Kimmerling, Robert J.Szeto, Gregory LeeLi, Jennifer W.Genshaft, Alex S.Kazer, Samuel W.Payer, Kristofor R.de Riba Borrajo, JacobBlainey, Paul C.Irvine, Darrell J.Shalek, Alex K.Manalis, Scott R.2016-03-012016Kimmerling, R. J., G. L. Szeto, J. W. Li, A. S. Genshaft, S. W. Kazer, K. R. Payer, J. de Riba Borrajo, et al. 2016. “A microfluidic platform enabling single-cell RNA-seq of multigenerational lineages.” Nature communications 7 (1): 10220. doi:10.1038/ncomms10220. http://dx.doi.org/10.1038/ncomms10220.2041-1723http://nrs.harvard.edu/urn-3:HUL.InstRepos:25658386We introduce a microfluidic platform that enables off-chip single-cell RNA-seq after multi-generational lineage tracking under controlled culture conditions. We use this platform to generate whole-transcriptome profiles of primary, activated murine CD8+ T-cell and lymphocytic leukemia cell line lineages. Here we report that both cell types have greater intra- than inter-lineage transcriptional similarity. For CD8+ T-cells, genes with functional annotation relating to lymphocyte differentiation and function—including Granzyme B—are enriched among the genes that demonstrate greater intra-lineage expression level similarity. Analysis of gene expression covariance with matched measurements of time since division reveals cell type-specific transcriptional signatures that correspond with cell cycle progression. We believe that the ability to directly measure the effects of lineage and cell cycle-dependent transcriptional profiles of single cells will be broadly useful to fields where heterogeneous populations of cells display distinct clonal trajectories, including immunology, cancer, and developmental biology.en-USJournal Article2016-03-0110.1038/ncomms10220