Question: Are fresh-frozen tissue samples compatible with Single Cell RNA sequencing?
Answer: If it is not feasible to process fresh tissue, fresh-frozen tissue samples can be used for Single Cell RNA sequencing. Before freezing, the tissue could be dissociated into a single-cell suspension. Cells can then be cryopreserved in a suitable freezing medium. When freezing cells, we recommend starting with at least 1 million total cells to recover sufficient numbers post-thaw since almost half may be lost in the freeze-thaw process and during the wash and centrifugation steps.
If the tissue is frozen whole, it is more challenging to isolate viable single cells after thawing. In this case, it is recommended to extract nuclei from the snap-frozen tissue. Please refer to this article: How do you isolate nuclei from snap-frozen tissue for 3’ gene expression profiling?
The choice of one method over the other(dissociating and then cryopreserving vs. snap-freezing whole tissue) would depend on the sample type. If a well-optimized tissue dissociation protocol is already available that yields >90% viable cells with no cell type bias, then dissociation followed by cryopreservation is preferred. However, if the tissue dissociation protocol is not optimized then it may be better to snap-freeze the tissue whole. It is recommended to try both approaches with a non-precious sample before the actual experiment to know which approach is giving better yields.
Products: Single Cell Gene Expression, Single Cell Immune Profiling