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 can result in lower transcriptome complexity. This decrease in complexity is expected to have a significant impact on the VDJ-enrichment steps of the assay, as they rely on the presence of lowly expressed transcripts. It is possible that methanol fixation may be compatible with VDJ-enrichment, but this will likely require further optimization and we do not recommend it with our current methanol fixation protocol.
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, but at this point we cannot guarantee assay performance of methanol fixation 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