CEL-Seq2: Sensitive highly-multiplexed single-cell RNA-Seq

Tamar Hashimshony; Naftalie Senderovich; Gal Avital; Agnes Klochendler; Yaron de Leeuw; Leon Anavy; Dave Gennert; Shuqiang Li; Kenneth J. Livak; Orit Rozenblatt-Rosen; Yuval Dor; Aviv Regev; Itai Yanai

doi:10.1186/s13059-016-0938-8

CEL-Seq2: Sensitive highly-multiplexed single-cell RNA-Seq

Tamar Hashimshony, Naftalie Senderovich, Gal Avital, Agnes Klochendler, Yaron de Leeuw, Leon Anavy, Dave Gennert, Shuqiang Li, Kenneth J. Livak, Orit Rozenblatt-Rosen, Yuval Dor, Aviv Regev, Itai Yanai^*

^*Corresponding author for this work

Department of Developmental Biology and Cancer Research

Research output: Contribution to journal › Article › peer-review

660 Scopus citations

Abstract

Single-cell transcriptomics requires a method that is sensitive, accurate, and reproducible. Here, we present CEL-Seq2, a modified version of our CEL-Seq method, with threefold higher sensitivity, lower costs, and less hands-on time. We implemented CEL-Seq2 on Fluidigm's C1 system, providing its first single-cell, on-chip barcoding method, and we detected gene expression changes accompanying the progression through the cell cycle in mouse fibroblast cells. We also compare with Smart-Seq to demonstrate CEL-Seq2's increased sensitivity relative to other available methods. Collectively, the improvements make CEL-Seq2 uniquely suited to single-cell RNA-Seq analysis in terms of economics, resolution, and ease of use.

Original language	American English
Article number	77
Journal	Genome Biology
Volume	17
Issue number	1
DOIs	https://doi.org/10.1186/s13059-016-0938-8
State	Published - 28 Apr 2016

Bibliographical note

Funding Information:
The research leading to these results has received funding from the European Research Council under the European Union’s Seventh Framework Programme (FP/2007-2013) under grant agreement number 310927. This work was also supported by the Israel Science Foundation (grant 1457/14).

Publisher Copyright:
© 2016 Hashimshony et al.

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title = "CEL-Seq2: Sensitive highly-multiplexed single-cell RNA-Seq",

abstract = "Single-cell transcriptomics requires a method that is sensitive, accurate, and reproducible. Here, we present CEL-Seq2, a modified version of our CEL-Seq method, with threefold higher sensitivity, lower costs, and less hands-on time. We implemented CEL-Seq2 on Fluidigm's C1 system, providing its first single-cell, on-chip barcoding method, and we detected gene expression changes accompanying the progression through the cell cycle in mouse fibroblast cells. We also compare with Smart-Seq to demonstrate CEL-Seq2's increased sensitivity relative to other available methods. Collectively, the improvements make CEL-Seq2 uniquely suited to single-cell RNA-Seq analysis in terms of economics, resolution, and ease of use.",

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note = "Funding Information: The research leading to these results has received funding from the European Research Council under the European Union{\textquoteright}s Seventh Framework Programme (FP/2007-2013) under grant agreement number 310927. This work was also supported by the Israel Science Foundation (grant 1457/14). Publisher Copyright: {\textcopyright} 2016 Hashimshony et al.",

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doi = "10.1186/s13059-016-0938-8",

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AU - Hashimshony, Tamar

AU - Senderovich, Naftalie

AU - Avital, Gal

AU - Klochendler, Agnes

AU - de Leeuw, Yaron

AU - Anavy, Leon

AU - Gennert, Dave

AU - Li, Shuqiang

AU - Livak, Kenneth J.

AU - Rozenblatt-Rosen, Orit

AU - Dor, Yuval

AU - Regev, Aviv

AU - Yanai, Itai

N1 - Funding Information: The research leading to these results has received funding from the European Research Council under the European Union’s Seventh Framework Programme (FP/2007-2013) under grant agreement number 310927. This work was also supported by the Israel Science Foundation (grant 1457/14). Publisher Copyright: © 2016 Hashimshony et al.

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AB - Single-cell transcriptomics requires a method that is sensitive, accurate, and reproducible. Here, we present CEL-Seq2, a modified version of our CEL-Seq method, with threefold higher sensitivity, lower costs, and less hands-on time. We implemented CEL-Seq2 on Fluidigm's C1 system, providing its first single-cell, on-chip barcoding method, and we detected gene expression changes accompanying the progression through the cell cycle in mouse fibroblast cells. We also compare with Smart-Seq to demonstrate CEL-Seq2's increased sensitivity relative to other available methods. Collectively, the improvements make CEL-Seq2 uniquely suited to single-cell RNA-Seq analysis in terms of economics, resolution, and ease of use.

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CEL-Seq2: Sensitive highly-multiplexed single-cell RNA-Seq

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