title: A microfluidic platform enabling single-cell RNA-seq of multigenerational lineages.
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.
authors.affiliation: Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachussets 02139, USA.|Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachussets 02139, USA.
authors.forename: Robert J
authors.initials: RJ
authors.lastname: Kimmerling
authors.affiliation: Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachussets 02139, USA.|Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachussets 02139, USA.|Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachussets 02139, USA.|Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, Cambridge, Massachussets 02139, USA.
authors.forename: Gregory
authors.initials: G
authors.lastname: Lee Szeto
authors.affiliation: Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachussets 02139, USA.
authors.forename: Jennifer W
authors.initials: JW
authors.lastname: Li
authors.affiliation: Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, Cambridge, Massachussets 02139, USA.|Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachussets 02139, USA.|Institute for Medical Engineering &Science, Massachusetts Institute of Technology, Cambridge, Massachussets 02139, USA.|Broad Institute of MIT and Harvard, Cambridge, Massachussets 02142, USA.
authors.forename: Alex S
authors.initials: AS
authors.lastname: Genshaft
authors.affiliation: Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, Cambridge, Massachussets 02139, USA.|Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachussets 02139, USA.|Institute for Medical Engineering &Science, Massachusetts Institute of Technology, Cambridge, Massachussets 02139, USA.|Broad Institute of MIT and Harvard, Cambridge, Massachussets 02142, USA.
authors.forename: Samuel W
authors.initials: SW
authors.lastname: Kazer
authors.affiliation: Microsystems Technology Laboratory, Massachusetts Institute of Technology, Cambridge, Massachussets 02139, USA.
authors.forename: Kristofor R
authors.initials: KR
authors.lastname: Payer
authors.affiliation: Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachussets 02139, USA.|Broad Institute of MIT and Harvard, Cambridge, Massachussets 02142, USA.
authors.forename: Jacob
authors.initials: J
authors.lastname: de Riba Borrajo
authors.affiliation: Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachussets 02139, USA.|Broad Institute of MIT and Harvard, Cambridge, Massachussets 02142, USA.
authors.forename: Paul C
authors.initials: PC
authors.lastname: Blainey
authors.affiliation: Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachussets 02139, USA.|Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachussets 02139, USA.|Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachussets 02139, USA.|Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, Cambridge, Massachussets 02139, USA.|Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA.
authors.forename: Darrell J
authors.initials: DJ
authors.lastname: Irvine
authors.affiliation: Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, Cambridge, Massachussets 02139, USA.|Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachussets 02139, USA.|Institute for Medical Engineering &Science, Massachusetts Institute of Technology, Cambridge, Massachussets 02139, USA.|Broad Institute of MIT and Harvard, Cambridge, Massachussets 02142, USA.|Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, Massachussets 02139, USA.|Department of Immunology, Massachusetts General Hospital, Boston, Massachussets 02114, USA.
authors.forename: Alex K
authors.initials: AK
authors.lastname: Shalek
authors.affiliation: Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachussets 02139, USA.|Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachussets 02139, USA.|Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, Massachussets 02139, USA.
authors.forename: Scott R
authors.initials: SR
authors.lastname: Manalis
mesh_terms: D000818:Animals; D018414:CD8-Positive T-Lymphocytes / Q000378:metabolism*; D002453:Cell Cycle / Q000502:physiology; D045744:Cell Line, Tumor; D051379:Mice; D046210:Microfluidic Analytical Techniques / Q000295:instrumentation* / Q000379:methods; D012313:RNA / Q000235:genetics*; D014158:Transcription, Genetic
chemical_list: D012313:RNA