title: Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets.
abstract: Cells, the basic units of biological structure and function, vary broadly in type and state. Single-cell genomics can characterize cell identity and function, but limitations of ease and scale have prevented its broad application. Here we describe Drop-seq, a strategy for quickly profiling thousands of individual cells by separating them into nanoliter-sized aqueous droplets, associating a different barcode with each cell's RNAs, and sequencing them all together. Drop-seq analyzes mRNA transcripts from thousands of individual cells simultaneously while remembering transcripts' cell of origin. We analyzed transcriptomes from 44,808 mouse retinal cells and identified 39 transcriptionally distinct cell populations, creating a molecular atlas of gene expression for known retinal cell classes and novel candidate cell subtypes. Drop-seq will accelerate biological discovery by enabling routine transcriptional profiling at single-cell resolution. VIDEO ABSTRACT.
authors.affiliation: Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA. Electronic address: emacosko@genetics.med.harvard.edu.
authors.forename: Evan Z
authors.initials: EZ
authors.lastname: Macosko
authors.affiliation: Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA.
authors.forename: Anindita
authors.initials: A
authors.lastname: Basu
authors.affiliation: Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; New York Genome Center, New York, NY 10013, USA; Department of Biology, New York University, New York, NY 10003, USA.
authors.forename: Rahul
authors.initials: R
authors.lastname: Satija
authors.affiliation: Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
authors.forename: James
authors.initials: J
authors.lastname: Nemesh
authors.affiliation: Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
authors.forename: Karthik
authors.initials: K
authors.lastname: Shekhar
authors.affiliation: Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
authors.forename: Melissa
authors.initials: M
authors.lastname: Goldman
authors.affiliation: Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
authors.forename: Itay
authors.initials: I
authors.lastname: Tirosh
authors.affiliation: The Program in Cellular and Molecular Medicine, Children's Hospital Boston, Boston, MA 02115, USA.
authors.forename: Allison R
authors.initials: AR
authors.lastname: Bialas
authors.affiliation: Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
authors.forename: Nolan
authors.initials: N
authors.lastname: Kamitaki
authors.affiliation: Department of Molecular and Cellular Biology and Center for Brain Science, Harvard University, Cambridge, MA 02138, USA.
authors.forename: Emily M
authors.initials: EM
authors.lastname: Martersteck
authors.affiliation: Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
authors.forename: John J
authors.initials: JJ
authors.lastname: Trombetta
authors.affiliation: School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA; Department of Physics, Harvard University, Cambridge, MA 02138, USA.
authors.forename: David A
authors.initials: DA
authors.lastname: Weitz
authors.affiliation: Department of Molecular and Cellular Biology and Center for Brain Science, Harvard University, Cambridge, MA 02138, USA.
authors.forename: Joshua R
authors.initials: JR
authors.lastname: Sanes
authors.affiliation: Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA; Institute for Medical Engineering and Science and Department of Chemistry, MIT, Cambridge, MA 02139, USA.
authors.forename: Alex K
authors.initials: AK
authors.lastname: Shalek
authors.affiliation: Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Biology, MIT, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
authors.forename: Aviv
authors.initials: A
authors.lastname: Regev
authors.affiliation: Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA. Electronic address: mccarroll@genetics.med.harvard.edu.
authors.forename: Steven A
authors.initials: SA
authors.lastname: McCarroll
mesh_terms: D000818:Animals; D020869:Gene Expression Profiling / Q000379:methods*; D055106:Genome-Wide Association Study; D059014:High-Throughput Nucleotide Sequencing; D051379:Mice; D046210:Microfluidic Analytical Techniques; D012160:Retina / Q000166:cytology*; D017423:Sequence Analysis, RNA; D059010:Single-Cell Analysis