Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells

Alex K. Shalek, Rahul Satija, Xian Adiconis, Rona S. Gertner, Jellert T. Gaublomme, Raktima Raychowdhury, Schraga Schwartz, Nir Yosef, Christine Malboeuf, Diana Lu, John J. Trombetta, Dave Gennert, Andreas Gnirke, Alon Goren, Nir Hacohen, Joshua Z. Levin, Hongkun Park () and Aviv Regev ()
Additional contact information
Alex K. Shalek: Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA
Rahul Satija: Broad Institute of MIT and Harvard, 7 Cambridge Center
Xian Adiconis: Broad Institute of MIT and Harvard, 7 Cambridge Center
Rona S. Gertner: Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA
Jellert T. Gaublomme: Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA
Raktima Raychowdhury: Broad Institute of MIT and Harvard, 7 Cambridge Center
Schraga Schwartz: Broad Institute of MIT and Harvard, 7 Cambridge Center
Nir Yosef: Broad Institute of MIT and Harvard, 7 Cambridge Center
Christine Malboeuf: Broad Institute of MIT and Harvard, 7 Cambridge Center
Diana Lu: Broad Institute of MIT and Harvard, 7 Cambridge Center
John J. Trombetta: Broad Institute of MIT and Harvard, 7 Cambridge Center
Dave Gennert: Broad Institute of MIT and Harvard, 7 Cambridge Center
Andreas Gnirke: Broad Institute of MIT and Harvard, 7 Cambridge Center
Alon Goren: Broad Institute of MIT and Harvard, 7 Cambridge Center
Nir Hacohen: Broad Institute of MIT and Harvard, 7 Cambridge Center
Joshua Z. Levin: Broad Institute of MIT and Harvard, 7 Cambridge Center
Hongkun Park: Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA
Aviv Regev: Broad Institute of MIT and Harvard, 7 Cambridge Center

Nature, 2013, vol. 498, issue 7453, 236-240

Abstract: Single-cell RNA sequencing is used to investigate the transcriptional response of 18 mouse bone-marrow-derived dendritic cells after lipopolysaccharide stimulation; many highly expressed genes, such as key immune genes and cytokines, show bimodal variation in both transcript abundance and splicing patterns. This variation reflects differences in both cell state and usage of an interferon-driven pathway involving Stat2 and Irf7.

Date: 2013
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DOI: 10.1038/nature12172

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