Question: Is Single Cell Immune Profiling Solution compatible with fixed cells?
Answer: Fixed cell samples (methanol, FFPE, etc) have not been tested for compatibility with Single Cell V(D)J reagent kits and are not supported at this time.
Methanol makes the cell membrane permeable and prone to RNA leakage, which results in lower sensitivity. This decrease in sensitivity is expected to have a significant impact on the VDJ-enrichment aspect of the assay. Although we have only tested methanol fixation on our 3' Gene Expression assay, we expect that the performance of 5' Gene Expression libraries would be similar to 3' Gene Expression libraries and may be compatible.
It is possible that methanol fixation may be compatible with the VDJ-enrichment aspect of the Immune Profiling assay as well, but this will likely require further optimization. Although we have seen good results with methanol fixation on our Gene Expression assay, at this point we cannot guarantee assay performance with our Immune Profiling Assay.
If you are interested in methanol fixation as a means for processing infectious samples, you may be interested in our page on Processing Samples Containing Infectious Agents using the 10x Genomics Chromium Controller and Protocols.
Products: Single Cell Immune Profiling