Q: How should I store my single-cell suspension?
A: In general, freshly prepared samples will give the best data, followed by cryopreserved and then methanol-fixed samples. Cryopreserved will cause you to lose some cells during the thawing process, but the transcriptomes are comparable (sample-specific). Once you get to methanol fixed, it can be harsh on the cell membranes so you get lots of cell lysis and cell loss. We have successfully fixed Jurkat cells and fresh mouse embryonic neuronal tissue and seen a strong correlation between the transcriptomes, but this will also be sample-type specific. Please note that methanol fixation is not supported with our Single Cell Immune Profiling Solution. It is also not supported with our Feature Barcoding technology.
We don't support other types of fixation such as formaldehyde--aldehydes will disrupt membrane stability, something necessary to retain the "single-cellness" of the assay. Additionally, the crosslinking and degradation of the nucleic acids may compromise data quality. Even in bulk RNA-Seq, you have lots of degraded RNA from formaldehyde-fixed samples, so these are not recommended for 10x assay.
Products: Single Cell Gene Expression, Single Cell Immune Profiling