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A variety of single-cell RNA preparation procedures have been described. So far, protocols require fresh material, which hinders complex study designs. We describe a sample preservation method that maintains transcripts in viable single cells, allowing one to disconnect time and place of sampling from subsequent processing steps. We sequence single-cell transcriptomes from >1000 fresh and cryopreserved cells using 3'-end and full-length RNA preparation methods. Our results confirm that thedoi:10.1186/s13059-017-1171-9 pmid:28249587 pmcid:PMC5333448 fatcat:kpufju3zvvbcvni4t6e3atuo34