomics, we have developed additional resources to help enable these experiments using TotalSeq™-C antibodies. Please refer to the article: Can I perform Cell Hashing in the 5’ workflow?
TotalSeq-C is compatible with 5’ CRISPR, and since cell hashing uses TotalSeq-C, it is theoretically possible to use cell hashing to recover more cells and CRISPR preturbations. This said, we have not tested the combination of Cell Hashing and 5’ CRISPR in-house. Therefore, this is untested and not officially supported. We would recommend a pilot experiment to determine feasibility. As with all single cell CRISPR experiments, careful experimental planning is critical for assay performance. What should I consider when designing my 3' or 5' CRISPR pool?
| Assays Compatible with 5' CRISPR | Compatibility |
| Chromium Single Cell 5' v3 | ✓ |
| Chromium Single Cell 5' v2 | ✓ |
| Chromium Single Cell 5' HT v2 | ✓ |
| V(D)J Receptor Sequences (TCR and BCR) | ✓ |
| Cell Surface Proteins (TotalSeq-C) | ✓ |
| 5' Cell Hashing | Untested |
Since hashing of 5’ Immune Profiling is not officially supported by 10x Genomics, the usual Cell Ranger pipelines are unable to demultiplex the samples. However, an unofficial workaround is available, and the tutorial is available here: Demultiplexing and Analyzing 5’ Immune Profiling Libraries Pooled with Hashtags.
Product: Single Cell Immune Profiling