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

Research output: Contribution to journalArticlepeer-review

716 Scopus citations


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 languageAmerican English
Article number77
JournalGenome Biology
Issue number1
StatePublished - 28 Apr 2016

Bibliographical note

Publisher Copyright:
© 2016 Hashimshony et al.


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