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Nat Commun. 2016 Jan 6;7:10220. doi: 10.1038/ncomms10220.

A microfluidic platform enabling single-cell RNA-seq of multigenerational lineages.

Kimmerling RJ1,2, Lee Szeto G1,2,3,4, Li JW2, Genshaft AS4,5,6,7, Kazer SW4,5,6,7, Payer KR8, de Riba Borrajo J2,7, Blainey PC2,7, Irvine DJ1,2,3,4,9, Shalek AK4,5,6,7,10,11, Manalis SR1,2,12.

Author information

1
Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachussets 02139, USA.
2
Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachussets 02139, USA.
3
Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachussets 02139, USA.
4
Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, Cambridge, Massachussets 02139, USA.
5
Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachussets 02139, USA.
6
Institute for Medical Engineering &Science, Massachusetts Institute of Technology, Cambridge, Massachussets 02139, USA.
7
Broad Institute of MIT and Harvard, Cambridge, Massachussets 02142, USA.
8
Microsystems Technology Laboratory, Massachusetts Institute of Technology, Cambridge, Massachussets 02139, USA.
9
Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA.
10
Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, Massachussets 02139, USA.
11
Department of Immunology, Massachusetts General Hospital, Boston, Massachussets 02114, USA.
12
Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, Massachussets 02139, USA.

Abstract

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.

PMID:
26732280
PMCID:
PMC4729820
DOI:
10.1038/ncomms10220
[Indexed for MEDLINE]
Free PMC Article

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