A microfluidic platform enabling single-cell RNA-seq of multigenerational lineages
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Kimmerling-2016-Microfluidic Platform.pdf
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Author(s)
Li, Jennifer W.
Genshaft, Alex S.
de Riba Borrajo, Jacob
Shalek, Alex K.
Kimmerling, Robert John
Kazer, Samuel Weisgurt
Payer, Kristofor Robert
Borrajo, Jacob de Riba
Blainey, Paul C
Irvine, Darrell J
Date Issued
January 2016
Journal
Nature Communications
Publisher
Nature Publishing Group
Citation
Kimmerling, Robert J., Gregory Lee Szeto, Jennifer W. Li, Alex S. Genshaft, Samuel W. Kazer, Kristofor R. Payer, Jacob de Riba Borrajo, et al. “A Microfluidic Platform Enabling Single-Cell RNA-Seq of Multigenerational Lineages.” Nat Comms 7 (January 6, 2016): 10220.
Version
Final published version
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.
MIT Department
Massachusetts Institute of Technology. Institute for Medical Engineering & Science
Harvard University--MIT Division of Health Sciences and Technology
Massachusetts Institute of Technology. Department of Biological Engineering
Massachusetts Institute of Technology. Department of Chemistry
Massachusetts Institute of Technology. Department of Materials Science and Engineering
Massachusetts Institute of Technology. Department of Mechanical Engineering
Massachusetts Institute of Technology. Microsystems Technology Laboratories
Koch Institute for Integrative Cancer Research at MIT
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DOI of Published Version
https://doi.org/10.1038/ncomms10220
