High-throughput single-cell labeling (Hi-SCL) for RNA-Seq using drop-based microfluidics

Assaf Rotem, Oren Ram, Noam Shoresh, Ralph A. Sperling, Michael Schnall-Levin, Huidan Zhang, Anindita Basu, Bradley E. Bernstein, David A. Weitz

Research output: Contribution to journalArticlepeer-review

61 Scopus citations

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.

Original languageAmerican English
Article numbere0116328
JournalPLoS ONE
Volume10
Issue number5
DOIs
StatePublished - 22 May 2015
Externally publishedYes

Bibliographical note

Publisher Copyright:
© 2015 Rotem et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

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