ACME dissociation: a versatile cell fixation-dissociation method for single-cell transcriptomics

Single-cell sequencing technologies are revolutionizing biology, but are limited by the need of dissociating fresh samples that can only be fixed at later stages. We present ACME (ACetic-MEthanol) dissociation, a species-versatile cell dissociation approach that fixes cells  as they are being dissociated. ACME-dissociated cells have high RNA integrity, can be cryopreserved multiple times, can be sorted by Fluorescence-Activated Cell Sorting (FACS) and are permeable, enabling combinatorial approaches of single-cell transcriptomics. ACME is based on cheap reagents and it can be done in most labs and even sampling trips. As a proof of principle, we have performed SPLiT-seq with ACME cells to obtain around ~35K cells from two planarian species and identified all previously described cell types in similar proportions. This technique allows fixed, dissociated cells to be obtained from diverse organisms  that can be cryopreserved and subjected to combinatorial barcoding methods for single-cell transcriptomics  and thus will accelerate our knowledge of cell types across the tree of life. Adult planarians were pooled, and cells disassociated using the novel ACME technique as described in Garcia-Castro et al 2020 (this manuscript). They were then used to perform SPLiTseq analysis. This sample was split into 3 sub-libraries for sequencing (Illumina Novaseq), however all sublibraries were derived from the same overall population.