Q: How should I store my single-cell suspension?
A: In general, freshly prepared samples will give the best data, followed by cryopreserved. Cryopreservation will cause you to lose some cells during the thawing process, but the transcriptomes are comparable (sample-specific).
We don't support other types of fixation in either the Single Cell Gene Expression or Single Cell Immune Profiling assays, such as formaldehyde which disrupt membrane stability, something necessary to retain the "single cell-ness" of the assay. Additionally, the crosslinking and degradation of the nucleic acids may compromise data quality. Even in bulk RNA-Seq, it is common to get degraded RNA from formaldehyde-fixed samples, so these are not recommended in these 10x single cell RNA-seq assays.
However, if you are interested in sample fixation for human or mouse samples using formaldehyde, the Chromium Fixed RNA Profiling assay may be of interest. This whole human or mouse transcriptome probe-based assay offers comprehensive, scalable solutions to measure gene expression in formaldehyde-fixed samples. Fixation at the point of sample collection preserves fragile biology and greatly streamlines workflows to provide critical insights into more samples. For more information, please review the product page for Chromium Fixed RNA Profiling.
Products: Single Cell Gene Expression, Single Cell Immune Profiling, Fixed RNA Profiling, Single Cell Gene Expression Flex