title: High-Throughput Single-Cell Labeling (Hi-SCL) for RNA-Seq Using Drop-Based Microfluidics.
abstract: The importance of single-cell level data is increasingly appreciated, and significant advances in this direction have been made in recent years. Common to these technologies is the need to physically segregate individual cells into containers, such as wells or chambers of a micro-fluidics chip. High-throughput Single-Cell Labeling (Hi-SCL) in drops is a novel method that uses drop-based libraries of oligonucleotide barcodes to index individual cells in a population. The use of drops as containers, and a microfluidics platform to manipulate them en-masse, yields a highly scalable methodological framework. Once tagged, labeled molecules from different cells may be mixed without losing the cell-of-origin information. Here we demonstrate an application of the method for generating RNA-sequencing data for multiple individual cells within a population. Barcoded oligonucleotides are used to prime cDNA synthesis within drops. Barcoded cDNAs are then combined and subjected to second generation sequencing. The data are deconvoluted based on the barcodes, yielding single-cell mRNA expression data. In a proof-of-concept set of experiments we show that this method yields data comparable to other existing methods, but with unique potential for assaying very large numbers of cells.
authors.affiliation: Department of Physics and School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts, United States of America; Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America.
authors.forename: Assaf
authors.initials: A
authors.lastname: Rotem
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America; Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, United States of America.
authors.forename: Oren
authors.initials: O
authors.lastname: Ram
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America.
authors.forename: Noam
authors.initials: N
authors.lastname: Shoresh
authors.affiliation: Department of Physics and School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts, United States of America.
authors.forename: Ralph A
authors.initials: RA
authors.lastname: Sperling
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America.
authors.forename: Michael
authors.initials: M
authors.lastname: Schnall-Levin
authors.affiliation: Department of Physics and School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts, United States of America.
authors.forename: Huidan
authors.initials: H
authors.lastname: Zhang
authors.affiliation: Department of Physics and School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts, United States of America; Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America.
authors.forename: Anindita
authors.initials: A
authors.lastname: Basu
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America; Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America; Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, United States of America; Center for Systems Biology and Center for Cancer Research, Massachusetts General Hospital, Boston, Massachusetts, United States of America.
authors.forename: Bradley E
authors.initials: BE
authors.lastname: Bernstein
authors.affiliation: Department of Physics and School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts, United States of America.
authors.forename: David A
authors.initials: DA
authors.lastname: Weitz
mesh_terms: D018076:DNA, Complementary / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing; D044085:Microfluidics / Q000379:methods*; D020411:Oligonucleotide Array Sequence Analysis; D017423:Sequence Analysis, RNA / Q000379:methods
chemical_list: D018076:DNA, Complementary