We 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.

NOTE: This protocol has not been validated with clinical samples. To facilitate collaborations with interested parties to jointly advance the fight against the current coronavirus pandemic, wehave set up a public forum on www.LAMP-Seq.org.

the global spread of a novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has resulted in over 109 million confirmed cases, and approximately 2.4 million deaths have been attributed to Coronavirus Disease 2019 (COVID-19) 1 . Current containment strategies based on 'test-trace-isolate' face major issues: (1) many infected individuals do not show any symptoms and, therefore, remain untested 2 ; (2) supply chain issues limit testing capacity; and(3) the successive (rather than parallel) testing of contact individuals causes a substantial lag in identifying infection chains, resulting in undetected spread due to delayed diagnosis. By contrast, repeated testing of large groups of individuals, regardless of symptoms or