Question: Can I use methanol fixation with the 3’ Single Cell Gene Expression assay?
Answer: Our 3’ Single Cell Gene Expression assay was optimized for use with single cell or single nuclei suspensions prepared from fresh cells/tissues. If processing fresh samples is not feasible, it may be possible to perform methanol fixation on cell suspensions and to store the methanol-fixed cells for later use with the 3’ GEX assay. However, methanol fixation is harsh and can lead to cell loss and cell lysis, and may not be suitable for all sample types. 10x Genomics developed a methanol fixation protocol that was tested with a few sample types (eg. PBMCs, Jurkat cells) with version 2 of our 3’ GEX assay (3’v2). This protocol is available from our Technical Support team upon request. Customers interested in using this protocol are encouraged to perform pilot experiments to determine if methanol fixation is suitable for their sample type. Furthermore, as an alternative to methanol fixation, we recommend customers use our Fixed RNA Profiling assay, which was optimized for use with formaldehyde-fixed samples and shows robust data quality across a range of sample types.
Products: Single Cell Gene Expression