SIS-seq, a molecular 'time machine', connects single cell fate with gene programs

Conventional single cell RNA-seq methods are destructive, such that a given cell cannot also then be tested for fate and function, without a time machine. Here, we develop a clonal method SIS-seq, whereby single cells are allowed to divide, and progeny cells are assayed separately in SISter conditions; some for fate, others by RNA-seq. By cross-correlating fate and gene expression within a clone, and doing this for many clones, we can identify the earliest gene expression signatures of dendritic cell subset development. SIS-seq could be used to study other populations harboring clonal heterogeneity, including stem, reprogrammed and cancer cells to reveal the transcriptional origins of fate decisions. Overall design: Single ubiquitin C-GFP+ Sca1+ ckit+ HSPCs were isolated from BM and cultured amongst a pool of BM filler cells from C57BL/6 mice, and supplemented with Flt3 ligand. After 2.5 days, wells were visually inspected for GFP+ clones, and those with 10 or more cells were mixed by pipetting, followed by equal volume separation into three parts; two replicate wells for further culture to test for fate at day 8, and the remaining fraction for single cell, or small cell number RNA-seq, using CEL-Seq2 to provide a transcriptional 'snapshot' of the clone prior to fate acquisition.